Pierrick Roger
| Snapshot Date: 2024-07-05 14:00 -0400 (Fri, 05 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: devel |
| git_last_commit: dfe3f6c |
| git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-06 11:38 -0400 (Sat, 06 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 197/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.11.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.11.0.tar.gz |
| StartedAt: 2024-07-05 20:51:22 -0400 (Fri, 05 Jul 2024) |
| EndedAt: 2024-07-05 20:53:46 -0400 (Fri, 05 Jul 2024) |
| EllapsedTime: 143.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-07-05 20:52:07.139][biodb::testContext]
biodb.INFO [2024-07-05 20:52:07.142][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-05 20:52:07.143][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-07-05 20:52:07.144][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-05 20:52:07.145][biodb::testContext]
biodb.INFO [2024-07-05 20:52:07.153][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-05 20:52:07.155][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-05 20:52:07.164][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-05 20:52:07.165][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-05 20:52:07.166][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-05 20:52:07.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.170][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-05 20:52:07.191][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-05 20:52:07.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.198][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-05 20:52:07.200][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-05 20:52:07.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.203][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-05 20:52:07.204][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-05 20:52:07.206][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-05 20:52:07.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.209][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-05 20:52:07.210][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-05 20:52:07.211][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-05 20:52:07.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.215][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-05 20:52:07.216][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-05 20:52:07.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.220][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-05 20:52:07.221][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-05 20:52:07.222][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-05 20:52:07.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.226][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-05 20:52:07.227][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-05 20:52:07.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.230][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-05 20:52:07.232][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-05 20:52:07.233][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-05 20:52:07.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.236][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-05 20:52:07.237][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-05 20:52:07.238][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-05 20:52:07.239][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-05 20:52:07.240][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-05 20:52:07.241][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-05 20:52:07.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.245][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-05 20:52:07.246][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-05 20:52:07.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.250][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-05 20:52:07.251][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-05 20:52:07.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.255][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-05 20:52:07.256][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-05 20:52:07.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.260][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-05 20:52:07.261][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-05 20:52:07.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.264][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-05 20:52:07.265][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-05 20:52:07.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.269][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-05 20:52:07.270][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-05 20:52:07.275][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-05 20:52:07.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.278][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-05 20:52:07.279][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-05 20:52:07.281][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-05 20:52:07.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.288][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-05 20:52:07.326][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:52:07.363][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-05 20:52:07.364][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.366][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:52:07.367][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.368][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.369][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:52:07.370][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.371][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-05 20:52:07.372][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:52:07.373][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.374][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-05 20:52:07.375][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:52:07.376][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:52:07.377][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.378][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-05 20:52:07.378][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-05 20:52:07.378][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-05 20:52:07.378][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-05 20:52:07.378][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-05 20:52:07.379][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:52:07.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:52:07.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:52:07.382][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:52:07.383][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:52:07.384][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:52:07.385][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.386][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:52:07.387][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:52:07.388][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:52:07.389][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:52:07.390][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:52:07.392][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-05 20:52:07.393][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:52:07.395][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-05 20:52:07.396][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.397][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:52:07.398][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.398][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.399][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:52:07.401][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.401][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-05 20:52:07.403][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:52:07.404][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.405][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-05 20:52:07.406][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:52:07.407][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:52:07.408][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.409][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-05 20:52:07.409][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-05 20:52:07.409][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-05 20:52:07.409][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-05 20:52:07.409][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-05 20:52:07.410][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:52:07.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:52:07.412][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:52:07.413][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:52:07.414][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:52:07.415][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:52:07.416][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.417][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:52:07.418][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:52:07.418][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:52:07.419][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:52:07.421][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:52:07.422][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-05 20:52:07.424][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.425][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-05 20:52:07.426][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.427][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:52:07.428][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.429][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.430][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:52:07.431][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.432][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-05 20:52:07.433][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:52:07.434][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:52:07.435][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-05 20:52:07.436][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:52:07.438][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:52:07.439][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.440][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:52:07.441][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:52:07.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:52:07.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:52:07.444][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:52:07.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:52:07.445][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:52:07.446][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.447][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:52:07.448][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:52:07.449][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:52:07.450][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:52:07.451][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:52:07.452][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-05 20:52:07.454][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.455][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-05 20:52:07.456][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.457][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:52:07.458][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.459][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.460][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:52:07.461][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.462][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-05 20:52:07.463][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:52:07.465][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:52:07.466][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-05 20:52:07.467][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:52:07.468][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:52:07.469][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.470][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:52:07.471][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:52:07.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:52:07.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:52:07.474][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:52:07.475][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:52:07.476][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:52:07.477][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.478][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:52:07.479][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:52:07.480][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:52:07.481][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:52:07.482][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:52:07.486][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-05 20:52:07.487][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.568][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-05 20:52:07.574][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-05 20:52:07.575][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-05 20:52:07.577][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-05 20:52:07.578][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-05 20:52:07.580][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-05 20:52:07.581][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-05 20:52:07.583][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-05 20:52:07.584][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-05 20:52:07.586][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-05 20:52:07.587][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-05 20:52:07.589][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-05 20:52:07.590][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-05 20:52:07.592][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-05 20:52:07.593][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-05 20:52:07.595][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-05 20:52:07.596][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-05 20:52:07.598][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-05 20:52:07.599][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-05 20:52:07.601][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-05 20:52:07.602][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-05 20:52:07.604][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-05 20:52:07.605][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-05 20:52:07.607][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-05 20:52:07.608][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-05 20:52:07.610][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-05 20:52:07.611][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-05 20:52:07.613][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-05 20:52:07.614][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-05 20:52:07.616][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-05 20:52:07.617][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-05 20:52:07.618][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-05 20:52:07.620][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-05 20:52:07.621][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-05 20:52:07.623][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-05 20:52:07.624][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-05 20:52:07.633][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-05 20:52:07.635][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-05 20:52:07.636][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-05 20:52:07.638][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-05 20:52:07.639][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-05 20:52:07.640][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-05 20:52:07.642][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-05 20:52:07.643][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-05 20:52:07.645][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-05 20:52:07.646][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-05 20:52:07.648][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-05 20:52:07.649][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-05 20:52:07.651][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-05 20:52:07.652][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-05 20:52:07.654][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-05 20:52:07.655][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-05 20:52:07.656][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-05 20:52:07.658][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-05 20:52:07.659][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-05 20:52:07.661][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-05 20:52:07.662][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-05 20:52:07.664][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-05 20:52:07.665][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-05 20:52:07.667][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-05 20:52:07.668][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-05 20:52:07.670][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-05 20:52:07.671][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-05 20:52:07.672][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-05 20:52:07.674][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-05 20:52:07.675][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-05 20:52:07.677][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-05 20:52:07.678][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-05 20:52:07.680][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-05 20:52:07.681][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-05 20:52:07.683][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-05 20:52:07.684][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-05 20:52:07.685][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-05 20:52:07.687][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-05 20:52:07.688][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-05 20:52:07.690][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-05 20:52:07.691][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-05 20:52:07.693][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-05 20:52:07.694][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-05 20:52:07.695][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-05 20:52:07.697][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-05 20:52:07.698][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-05 20:52:07.700][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-05 20:52:07.706][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-05 20:52:07.708][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-05 20:52:07.712][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-05 20:52:07.713][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.715][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:52:07.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:07.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:07.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:07.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:07.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:07.840][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-05 20:52:07.852][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-05 20:52:07.854][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:52:07.856][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.857][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.858][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:52:07.859][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.860][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.861][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.862][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-05 20:52:07.863][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-05 20:52:07.864][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:52:07.865][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.866][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-05 20:52:07.867][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:52:07.868][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-05 20:52:07.868][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-05 20:52:07.868][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-05 20:52:07.868][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-05 20:52:07.868][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-05 20:52:07.868][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-05 20:52:07.868][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-05 20:52:07.868][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-05 20:52:07.868][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-05 20:52:07.868][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-05 20:52:07.868][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-05 20:52:07.870][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-05 20:52:07.871][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-05 20:52:07.871][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-05 20:52:07.871][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-05 20:52:07.872][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-05 20:52:07.873][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:52:07.874][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:52:07.874][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:52:07.875][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:52:07.876][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:52:07.877][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:52:07.878][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:07.878][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-05 20:52:07.879][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:52:07.880][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:52:07.881][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-05 20:52:07.882][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-05 20:52:07.882][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-05 20:52:07.889][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-05 20:52:07.891][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-05 20:52:07.893][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-05 20:52:07.894][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-05 20:52:07.896][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-05 20:52:07.897][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-05 20:52:07.934][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-05 20:52:07.936][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-05 20:52:07.941][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-05 20:52:07.945][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-05 20:52:07.951][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-05 20:52:07.952][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-05 20:52:07.953][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-05 20:52:07.954][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-05 20:52:07.965][biodb::testThat]
biodb.INFO [2024-07-05 20:52:07.966][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-07-05 20:52:07.967][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:52:07.968][biodb::testThat]
biodb.TRACE[2024-07-05 20:52:07.972][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-07-05 20:52:07.974][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:07.979][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:07.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:07.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:07.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:08.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:08.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:08.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:08.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:08.022][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.023][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.025][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.046][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:08.047][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:08.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.049][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.082][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:08.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:08.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.087][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:08.089][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:08.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.091][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.092][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:08.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:08.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.097][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:08.098][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:08.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.100][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:08.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:08.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.106][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.107][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.109][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.115][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.116][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.118][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.119][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.124][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:08.125][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.127][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.128][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:08.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.132][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.133][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.135][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.141][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:08.142][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:08.143][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.144][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:08.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:08.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.149][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:08.150][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:08.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.152][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.153][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:08.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:08.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.158][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:08.159][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:08.159][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.160][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.162][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:08.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:08.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:08.255][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-07-05 20:52:08.258][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:08.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:08.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:08.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:08.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.290][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.294][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.306][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-05 20:52:08.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-05 20:52:08.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.310][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-05 20:52:08.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-05 20:52:08.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.314][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-05 20:52:08.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-05 20:52:08.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.318][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-05 20:52:08.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-05 20:52:08.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.422][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.423][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.425][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.488][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.489][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.491][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:08.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:08.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:08.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:08.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:08.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.512][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:08.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:08.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.516][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:08.517][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:08.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.519][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.520][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:08.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:08.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.532][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:08.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:08.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.536][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:08.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:08.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.540][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:08.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:08.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.544][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:08.545][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:08.546][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.547][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.548][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:08.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:08.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.573][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.574][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.576][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.602][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.603][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.605][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.617][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:08.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:08.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.621][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:08.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:08.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.625][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:08.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:08.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.629][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:08.630][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:08.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.632][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.633][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:08.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:08.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.645][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-05 20:52:08.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:08.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.649][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-05 20:52:08.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:08.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.653][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-05 20:52:08.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:08.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.657][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-05 20:52:08.658][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:08.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.660][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.661][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-05 20:52:08.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:08.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.674][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.678][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.682][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.686][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.687][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.689][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.690][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.702][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:08.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:08.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.706][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:08.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:08.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.718][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:08.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:08.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.722][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:08.723][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:08.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.725][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.726][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:08.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:08.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.751][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.752][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.754][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.768][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:08.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:08.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.772][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:08.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:08.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:08.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:08.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.780][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:08.781][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:08.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.783][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.784][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:08.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:08.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.796][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:08.797][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:08.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.799][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.804][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:08.805][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:08.806][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.807][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.811][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:08.812][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:08.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.814][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.819][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:08.820][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:08.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.822][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.826][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.828][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:08.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.830][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.834][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.836][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:08.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.838][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.843][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.844][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:08.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.846][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.851][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.852][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:08.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.854][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.859][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-05 20:52:08.860][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:08.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.862][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.866][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:08.868][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:08.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.870][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:08.875][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:08.876][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:08.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:08.878][ef$get] fields variable is a list.
biodb.INFO [2024-07-05 20:52:08.886][biodb::testThat]
biodb.INFO [2024-07-05 20:52:08.887][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-05 20:52:08.888][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:52:08.889][biodb::testThat]
biodb.DEBUG[2024-07-05 20:52:08.905][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-07-05 20:52:08.914][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:08.920][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.INFO [2024-07-05 20:52:08.922][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-07-05 20:52:08.923][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:08.924][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:08.926][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:08.927][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:08.928][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:08.929][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:08.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:08.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:08.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:08.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:08.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:08.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:08.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:08.947][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
biodb.DEBUG[2024-07-05 20:52:08.979][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:08.980][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:08.981][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
biodb.TRACE[2024-07-05 20:52:09.488][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
biodb.DEBUG[2024-07-05 20:52:10.079][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:10.085][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5c6fb88c946e8568cc03c0d73dc5603e.content"
biodb.TRACE[2024-07-05 20:52:10.119][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5c6fb88c946e8568cc03c0d73dc5603e.request"
biodb.TRACE[2024-07-05 20:52:10.124][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml"
biodb.DEBUG[2024-07-05 20:52:10.126][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:10.160][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:10.161][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:10.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:10.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:10.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:10.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:10.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:10.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:10.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:10.176][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:10.177][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:10.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.179][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:10.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:10.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.220][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:10.221][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:10.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.223][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.225][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:10.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:10.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.229][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:10.230][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:10.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.232][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.234][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:10.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:10.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.238][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:10.239][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:10.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.241][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:10.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:10.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.246][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:10.248][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:10.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.249][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:10.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:10.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.255][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:10.256][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:10.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.258][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.259][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:10.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:10.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.263][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:10.264][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:10.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.266][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.268][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:10.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:10.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.272][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:10.273][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:10.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.275][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:10.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:10.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.280][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:10.281][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:10.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.283][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:10.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:10.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.289][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:10.290][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:10.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.292][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.293][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:10.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:10.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.297][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:10.298][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:10.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.300][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.301][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:10.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:10.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:10.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:10.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:10.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:10.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:10.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:10.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:10.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:10.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:10.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:10.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:10.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:10.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:10.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:10.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:10.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:10.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:10.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:10.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:10.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:10.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:10.346][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-07-05 20:52:10.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-05 20:52:10.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-05 20:52:10.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-05 20:52:10.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-05 20:52:10.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-05 20:52:10.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-05 20:52:10.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-05 20:52:10.367][biodb::testThat]
biodb.INFO [2024-07-05 20:52:10.369][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-05 20:52:10.370][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:52:10.370][biodb::testThat]
biodb.TRACE[2024-07-05 20:52:10.374][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:10.375][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:10.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.377][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:10.378][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-07-05 20:52:10.411][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:10.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:10.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.415][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:10.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:10.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:10.419][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:10.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:10.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:10.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:10.427][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-07-05 20:52:10.450][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-05 20:52:10.467][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:10.468][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:10.484][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-07-05 20:52:10.867][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-07-05 20:52:11.453][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-07-05 20:52:11.457][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-07-05 20:52:11.461][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-07-05 20:52:11.469][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-07-05 20:52:11.478][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:52:11.486][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:11.488][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:11.492][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-05 20:52:19.426][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-05 20:52:20.002][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:20.007][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-07-05 20:52:20.016][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-07-05 20:52:20.022][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-07-05 20:52:20.047][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:20.049][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:20.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.053][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.055][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:20.056][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:20.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.060][ef$get] fields variable is a list.
biodb.INFO [2024-07-05 20:52:20.066][biodb::testThat]
biodb.INFO [2024-07-05 20:52:20.068][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-07-05 20:52:20.069][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:52:20.071][biodb::testThat]
biodb.TRACE[2024-07-05 20:52:20.101][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:20.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:20.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.106][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:20.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:20.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.110][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:20.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:20.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:20.256][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:52:20.260][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:52:20.278][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-05 20:52:20.280][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:52:20.281][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-07-05 20:52:20.298][biodb::testThat]
biodb.INFO [2024-07-05 20:52:20.299][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-07-05 20:52:20.300][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:52:20.301][biodb::testThat]
biodb.TRACE[2024-07-05 20:52:20.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:20.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:20.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.328][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:20.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:20.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.332][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:20.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:20.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:20.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:20.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:20.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:20.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:20.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:20.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.349][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-05 20:52:20.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-05 20:52:20.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.353][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-05 20:52:20.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-05 20:52:20.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.358][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-05 20:52:20.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-05 20:52:20.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.362][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-05 20:52:20.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-05 20:52:20.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.398][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:20.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:20.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:20.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:20.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:20.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:20.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:20.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:20.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:20.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:20.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:20.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:20.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.421][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-05 20:52:20.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-05 20:52:20.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.425][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-05 20:52:20.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-05 20:52:20.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.429][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-05 20:52:20.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-05 20:52:20.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:20.433][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-05 20:52:20.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-05 20:52:20.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:20.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-05 20:52:20.442][biodb::testThat]
biodb.INFO [2024-07-05 20:52:20.443][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-05 20:52:20.444][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:52:20.445][biodb::testThat]
biodb.INFO [2024-07-05 20:52:20.453][biodb::testThat]
biodb.INFO [2024-07-05 20:52:20.454][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-05 20:52:20.455][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:52:20.456][biodb::testThat]
biodb.INFO [2024-07-05 20:52:20.464][biodb::testThat]
biodb.INFO [2024-07-05 20:52:20.465][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-05 20:52:20.466][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:52:20.467][biodb::testThat]
biodb.DEBUG[2024-07-05 20:52:20.470][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-07-05 20:52:20.993][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-07-05 20:52:22.133][biodb::testThat]
biodb.INFO [2024-07-05 20:52:22.135][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-05 20:52:22.137][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:52:22.139][biodb::testThat]
biodb.DEBUG[2024-07-05 20:52:22.578][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-07-05 20:52:23.040][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:23.042][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:23.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:23.043][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:23.044][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:23.045][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:23.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:23.047][ef$get] fields variable is a list.
biodb.INFO [2024-07-05 20:52:23.049][biodb::testThat]
biodb.INFO [2024-07-05 20:52:23.050][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-07-05 20:52:23.051][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:52:23.052][biodb::testThat]
biodb.TRACE[2024-07-05 20:52:23.062][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:23.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:23.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:23.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:23.065][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:23.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:23.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:23.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:23.069][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:23.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:23.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:23.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:23.164][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:52:23.167][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:52:23.169][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-05 20:52:23.170][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:52:23.171][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-05 20:52:23.230][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:52:23.233][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:52:23.234][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-05 20:52:23.236][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:52:23.237][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-07-05 20:52:23.250][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-05 20:52:23.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-05 20:52:23.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:23.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:23.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:23.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:23.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:23.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:23.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:23.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:23.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:23.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:23.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:23.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:23.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:23.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:23.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:23.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:23.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:23.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:23.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:23.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:23.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:23.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:23.283][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:52:23.286][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:23.287][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:23.289][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-05 20:52:23.686][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-05 20:52:24.080][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:24.084][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-07-05 20:52:24.090][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-07-05 20:52:24.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:24.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:24.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:24.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:24.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:24.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:24.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:24.163][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-07-05 20:52:24.217][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:24.219][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-07-05 20:52:24.221][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:24.222][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:24.223][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:24.224][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:24.225][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:24.226][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:24.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:24.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:24.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:24.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:24.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:24.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:24.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:24.252][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-07-05 20:52:24.255][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:24.256][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:24.258][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-07-05 20:52:24.645][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-07-05 20:52:25.070][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:25.073][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-07-05 20:52:25.077][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-07-05 20:52:25.079][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-07-05 20:52:25.081][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:25.082][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:25.083][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:25.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:25.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:25.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:25.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:25.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:25.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:25.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:25.098][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:25.099][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:25.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.101][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:25.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:25.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.107][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:25.108][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:25.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.110][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.111][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:25.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:25.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.116][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:25.117][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:25.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.119][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.121][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:25.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:25.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.126][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:25.127][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:25.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.129][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:25.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:25.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.135][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:25.136][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:25.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.138][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.152][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:25.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:25.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.157][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:25.159][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:25.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.161][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.162][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:25.163][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:25.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.165][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.166][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:25.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:25.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.171][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:25.172][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:25.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.174][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:25.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:25.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.179][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:25.180][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:25.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.182][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:25.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:25.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.187][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:25.188][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:25.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.190][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.192][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:25.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:25.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.196][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:25.196][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:25.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.198][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.199][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:25.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:25.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:25.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:25.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:25.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:25.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:25.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:25.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:25.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:25.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:25.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:25.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:25.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:25.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:25.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:25.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:25.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:25.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:25.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:25.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:25.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:25.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:25.241][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-07-05 20:52:25.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:25.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:25.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:25.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:25.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:25.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:25.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:25.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:25.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:25.263][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:52:25.266][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:25.267][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:25.268][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-05 20:52:25.693][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-05 20:52:26.085][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:26.089][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-07-05 20:52:26.096][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-07-05 20:52:26.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:26.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:26.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:26.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:26.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:26.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:26.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:26.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:26.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:26.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:26.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:26.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:26.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:26.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:26.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:26.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:26.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:26.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:26.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:26.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:26.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:26.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:26.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:26.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:26.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:26.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:26.162][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-07-05 20:52:26.163][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:26.165][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-07-05 20:52:26.166][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:26.167][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:26.169][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:26.170][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:26.171][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:26.172][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:26.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:26.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:26.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:26.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:26.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:26.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:26.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:26.185][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-07-05 20:52:26.188][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:26.189][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:26.190][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-07-05 20:52:26.576][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-07-05 20:52:26.990][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:26.994][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-07-05 20:52:26.999][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-07-05 20:52:27.002][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-07-05 20:52:27.004][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:27.005][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:27.007][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:27.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:27.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:27.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:27.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:27.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:27.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:27.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:27.025][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:27.026][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:27.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.028][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:27.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:27.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.035][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:27.036][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:27.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.038][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.040][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:27.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:27.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.044][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:27.045][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:27.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.047][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.049][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:27.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:27.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.054][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:27.055][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:27.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.057][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.058][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:27.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:27.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.062][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:27.063][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:27.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.065][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:27.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:27.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.071][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:27.072][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:27.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.074][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.075][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:27.076][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:27.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.078][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.080][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:27.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:27.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.084][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:27.085][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:27.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.087][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:27.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:27.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.092][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:27.094][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:27.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.095][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:27.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:27.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.101][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:27.102][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:27.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.104][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.106][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:27.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:27.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.110][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:27.111][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:27.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.113][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.114][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:27.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:27.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:27.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:27.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:27.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:27.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:27.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:27.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:27.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:27.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:27.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:27.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:27.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:27.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:27.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:27.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:27.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:27.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:27.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:27.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:27.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:27.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:27.181][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-07-05 20:52:27.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:27.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:27.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:27.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:27.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:27.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:27.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:27.215][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:52:27.219][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:52:27.220][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-05 20:52:27.221][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:52:27.223][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-05 20:52:27.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:27.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:27.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:27.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:27.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:27.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:27.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:27.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:27.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:27.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:27.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:27.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:27.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:27.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:27.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:27.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:27.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:27.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:27.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:27.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:27.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:27.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:27.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:27.259][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-07-05 20:52:27.260][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:27.262][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-07-05 20:52:27.263][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:27.264][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:27.265][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:27.266][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:27.267][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:27.268][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:27.271][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:27.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:27.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:27.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:27.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:27.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:27.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:27.280][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-07-05 20:52:27.283][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:27.284][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:27.285][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-07-05 20:52:27.687][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-07-05 20:52:28.075][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:28.079][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-07-05 20:52:28.085][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-07-05 20:52:28.090][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-07-05 20:52:28.093][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:28.095][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:28.097][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:28.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:28.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:28.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:28.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:28.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:28.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:28.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:28.121][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:28.123][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:28.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.126][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:28.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:28.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.134][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:28.135][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:28.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.138][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.140][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:28.141][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:28.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.143][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.145][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:28.147][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:28.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.149][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.150][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:28.152][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:28.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.154][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.155][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:28.157][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:28.159][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.160][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.162][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:28.163][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:28.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.179][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.181][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:28.182][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:28.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.184][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.186][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:28.187][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:28.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.189][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:28.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:28.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.195][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:28.196][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:28.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.198][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.199][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:28.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:28.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.203][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:28.204][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:28.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.206][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:28.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:28.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:28.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:28.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:28.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:28.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:28.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:28.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:28.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:28.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:28.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:28.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:28.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:28.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:28.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:28.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:28.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:28.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:28.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:28.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:28.249][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-07-05 20:52:28.250][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:28.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:28.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:28.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:28.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:28.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:28.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:28.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:28.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:28.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:28.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:28.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:28.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:28.269][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:28.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:28.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:28.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:28.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:28.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:28.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:28.278][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-07-05 20:52:28.279][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:28.281][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-07-05 20:52:28.282][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:28.283][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:28.284][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:28.285][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:28.286][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:28.287][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:28.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:28.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:28.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:28.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:28.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:28.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:28.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:28.299][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-07-05 20:52:28.302][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:28.303][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:28.304][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-07-05 20:52:28.711][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-07-05 20:52:29.189][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:29.191][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-07-05 20:52:29.195][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-07-05 20:52:29.198][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-07-05 20:52:29.199][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:29.201][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:29.202][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:29.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:29.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:29.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:29.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:29.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:29.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:29.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:29.216][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:29.218][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:29.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.220][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:29.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:29.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.225][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:29.227][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:29.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.229][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.231][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:29.232][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:29.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.234][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.235][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:29.236][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:29.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.238][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.245][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:29.250][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:29.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.252][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.253][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:29.254][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:29.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.256][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.258][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:29.258][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:29.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.260][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.261][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:29.262][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:29.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.264][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.265][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:29.266][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:29.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.268][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.270][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:29.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:29.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.274][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:29.275][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:29.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.276][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.278][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:29.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:29.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.281][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:29.282][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:29.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.284][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:29.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:29.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:29.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:29.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:29.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:29.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:29.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:29.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:29.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:29.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:29.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:29.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:29.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:29.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:29.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:29.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:29.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:29.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:29.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:29.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:29.322][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-07-05 20:52:29.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:29.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:29.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:29.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:29.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:29.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:29.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:29.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:29.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:29.338][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:29.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:29.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:29.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:29.342][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:29.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:29.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:29.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:29.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:29.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:29.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:29.351][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-07-05 20:52:29.352][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:29.354][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-07-05 20:52:29.355][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:29.356][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:29.357][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:29.358][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:29.359][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:29.360][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:29.363][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:29.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:29.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:29.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:29.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:29.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:29.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:29.373][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-07-05 20:52:29.375][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:29.376][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:29.377][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-07-05 20:52:29.787][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-07-05 20:52:30.187][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:30.192][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-07-05 20:52:30.196][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-07-05 20:52:30.199][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-07-05 20:52:30.201][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:30.203][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:30.204][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:30.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:30.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:30.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:30.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:30.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:30.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:30.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:30.222][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:30.223][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:30.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.226][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:30.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:30.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.231][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:30.248][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:30.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.254][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.256][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:30.257][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:30.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.259][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.261][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:30.262][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:30.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.264][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.265][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:30.266][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:30.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.268][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.269][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:30.270][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:30.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.272][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.274][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:30.275][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:30.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.277][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.278][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:30.279][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:30.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.281][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.282][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:30.283][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:30.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.285][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.287][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:30.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:30.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.291][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:30.292][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:30.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.294][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.295][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:30.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:30.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.299][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:30.300][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:30.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.302][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:30.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:30.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:30.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:30.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:30.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:30.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:30.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:30.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:30.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:30.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:30.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:30.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:30.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:30.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:30.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:30.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:30.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:30.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:30.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:30.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:30.342][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-07-05 20:52:30.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:30.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:30.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:30.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:30.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:30.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:30.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:30.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:30.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:30.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:30.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:30.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:30.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:30.363][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:30.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:30.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:30.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:30.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:30.372][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:30.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:30.374][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-07-05 20:52:30.375][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:30.376][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-07-05 20:52:30.377][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:30.379][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:30.380][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:30.381][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:30.382][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:30.383][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:30.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:30.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:30.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:30.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:30.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:30.394][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:30.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:30.395][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-07-05 20:52:30.398][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:30.399][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:30.400][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-07-05 20:52:30.787][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-07-05 20:52:31.178][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:31.181][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-07-05 20:52:31.184][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-07-05 20:52:31.187][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-07-05 20:52:31.188][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:31.189][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:31.190][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:31.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:31.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:31.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:31.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:31.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:31.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:31.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:31.213][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:31.214][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:31.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.215][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:31.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:31.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.221][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:31.222][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:31.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.223][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.225][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:31.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:31.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.229][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:31.230][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:31.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.231][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.233][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:31.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:31.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.237][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:31.238][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:31.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.240][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.241][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:31.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:31.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.245][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:31.246][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:31.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.248][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:31.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:31.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.253][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:31.254][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:31.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.256][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.257][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:31.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:31.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.261][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:31.262][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:31.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.264][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.266][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:31.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:31.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.270][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:31.271][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:31.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.273][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:31.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:31.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.278][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:31.279][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:31.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.281][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:31.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:31.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.286][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:31.287][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:31.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.289][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.290][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:31.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:31.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.294][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:31.295][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:31.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.297][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.298][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:31.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:31.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:31.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:31.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:31.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:31.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:31.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:31.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:31.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:31.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:31.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:31.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:31.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:31.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:31.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:31.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:31.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:31.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:31.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:31.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:31.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:31.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:31.340][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-07-05 20:52:31.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:31.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:31.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:31.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:31.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:31.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:31.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:31.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:31.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:31.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:31.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:31.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:31.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:31.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:31.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:31.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:31.364][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-07-05 20:52:31.365][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:31.367][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-07-05 20:52:31.369][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:31.370][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:31.371][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:31.372][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:31.373][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:31.374][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:31.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:31.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:31.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:31.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:31.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:31.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:31.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:31.396][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-07-05 20:52:31.398][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:31.399][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:31.401][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-07-05 20:52:31.799][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-07-05 20:52:32.249][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:32.254][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-07-05 20:52:32.262][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-07-05 20:52:32.267][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-07-05 20:52:32.270][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:32.273][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:32.276][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:32.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:32.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:32.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:32.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:32.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:32.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:32.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:32.299][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:32.300][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:32.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.302][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:32.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:32.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.308][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:32.309][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:32.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.311][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.312][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:32.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:32.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.316][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:32.317][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:32.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.319][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.320][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:32.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:32.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.324][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:32.325][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:32.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.327][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.328][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:32.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:32.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.333][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:32.334][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:32.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.336][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:32.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:32.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.341][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:32.342][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:32.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.343][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.344][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:32.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:32.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.349][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:32.350][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:32.350][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.351][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.352][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:32.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:32.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.356][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:32.358][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:32.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.359][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:32.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:32.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.364][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:32.365][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:32.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.367][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:32.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:32.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.373][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:32.374][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:32.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.375][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.376][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:32.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:32.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.380][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:32.381][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:32.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.383][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.384][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:32.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:32.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:32.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:32.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:32.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:32.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:32.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:32.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:32.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:32.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:32.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:32.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:32.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:32.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:32.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:32.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:32.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:32.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:32.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:32.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:32.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:32.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:32.426][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-07-05 20:52:32.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:32.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:32.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:32.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:32.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:32.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:32.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:32.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:32.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:32.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:32.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:32.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:32.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:32.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:32.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:32.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:32.460][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-07-05 20:52:32.461][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:32.462][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-07-05 20:52:32.463][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:32.464][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:32.465][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:32.466][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:32.467][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:32.468][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:32.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:32.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:32.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:32.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:32.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:32.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:32.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:32.489][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-07-05 20:52:32.492][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:32.493][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:32.494][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-07-05 20:52:32.905][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-07-05 20:52:33.324][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:33.327][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-07-05 20:52:33.332][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-07-05 20:52:33.335][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-07-05 20:52:33.336][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:33.338][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:33.340][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:33.342][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:33.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:33.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:33.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:33.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:33.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:33.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:33.357][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:33.359][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:33.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.361][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:33.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:33.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.368][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:33.369][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:33.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.371][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.373][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:33.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:33.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.378][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:33.379][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:33.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.381][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.383][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:33.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:33.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.388][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:33.389][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:33.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.391][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.393][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:33.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:33.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.398][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:33.399][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:33.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.401][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.403][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:33.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:33.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.408][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:33.409][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:33.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.411][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.413][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:33.414][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:33.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.417][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.418][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:33.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:33.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.423][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:33.424][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:33.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.427][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:33.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:33.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.433][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:33.434][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:33.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.437][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:33.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:33.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.443][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:33.445][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:33.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.447][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.449][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:33.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:33.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.454][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:33.455][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:33.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.457][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.459][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:33.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:33.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.464][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:33.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:33.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:33.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:33.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:33.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:33.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:33.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:33.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:33.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:33.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:33.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:33.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:33.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:33.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:33.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:33.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:33.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:33.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:33.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:33.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:33.546][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-07-05 20:52:33.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:33.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:33.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:33.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:33.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:33.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:33.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:33.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:33.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:33.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:33.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:33.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:33.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:33.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:33.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:33.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:33.569][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-07-05 20:52:33.570][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:33.571][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-07-05 20:52:33.572][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:33.573][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:33.574][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:33.575][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:33.576][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:33.577][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:33.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:33.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:33.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:33.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:33.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:33.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:33.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:33.590][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-07-05 20:52:33.593][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:33.594][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:33.595][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-07-05 20:52:33.986][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-07-05 20:52:34.407][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:34.410][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-07-05 20:52:34.416][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-07-05 20:52:34.421][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-07-05 20:52:34.423][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:34.425][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:34.427][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:34.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:34.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:34.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:34.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:34.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:34.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:34.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:34.450][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:34.451][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:34.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.454][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:34.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:34.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.462][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:34.463][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:34.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.466][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.468][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:34.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:34.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.472][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:34.474][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:34.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.476][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.477][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:34.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:34.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.481][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:34.482][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:34.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.484][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:34.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:34.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.490][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:34.491][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:34.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.492][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:34.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:34.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.497][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:34.498][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:34.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.500][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.501][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:34.502][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:34.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.504][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.505][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:34.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:34.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.509][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:34.510][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:34.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.512][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:34.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:34.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.517][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:34.530][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:34.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.532][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.534][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:34.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:34.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.538][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:34.539][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:34.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.541][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.542][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:34.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:34.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.546][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:34.547][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:34.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.549][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.551][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:34.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:34.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:34.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:34.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:34.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:34.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:34.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:34.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:34.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:34.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:34.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:34.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:34.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:34.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:34.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:34.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:34.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:34.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:34.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:34.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:34.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:34.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:34.594][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-07-05 20:52:34.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:34.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:34.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.599][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:34.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:34.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:34.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:34.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:34.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:34.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:34.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:34.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:34.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:34.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:34.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:34.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:34.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:34.616][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-07-05 20:52:34.617][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:34.619][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-07-05 20:52:34.620][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:34.621][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:34.622][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:34.623][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:34.624][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:34.625][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:34.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:34.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:34.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:34.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:34.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:34.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:34.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:34.639][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-07-05 20:52:34.642][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:34.643][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:34.644][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-07-05 20:52:35.047][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-07-05 20:52:35.496][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:35.507][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-07-05 20:52:35.514][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-07-05 20:52:35.517][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-07-05 20:52:35.518][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:35.520][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:35.522][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:35.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:35.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:35.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:35.541][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:35.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:35.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:35.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:35.548][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:35.549][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:35.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.552][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:35.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:35.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.558][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:35.559][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:35.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.561][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.563][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:35.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:35.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.567][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:35.569][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:35.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.571][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.572][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:35.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:35.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.577][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:35.578][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:35.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.580][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.581][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:35.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:35.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.608][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:35.609][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:35.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.611][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:35.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:35.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.616][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:35.617][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:35.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.619][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.620][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:35.622][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:35.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.624][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.625][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:35.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:35.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.629][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:35.630][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:35.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.632][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:35.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:35.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.638][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:35.639][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:35.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.641][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:35.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:35.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.647][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:35.648][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:35.649][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.650][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.651][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:35.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:35.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.655][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:35.656][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:35.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.658][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.660][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:35.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:35.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:35.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:35.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:35.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:35.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:35.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:35.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:35.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:35.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:35.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:35.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:35.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:35.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:35.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:35.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:35.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:35.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:35.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:35.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:35.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:35.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:35.706][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-07-05 20:52:35.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:35.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:35.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:35.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:35.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:35.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:35.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:35.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:35.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:35.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:35.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:35.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:35.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:35.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:35.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:35.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:35.730][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-07-05 20:52:35.731][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:35.733][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-07-05 20:52:35.734][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:35.735][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:35.736][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:35.737][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:35.738][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:35.739][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:35.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:35.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:35.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:35.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:35.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:35.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:35.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:35.752][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-07-05 20:52:35.755][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:35.756][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:35.757][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-07-05 20:52:36.147][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-07-05 20:52:36.582][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:36.586][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-07-05 20:52:36.592][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-07-05 20:52:36.596][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-07-05 20:52:36.599][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:36.601][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:36.603][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:36.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:36.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:36.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:36.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:36.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:36.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:36.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:36.670][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:36.671][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:36.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.673][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:36.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:36.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.678][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:36.679][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:36.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.681][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.682][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:36.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:36.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.686][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:36.687][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:36.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.689][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.690][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:36.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:36.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.694][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:36.695][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:36.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.697][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.698][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:36.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:36.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.702][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:36.703][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:36.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.705][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.706][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:36.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:36.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.710][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:36.711][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:36.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.712][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.713][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:36.714][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:36.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.716][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.717][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:36.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:36.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.721][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:36.722][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:36.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.724][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:36.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:36.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.729][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:36.730][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:36.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.732][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.733][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:36.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:36.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.737][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:36.738][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:36.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.740][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.741][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:36.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:36.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.745][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:36.746][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:36.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.748][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.749][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:36.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:36.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:36.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:36.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:36.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:36.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:36.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:36.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:36.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:36.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:36.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:36.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:36.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:36.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:36.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:36.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:36.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:36.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:36.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:36.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:36.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:36.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:36.792][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-07-05 20:52:36.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:36.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:36.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:36.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:36.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:36.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:36.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:36.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:36.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:36.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:36.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:36.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:36.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:36.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:36.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:36.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:36.814][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-07-05 20:52:36.815][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:36.816][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-07-05 20:52:36.817][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:36.818][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:36.819][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:36.820][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:36.821][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:36.822][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:36.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:36.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:36.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:36.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:36.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:36.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:36.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:36.841][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-07-05 20:52:36.844][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:36.845][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:36.846][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-07-05 20:52:37.237][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-07-05 20:52:37.664][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:37.666][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-07-05 20:52:37.669][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-07-05 20:52:37.672][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-07-05 20:52:37.674][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:37.675][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:37.676][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:37.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:37.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:37.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:37.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:37.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:37.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:37.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:37.689][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:37.690][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:37.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.692][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:37.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:37.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.697][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:37.698][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:37.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.699][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.701][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:37.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:37.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.704][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:37.705][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:37.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.707][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.708][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:37.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:37.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.712][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:37.713][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:37.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.715][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.716][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:37.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:37.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.720][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:37.721][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:37.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.723][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:37.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:37.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.728][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:37.729][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:37.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.731][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.732][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:37.733][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:37.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.735][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.736][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:37.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:37.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.740][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:37.741][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:37.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.742][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:37.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:37.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.747][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:37.749][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:37.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.750][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:37.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:37.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.756][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:37.757][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:37.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.758][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.760][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:37.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:37.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.764][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:37.765][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:37.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.766][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.768][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:37.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:37.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:37.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:37.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:37.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:37.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:37.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:37.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:37.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:37.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:37.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:37.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:37.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:37.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:37.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:37.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:37.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:37.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:37.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:37.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:37.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:37.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:37.815][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-07-05 20:52:37.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:37.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:37.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:37.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:37.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:37.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:37.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:37.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:37.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:37.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:37.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:37.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:37.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:37.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:37.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:37.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:37.846][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-07-05 20:52:37.847][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:37.849][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-07-05 20:52:37.850][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:37.851][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:37.852][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:37.853][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:37.854][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:37.855][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:37.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:37.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:37.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:37.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:37.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:37.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:37.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:37.868][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-07-05 20:52:37.871][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:37.872][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:37.873][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-07-05 20:52:38.262][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-07-05 20:52:38.673][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:38.680][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-07-05 20:52:38.687][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-07-05 20:52:38.692][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-07-05 20:52:38.695][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:38.697][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:38.700][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:38.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:38.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:38.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:38.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:38.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:38.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:38.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:38.730][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:38.732][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:38.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.735][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:38.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:38.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.743][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:38.745][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:38.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.747][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.749][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:38.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:38.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.754][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:38.755][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:38.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.758][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.759][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:38.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:38.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.765][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:38.766][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:38.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.768][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.770][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:38.771][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:38.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.774][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.775][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:38.777][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:38.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.779][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.781][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:38.782][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:38.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.784][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.786][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:38.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:38.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.791][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:38.793][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:38.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.795][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:38.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:38.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.802][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:38.803][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:38.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.806][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:38.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:38.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.813][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:38.815][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:38.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.817][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.819][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:38.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:38.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.824][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:38.825][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:38.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.828][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:38.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:38.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:38.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:38.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:38.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:38.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:38.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:38.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:38.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:38.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:38.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:38.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:38.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:38.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:38.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:38.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:38.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:38.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:38.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:38.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:38.913][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-07-05 20:52:38.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:38.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:38.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:38.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:38.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:38.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:38.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:38.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:38.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:38.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:38.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:38.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:38.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:38.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:38.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:38.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:38.944][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-07-05 20:52:38.945][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:38.947][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-07-05 20:52:38.949][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:38.950][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:38.951][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:38.953][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:38.954][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:38.955][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:38.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:38.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:38.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:38.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:38.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:38.969][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:38.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:38.971][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-07-05 20:52:38.974][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:38.975][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:38.977][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-07-05 20:52:39.377][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-07-05 20:52:39.815][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:39.820][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-07-05 20:52:39.827][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-07-05 20:52:39.832][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-07-05 20:52:39.835][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:39.838][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:39.840][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:39.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:39.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:39.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:39.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:39.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:39.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:39.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:39.866][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:39.868][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:39.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.871][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:39.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:39.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.880][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:39.881][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:39.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.884][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.885][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:39.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:39.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.890][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:39.891][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:39.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.894][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.895][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:39.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:39.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.899][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:39.901][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:39.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.902][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.904][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:39.905][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:39.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.907][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.908][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:39.909][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:39.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.911][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.912][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:39.913][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:39.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.914][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.916][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:39.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:39.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.919][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:39.920][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:39.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.922][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:39.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:39.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.927][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:39.928][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:39.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.930][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.931][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:39.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:39.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.935][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:39.936][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:39.937][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.938][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.939][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:39.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:39.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.943][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:39.944][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:39.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.946][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:39.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:39.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:39.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:39.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:39.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:39.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:39.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:39.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:39.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:39.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:39.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:39.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:39.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:39.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:39.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:39.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:39.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:39.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:39.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:39.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:39.993][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-07-05 20:52:39.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:39.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:39.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:39.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:39.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:39.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:40.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:40.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:40.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:40.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:40.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:40.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:40.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:40.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:40.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:40.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:40.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:40.014][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:40.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:40.016][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-07-05 20:52:40.017][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:40.018][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-07-05 20:52:40.020][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:40.021][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:40.022][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:40.023][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:40.024][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:40.025][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:40.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:40.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:40.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:40.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:40.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:40.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:40.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:40.037][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-07-05 20:52:40.040][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:40.041][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:40.042][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-07-05 20:52:40.457][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-07-05 20:52:40.904][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:40.909][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-07-05 20:52:40.915][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-07-05 20:52:40.920][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-07-05 20:52:40.923][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:40.926][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:40.928][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:40.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:40.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:40.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:40.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:40.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:40.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:40.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:40.953][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:40.954][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:40.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:40.957][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:40.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:40.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:40.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:40.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:40.965][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:40.967][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:40.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:40.969][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:40.971][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:40.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:40.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:40.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:40.976][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:40.977][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:40.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:40.979][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:40.981][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:40.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:40.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:40.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:40.985][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:40.986][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:40.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:40.988][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:40.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:40.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:40.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:40.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:40.994][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:40.995][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:40.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:40.997][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:40.998][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:40.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:41.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.002][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:41.003][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:41.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.005][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.006][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:41.007][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:41.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.009][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.010][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:41.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:41.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.014][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:41.015][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:41.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.017][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:41.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:41.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.022][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:41.023][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:41.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.024][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:41.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:41.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.030][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:41.042][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:41.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.044][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.045][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:41.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:41.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.049][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:41.050][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:41.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.052][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.054][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:41.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:41.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:41.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:41.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:41.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:41.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:41.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:41.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:41.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:41.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:41.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:41.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:41.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:41.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:41.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:41.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:41.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:41.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:41.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:41.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:41.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:41.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:41.099][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-07-05 20:52:41.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:41.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:41.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:41.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:41.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:41.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:41.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:41.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:41.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:41.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:41.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:41.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:41.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:41.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:41.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:41.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:41.122][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-07-05 20:52:41.123][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:41.125][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-07-05 20:52:41.126][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:41.127][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:41.128][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:41.129][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:41.130][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:41.131][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:41.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:41.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:41.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:41.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:41.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:41.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:41.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:41.144][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-07-05 20:52:41.147][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:41.148][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:41.149][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-07-05 20:52:41.549][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-07-05 20:52:41.990][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:41.994][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-07-05 20:52:41.999][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-07-05 20:52:42.002][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-07-05 20:52:42.004][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:42.006][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:42.008][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:42.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:42.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:42.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:42.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:42.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:42.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:42.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:42.028][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:42.030][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:42.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.032][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:42.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:42.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.039][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:42.041][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:42.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.043][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.045][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:42.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:42.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.050][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:42.051][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:42.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.053][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:42.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:42.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.060][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:42.061][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:42.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.063][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:42.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:42.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.070][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:42.071][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:42.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.074][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.075][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:42.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:42.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.106][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:42.107][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:42.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.110][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.111][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:42.112][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:42.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.115][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.116][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:42.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:42.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.121][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:42.122][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:42.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.125][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:42.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:42.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.131][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:42.132][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:42.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.135][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:42.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:42.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.142][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:42.143][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:42.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.145][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.147][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:42.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:42.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.152][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:42.153][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:42.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.155][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.157][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:42.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:42.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:42.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:42.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:42.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:42.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:42.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:42.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:42.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:42.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:42.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:42.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:42.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:42.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:42.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:42.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:42.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:42.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:42.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:42.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:42.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:42.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:42.208][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-07-05 20:52:42.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:42.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:42.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:42.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:42.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:42.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:42.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:42.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:42.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:42.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:42.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:42.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:42.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:42.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:42.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:42.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:42.235][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-07-05 20:52:42.236][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:42.238][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-07-05 20:52:42.239][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:42.240][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:42.242][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:42.243][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:42.244][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:42.245][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:42.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:42.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:42.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:42.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:42.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:42.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:42.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:42.260][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-07-05 20:52:42.264][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:42.265][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:42.267][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-07-05 20:52:42.659][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-07-05 20:52:43.072][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:43.077][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-07-05 20:52:43.086][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-07-05 20:52:43.092][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-07-05 20:52:43.095][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:43.098][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:43.101][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:43.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:43.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:43.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:43.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:43.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:43.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:43.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:43.130][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:43.132][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:43.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.135][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:43.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:43.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.158][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:43.159][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:43.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.161][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.163][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:43.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:43.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.167][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:43.169][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:43.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.170][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.172][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:43.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:43.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.176][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:43.177][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:43.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.179][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:43.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:43.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.185][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:43.187][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:43.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.189][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.190][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:43.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:43.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.194][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:43.196][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:43.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.198][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.199][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:43.200][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:43.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.202][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.204][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:43.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:43.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.208][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:43.209][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:43.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.211][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:43.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:43.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.218][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:43.219][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:43.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.221][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.223][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:43.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:43.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.227][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:43.228][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:43.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.230][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.231][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:43.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:43.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.236][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:43.237][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:43.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.239][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.240][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:43.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:43.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:43.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:43.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:43.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:43.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:43.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:43.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:43.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:43.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:43.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:43.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:43.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:43.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:43.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:43.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:43.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:43.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:43.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:43.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:43.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:43.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:43.287][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-07-05 20:52:43.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:43.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:43.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:43.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:43.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:43.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:43.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:43.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:43.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:43.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:43.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:43.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:43.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:43.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:43.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:43.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:43.313][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-07-05 20:52:43.315][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:43.317][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-07-05 20:52:43.318][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:43.320][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:43.321][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:43.322][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:43.323][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:43.324][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:43.328][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:43.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:43.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:43.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:43.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:43.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:43.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:43.340][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-07-05 20:52:43.344][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:43.345][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:43.346][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-07-05 20:52:43.782][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-07-05 20:52:44.186][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:44.191][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-07-05 20:52:44.199][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-07-05 20:52:44.204][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-07-05 20:52:44.207][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:44.210][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:44.213][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:44.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:44.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:44.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:44.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:44.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:44.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:44.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:44.237][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:44.239][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:44.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.242][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:44.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:44.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.249][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:44.251][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:44.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.253][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.255][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:44.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:44.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.260][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:44.261][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:44.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.263][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.265][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:44.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:44.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.269][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:44.270][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:44.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.272][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.274][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:44.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:44.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.278][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:44.279][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:44.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.281][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.282][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:44.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:44.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.287][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:44.288][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:44.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.290][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.291][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:44.292][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:44.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.294][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.296][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:44.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:44.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.305][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:44.308][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:44.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.310][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:44.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:44.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.317][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:44.318][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:44.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.320][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.322][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:44.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:44.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.326][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:44.327][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:44.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.330][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.331][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:44.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:44.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.335][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:44.336][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:44.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.338][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.340][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:44.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:44.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:44.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:44.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:44.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:44.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:44.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:44.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:44.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:44.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:44.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:44.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:44.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:44.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:44.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:44.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:44.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:44.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:44.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:44.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:44.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:44.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:44.388][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-07-05 20:52:44.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:44.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:44.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:44.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:44.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:44.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:44.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:44.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:44.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:44.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:44.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:44.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:44.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:44.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:44.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:44.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:44.439][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-07-05 20:52:44.440][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:44.442][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-07-05 20:52:44.444][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:44.445][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:44.446][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:44.447][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:44.448][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:44.449][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:44.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:44.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:44.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:44.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:44.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:44.462][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:44.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:44.464][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-07-05 20:52:44.468][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:44.469][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:44.470][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-07-05 20:52:44.859][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-07-05 20:52:45.269][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:45.272][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-07-05 20:52:45.277][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-07-05 20:52:45.281][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-07-05 20:52:45.284][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:45.285][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:45.287][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:45.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:45.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:45.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:45.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:45.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:45.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:45.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:45.307][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:45.309][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:45.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.312][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:45.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:45.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.319][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:45.321][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:45.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.323][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.325][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:45.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:45.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.330][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:45.331][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:45.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.333][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.334][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:45.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:45.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.339][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:45.340][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:45.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.342][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:45.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:45.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.347][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:45.348][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:45.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.349][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:45.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:45.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.354][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:45.355][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:45.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.357][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.358][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:45.359][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:45.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.361][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.362][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:45.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:45.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.366][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:45.367][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:45.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.369][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:45.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:45.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.374][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:45.375][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:45.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.376][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.378][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:45.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:45.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.382][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:45.383][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:45.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.385][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.386][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:45.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:45.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.390][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:45.391][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:45.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.392][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.393][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:45.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:45.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:45.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:45.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:45.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:45.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:45.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:45.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:45.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:45.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:45.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:45.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:45.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:45.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:45.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:45.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:45.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:45.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:45.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:45.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:45.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:45.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:45.443][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-07-05 20:52:45.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:45.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:45.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:45.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:45.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:45.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:45.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:45.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:45.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:45.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:45.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:45.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:45.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:45.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:45.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:45.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:45.465][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-07-05 20:52:45.466][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:45.467][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-07-05 20:52:45.469][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:45.470][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:45.471][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:45.472][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:45.472][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:45.473][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:45.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:45.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:45.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:45.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:45.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:45.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:45.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:45.486][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-07-05 20:52:45.488][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:45.489][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:45.491][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-07-05 20:52:45.877][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-07-05 20:52:46.348][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:46.350][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-07-05 20:52:46.354][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-07-05 20:52:46.357][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-07-05 20:52:46.358][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:46.359][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:46.360][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:46.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:46.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:46.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:46.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:46.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:46.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:46.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:46.373][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:46.374][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:46.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.375][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:46.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:46.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.380][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:46.382][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:46.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.384][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.385][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:46.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:46.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.390][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:46.391][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:46.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.394][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.395][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:46.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:46.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.400][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:46.401][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:46.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.403][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.404][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:46.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:46.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.408][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:46.409][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:46.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.411][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:46.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:46.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.416][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:46.417][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:46.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.419][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.421][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:46.423][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:46.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.426][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.428][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:46.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:46.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.434][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:46.436][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:46.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.439][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:46.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:46.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.447][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:46.448][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:46.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.451][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:46.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:46.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.460][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:46.461][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:46.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.463][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.464][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:46.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:46.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.468][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:46.469][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:46.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.471][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.482][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:46.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:46.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:46.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:46.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:46.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:46.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:46.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:46.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:46.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:46.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:46.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:46.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:46.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:46.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:46.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:46.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:46.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:46.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:46.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:46.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:46.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:46.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:46.525][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-07-05 20:52:46.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:46.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:46.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:46.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:46.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:46.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:46.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:46.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:46.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:46.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:46.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:46.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:46.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:46.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:46.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:46.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:46.546][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-07-05 20:52:46.547][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:46.549][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-07-05 20:52:46.550][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:46.551][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:46.552][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:46.553][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:46.554][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:46.555][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:46.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:46.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:46.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:46.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:46.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:46.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:46.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:46.573][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-07-05 20:52:46.577][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:46.579][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:46.581][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-07-05 20:52:47.760][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-07-05 20:52:48.175][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:48.180][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-07-05 20:52:48.186][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-07-05 20:52:48.189][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-07-05 20:52:48.191][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:48.193][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:48.194][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:48.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:48.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:48.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:48.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:48.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:48.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:48.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:48.218][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:48.219][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:48.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.223][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:48.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:48.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.230][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:48.232][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:48.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.234][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.236][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:48.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:48.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.241][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:48.242][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:48.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.245][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.247][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:48.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:48.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.252][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:48.254][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:48.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.256][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.258][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:48.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:48.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.265][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:48.267][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:48.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.270][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:48.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:48.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.281][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:48.283][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:48.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.287][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.289][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:48.291][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.295][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.333][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:48.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.343][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:48.346][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:48.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.349][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:48.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:48.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.359][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:48.361][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:48.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.365][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:48.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:48.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.374][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:48.376][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:48.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.379][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.381][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:48.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:48.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.387][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:48.389][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:48.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.393][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.395][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:48.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:48.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:48.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:48.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:48.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:48.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:48.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:48.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:48.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:48.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:48.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:48.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:48.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:48.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:48.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:48.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:48.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:48.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:48.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:48.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:48.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:48.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:48.472][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-07-05 20:52:48.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:48.531][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:52:48.535][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:52:48.538][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-05 20:52:48.541][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:52:48.544][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-05 20:52:48.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:48.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:48.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:48.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:48.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:48.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:48.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:48.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:48.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:48.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:48.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:48.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:48.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:48.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:48.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:48.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:48.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:48.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:48.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:48.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:48.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:48.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:48.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:48.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:48.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:48.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:48.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:48.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:48.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:48.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:48.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:48.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:48.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:48.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:48.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:48.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:48.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:48.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:48.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:48.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:48.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:48.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:48.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:48.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:48.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:48.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:48.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:48.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:48.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:48.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:48.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:48.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:48.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:48.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:48.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:48.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:48.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:48.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:48.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:48.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:48.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:48.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:48.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:48.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:48.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:48.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:48.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:48.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:48.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:48.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:48.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:48.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:48.986][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:48.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:48.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:48.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:49.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:49.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:49.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:49.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:49.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:49.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:49.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:49.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:49.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:49.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:49.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:49.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:49.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:49.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:49.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:49.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:49.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:49.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:49.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:49.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:49.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:49.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:49.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:49.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:49.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:49.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:49.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:49.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:49.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:49.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:49.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:49.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:49.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:49.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:49.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:49.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:49.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:49.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:49.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:49.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:49.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:49.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:49.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:49.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:49.249][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:49.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:49.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:49.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:49.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:49.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:49.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:49.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:49.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:49.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:49.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:49.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:49.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:49.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:49.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:49.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:49.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:49.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:49.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:49.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:49.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:49.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:49.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:49.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:49.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:49.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:49.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:49.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:49.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:49.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:49.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:49.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:49.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:49.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:49.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:49.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:49.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:49.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:49.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:49.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:49.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:49.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:49.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:49.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:49.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:49.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:49.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:49.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:49.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:49.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:49.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:49.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:49.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:49.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:49.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:49.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:49.608][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:52:49.612][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:49.614][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:49.617][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-05 20:52:54.613][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-05 20:52:55.005][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:55.009][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-07-05 20:52:55.015][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-07-05 20:52:55.020][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:52:55.025][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:55.026][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:55.029][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-05 20:52:55.418][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-05 20:52:55.910][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:55.915][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-07-05 20:52:55.970][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-07-05 20:52:55.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:55.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:55.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:55.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:56.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:56.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:56.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:56.007][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-07-05 20:52:56.009][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:56.012][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-07-05 20:52:56.015][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:56.017][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:56.019][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:56.020][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:56.022][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:56.024][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:56.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:56.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:56.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:56.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:56.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:56.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:56.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:56.048][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-07-05 20:52:56.053][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:56.055][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:56.057][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-07-05 20:52:56.509][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-07-05 20:52:56.938][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:56.944][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-07-05 20:52:56.953][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-07-05 20:52:56.960][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-07-05 20:52:56.964][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:56.966][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:56.968][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:56.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:56.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:56.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:56.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:56.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:56.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:56.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:56.993][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:56.995][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:56.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:56.998][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:56.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:57.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:57.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.005][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:57.006][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:57.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.009][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.011][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:57.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:57.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.016][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:57.018][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:57.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.020][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.022][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:57.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:57.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.028][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:57.030][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:57.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.032][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.034][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:57.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:57.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.039][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:57.041][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:57.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.043][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:57.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:57.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.050][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:57.052][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:57.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.054][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.056][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:57.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:57.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.061][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:57.063][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:57.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.065][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.067][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:57.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:57.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.072][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.074][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.076][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.083][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:57.084][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:57.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.086][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:57.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:57.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.094][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:57.095][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:57.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.098][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.100][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:57.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:57.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.105][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:57.106][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:57.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.108][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.110][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:57.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:57.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:57.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:57.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:57.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:57.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:57.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:57.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:57.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:57.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:57.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:57.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:57.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:57.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:57.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:57.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:57.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:57.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:57.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:57.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:57.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:57.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:57.201][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-07-05 20:52:57.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:57.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:57.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:57.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:57.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:57.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:57.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:57.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:57.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:57.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:57.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:57.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:57.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:57.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:57.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:57.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:57.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:57.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:57.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:57.261][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-07-05 20:52:57.262][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:52:57.264][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-07-05 20:52:57.266][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:52:57.267][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:52:57.269][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:52:57.270][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:52:57.272][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:52:57.273][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:52:57.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:57.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:57.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:57.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:57.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:57.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:57.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:57.292][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-07-05 20:52:57.296][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:52:57.297][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:52:57.299][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-07-05 20:52:57.721][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-07-05 20:52:58.141][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:52:58.144][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-07-05 20:52:58.148][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-07-05 20:52:58.152][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-07-05 20:52:58.153][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:52:58.155][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:52:58.156][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:52:58.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.172][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:58.174][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:58.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.176][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:58.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:58.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.183][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:58.184][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:58.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.187][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.188][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:52:58.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:52:58.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.195][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:58.197][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:58.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.200][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.202][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:52:58.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:52:58.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.210][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:58.211][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:58.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.214][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.216][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:52:58.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:52:58.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.222][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:58.224][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:58.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.227][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.229][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:52:58.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:52:58.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.236][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:58.246][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:52:58.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.259][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.262][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:58.264][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:58.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.267][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.269][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:52:58.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:58.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.273][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.274][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.276][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.281][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:58.282][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:58.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.284][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.286][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:52:58.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:52:58.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.290][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:58.291][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:58.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.293][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.294][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:52:58.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:52:58.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.298][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:58.299][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:58.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.301][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.303][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:52:58.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:52:58.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:58.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:58.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:58.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:58.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:58.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:58.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:58.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:58.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:58.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:58.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:58.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:58.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:58.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:58.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:58.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:58.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:58.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:58.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:52:58.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:52:58.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.349][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-07-05 20:52:58.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.383][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:52:58.387][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:52:58.388][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-05 20:52:58.390][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:52:58.391][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-05 20:52:58.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.421][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.428][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.532][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.543][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.644][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.645][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.738][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.758][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.759][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.769][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:58.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:58.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:58.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:58.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:58.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:58.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:58.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:58.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:58.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:58.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:58.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.077][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:52:59.081][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:52:59.083][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-05 20:52:59.084][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:52:59.086][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-05 20:52:59.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.199][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.305][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.352][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.498][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.499][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.557][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:52:59.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.733][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-05 20:52:59.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-05 20:52:59.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-05 20:52:59.748][biodb::testThat]
biodb.INFO [2024-07-05 20:52:59.749][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-07-05 20:52:59.751][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:52:59.752][biodb::testThat]
biodb.TRACE[2024-07-05 20:52:59.756][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-05 20:52:59.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-05 20:52:59.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:52:59.804][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:52:59.808][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:52:59.810][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-07-05 20:52:59.811][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:52:59.813][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-07-05 20:52:59.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.849][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:52:59.853][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:52:59.855][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-07-05 20:52:59.856][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:52:59.858][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-07-05 20:52:59.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:52:59.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:52:59.935][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-05 20:52:59.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:52:59.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:52:59.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:52:59.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:52:59.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:52:59.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:52:59.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:52:59.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:59.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:59.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:59.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:59.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.963][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:52:59.964][private$selectFields]
biodb.TRACE[2024-07-05 20:52:59.966][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:52:59.967][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:52:59.968][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:52:59.970][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:59.971][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:59.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.974][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.975][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:59.977][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:59.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.979][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.981][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:52:59.982][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:52:59.983][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:59.985][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:59.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.988][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.989][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:52:59.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:59.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:59.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:52:59.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:52:59.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:52:59.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:52:59.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.021][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-05 20:53:00.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:00.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:00.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:00.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:00.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:00.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:00.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:00.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.054][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:00.055][private$selectFields]
biodb.TRACE[2024-07-05 20:53:00.056][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:00.058][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:00.059][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:00.060][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.062][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.064][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.066][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.067][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.069][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.071][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:00.072][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:00.074][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.075][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.078][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.079][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:00.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.096][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-05 20:53:00.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:00.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:00.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:00.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:00.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:00.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:00.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:00.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.136][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:00.138][private$selectFields]
biodb.TRACE[2024-07-05 20:53:00.139][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:00.141][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:00.142][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:00.144][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.145][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.148][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.149][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.151][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.152][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.154][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.155][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:00.156][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:00.157][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.159][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.161][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.163][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:00.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:00.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.181][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-05 20:53:00.182][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-05 20:53:00.184][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-05 20:53:00.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:00.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:00.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:00.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:00.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:00.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:00.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:00.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:00.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:00.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:00.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:00.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:00.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:00.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:00.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:00.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:00.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:00.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:00.279][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:00.282][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:53:00.283][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:53:00.285][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-05 20:53:00.673][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-05 20:53:01.094][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:53:01.097][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-07-05 20:53:01.105][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-07-05 20:53:01.111][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:01.116][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:53:01.118][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:53:01.121][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-05 20:53:01.534][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-05 20:53:01.945][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:53:01.950][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-07-05 20:53:01.960][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-07-05 20:53:01.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:01.969][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:01.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:01.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:01.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:01.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:01.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:01.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:01.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:01.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:01.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:01.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:02.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.020][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:02.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:02.086][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-05 20:53:02.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.127][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.128][private$selectFields]
biodb.TRACE[2024-07-05 20:53:02.129][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:02.130][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:02.131][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.132][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.133][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.134][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.135][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.136][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.138][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.139][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.155][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.158][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.161][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.164][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.165][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:02.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.182][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-05 20:53:02.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.244][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.245][private$selectFields]
biodb.TRACE[2024-07-05 20:53:02.246][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:02.247][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:02.248][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.249][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.250][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.252][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.253][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.254][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.256][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.258][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.270][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.271][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.272][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.274][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.275][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:02.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.290][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-05 20:53:02.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.310][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.311][private$selectFields]
biodb.TRACE[2024-07-05 20:53:02.312][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:02.313][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:02.314][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.315][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.316][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.318][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.319][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.320][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.322][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.324][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.325][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.326][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.327][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.329][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.330][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:02.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.360][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-05 20:53:02.360][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-05 20:53:02.361][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-05 20:53:02.369][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-05 20:53:02.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-05 20:53:02.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-05 20:53:02.376][biodb::testThat]
biodb.INFO [2024-07-05 20:53:02.377][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-07-05 20:53:02.378][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:53:02.379][biodb::testThat]
biodb.TRACE[2024-07-05 20:53:02.382][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-05 20:53:02.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-05 20:53:02.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:02.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:02.415][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:02.419][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:02.420][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-07-05 20:53:02.421][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:02.422][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-07-05 20:53:02.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:02.446][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:02.450][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:02.451][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-07-05 20:53:02.452][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:02.453][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-07-05 20:53:02.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.473][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:02.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:02.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:02.498][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-05 20:53:02.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.523][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.524][private$selectFields]
biodb.TRACE[2024-07-05 20:53:02.525][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:02.526][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:02.527][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.528][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.529][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.530][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.531][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.532][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.534][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.535][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.536][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.537][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.538][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.540][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.541][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:02.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.554][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-05 20:53:02.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.571][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.572][private$selectFields]
biodb.TRACE[2024-07-05 20:53:02.573][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:02.574][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:02.575][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.576][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.577][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.579][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.579][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.580][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.582][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.583][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.584][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.585][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.586][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.587][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.588][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:02.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.601][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-05 20:53:02.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.607][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.618][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.619][private$selectFields]
biodb.TRACE[2024-07-05 20:53:02.620][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:02.621][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:02.622][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.623][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.624][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.625][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.626][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.627][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.628][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.629][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.630][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.631][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.632][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.633][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.634][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.635][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:02.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.648][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-05 20:53:02.649][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-05 20:53:02.649][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-05 20:53:02.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:02.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:02.692][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:02.695][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:02.696][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-07-05 20:53:02.698][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:02.699][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-07-05 20:53:02.703][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:02.708][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:02.710][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-07-05 20:53:02.711][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:02.713][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-07-05 20:53:02.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:02.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:02.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.798][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:02.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:02.837][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-05 20:53:02.839][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.864][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.867][private$selectFields]
biodb.TRACE[2024-07-05 20:53:02.869][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:02.871][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:02.873][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.874][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.876][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.878][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.879][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.880][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.882][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.884][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.885][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.886][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.888][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.890][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.891][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:02.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.908][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-05 20:53:02.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:02.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:02.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:02.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:02.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:02.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:02.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:02.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.954][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.957][private$selectFields]
biodb.TRACE[2024-07-05 20:53:02.959][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:02.961][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:02.962][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.976][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.978][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.982][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.984][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.986][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:02.989][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:02.993][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.995][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:02.996][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:02.998][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.003][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.005][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:03.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.028][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-05 20:53:03.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:03.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.050][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.051][private$selectFields]
biodb.TRACE[2024-07-05 20:53:03.052][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:03.053][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:03.054][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.055][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.056][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.058][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.059][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.060][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.062][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.063][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.064][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.065][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.066][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.068][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.069][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:03.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.091][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-05 20:53:03.093][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-05 20:53:03.095][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-05 20:53:03.114][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-05 20:53:03.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-05 20:53:03.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-05 20:53:03.128][biodb::testThat]
biodb.INFO [2024-07-05 20:53:03.131][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-07-05 20:53:03.132][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:53:03.133][biodb::testThat]
biodb.TRACE[2024-07-05 20:53:03.141][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-05 20:53:03.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-05 20:53:03.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:03.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:03.202][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:03.206][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:03.207][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-07-05 20:53:03.208][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:03.210][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-07-05 20:53:03.213][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:03.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:03.244][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:03.249][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:03.251][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-07-05 20:53:03.252][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:03.254][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-07-05 20:53:03.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:03.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:03.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:03.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:03.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:03.313][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-05 20:53:03.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:03.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.338][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.339][private$selectFields]
biodb.TRACE[2024-07-05 20:53:03.341][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:03.342][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:03.343][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.344][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.345][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.348][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.349][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.351][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.354][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.355][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.356][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.358][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.359][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.362][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.363][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:03.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.381][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-05 20:53:03.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.383][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.394][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:03.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.409][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.410][private$selectFields]
biodb.TRACE[2024-07-05 20:53:03.411][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:03.412][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:03.414][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.415][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.417][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.420][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.421][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.422][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.424][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.425][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.427][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.428][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.429][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.431][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.432][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:03.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.459][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-05 20:53:03.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:03.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.505][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.507][private$selectFields]
biodb.TRACE[2024-07-05 20:53:03.508][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:03.510][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:03.511][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.513][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.514][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.518][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.519][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.521][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.524][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.526][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.528][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.529][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.531][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.535][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.537][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:03.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.557][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-05 20:53:03.558][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-05 20:53:03.559][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-05 20:53:03.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:03.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:03.613][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:03.617][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:03.618][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-07-05 20:53:03.620][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:03.621][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-07-05 20:53:03.626][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:03.631][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:03.633][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-07-05 20:53:03.635][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:03.637][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-07-05 20:53:03.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:03.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:03.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:03.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:03.702][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.703][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:03.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:03.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:03.735][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-05 20:53:03.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:03.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.759][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.760][private$selectFields]
biodb.TRACE[2024-07-05 20:53:03.761][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:03.762][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:03.763][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.764][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.766][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.768][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.770][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.771][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.774][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.775][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.776][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.778][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.779][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.782][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.783][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:03.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.799][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-05 20:53:03.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:03.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.821][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.822][private$selectFields]
biodb.TRACE[2024-07-05 20:53:03.823][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:03.824][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:03.825][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.826][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.827][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.830][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.832][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.834][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.836][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.837][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.838][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.839][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.840][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.842][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.843][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:03.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.859][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-05 20:53:03.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:03.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:03.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:03.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:03.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:03.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.883][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.884][private$selectFields]
biodb.TRACE[2024-07-05 20:53:03.885][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-05 20:53:03.886][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-05 20:53:03.888][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.889][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.890][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.893][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.894][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.896][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.898][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.900][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.901][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-05 20:53:03.902][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.904][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.906][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.907][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-05 20:53:03.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:03.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:03.924][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-05 20:53:03.925][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-05 20:53:03.935][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-05 20:53:03.963][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-05 20:53:03.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-05 20:53:03.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:03.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-05 20:53:03.974][biodb::testThat]
biodb.INFO [2024-07-05 20:53:03.975][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-07-05 20:53:03.976][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:53:03.978][biodb::testThat]
biodb.DEBUG[2024-07-05 20:53:03.980][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-07-05 20:53:03.982][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:53:03.984][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-07-05 20:53:03.985][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:53:03.987][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:53:03.988][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:53:03.989][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:53:03.991][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:53:03.992][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:53:03.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:03.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:03.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:04.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:04.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:04.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:04.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:04.007][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-07-05 20:53:04.010][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:53:04.012][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:53:04.013][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-07-05 20:53:04.420][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-07-05 20:53:04.864][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:53:04.870][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-07-05 20:53:04.877][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-07-05 20:53:04.881][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-07-05 20:53:04.883][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:53:04.884][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:53:04.886][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:53:04.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:04.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:04.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:04.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:04.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:04.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:04.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:04.910][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:04.911][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:04.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:04.913][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:04.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:04.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:04.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:04.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:04.920][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:53:04.921][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:53:04.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:04.923][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:04.925][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:53:04.927][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:53:04.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:04.930][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:04.932][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:53:04.934][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:53:04.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:04.936][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:04.938][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:53:04.939][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:53:04.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:04.942][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:04.944][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:04.946][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:04.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:04.948][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:04.949][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:53:04.950][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:04.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:04.952][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:04.954][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:04.956][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:04.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:04.960][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:04.962][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:53:04.964][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:53:04.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:04.967][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:04.970][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:53:04.972][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:53:04.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:04.975][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:04.977][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:53:04.979][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:53:04.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:04.983][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:04.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:04.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:04.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:04.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:04.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:04.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:04.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:04.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:04.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:05.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:05.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:05.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:05.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:05.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:05.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:05.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:05.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:05.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:05.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:05.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:05.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:05.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:05.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:05.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:05.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:05.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:05.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:05.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:05.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:05.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:05.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:05.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:05.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:05.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:05.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:05.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:05.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:05.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:05.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:05.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:05.078][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-07-05 20:53:05.080][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-07-05 20:53:05.095][biodb::testThat]
biodb.INFO [2024-07-05 20:53:05.097][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-07-05 20:53:05.098][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:53:05.100][biodb::testThat]
biodb.DEBUG[2024-07-05 20:53:05.113][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-07-05 20:53:05.116][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-07-05 20:53:05.117][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-07-05 20:53:05.120][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-07-05 20:53:05.121][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-07-05 20:53:05.123][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:53:05.125][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:53:05.127][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:53:05.128][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:53:05.130][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:53:05.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:05.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:05.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:05.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:05.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:05.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:05.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:05.155][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-07-05 20:53:05.158][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:53:05.159][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:53:05.161][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-07-05 20:53:05.586][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-07-05 20:53:06.094][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:53:06.098][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-07-05 20:53:06.101][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-07-05 20:53:06.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:06.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:06.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:06.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:06.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:06.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:06.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:06.119][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-07-05 20:53:06.123][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:53:06.125][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:53:06.127][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-07-05 20:53:06.558][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-07-05 20:53:06.981][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:53:06.984][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-07-05 20:53:06.988][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-07-05 20:53:06.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:06.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:06.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:06.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:07.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:07.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:07.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:07.006][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-07-05 20:53:07.010][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:53:07.012][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:53:07.014][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-07-05 20:53:07.428][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-07-05 20:53:07.860][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:53:07.863][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-07-05 20:53:07.866][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-07-05 20:53:07.869][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-07-05 20:53:07.872][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:53:07.874][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-07-05 20:53:07.877][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-07-05 20:53:07.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:07.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:07.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:07.891][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:07.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:07.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:07.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:07.900][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:07.902][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:07.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:07.905][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:07.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:07.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:07.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:07.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:07.913][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:53:07.915][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:53:07.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:07.917][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:07.919][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:53:07.922][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:53:07.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:07.925][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:07.926][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:53:07.927][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:53:07.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:07.930][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:07.932][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:53:07.933][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:53:07.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:07.937][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:07.939][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:07.941][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:07.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:07.944][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:07.946][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:53:07.948][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:07.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:07.951][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:07.953][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:07.978][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:07.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:07.983][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:07.986][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:53:07.988][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:53:07.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:07.991][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:07.993][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:53:07.994][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:53:07.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:07.996][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:07.997][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:53:07.998][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:53:07.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.000][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:08.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:08.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:08.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:08.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:08.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:08.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:08.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:08.074][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.076][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.080][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.090][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:53:08.091][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:53:08.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.094][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.095][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:53:08.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:53:08.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.099][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:53:08.101][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:53:08.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.104][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.107][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:53:08.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:53:08.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.114][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:53:08.116][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:53:08.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.120][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:53:08.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:53:08.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.128][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:53:08.130][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:53:08.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.132][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:53:08.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:53:08.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.139][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:08.141][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:08.143][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.144][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.145][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:08.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:08.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.150][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:53:08.152][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:08.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.155][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.158][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:53:08.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:08.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.166][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:08.168][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:08.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.171][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:08.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:08.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.178][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:53:08.179][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:53:08.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.181][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:53:08.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:53:08.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.187][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:53:08.189][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:53:08.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.191][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.193][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:53:08.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:53:08.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.200][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:53:08.202][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:53:08.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.205][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.208][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:53:08.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:53:08.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:08.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:08.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:08.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:08.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:08.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:08.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:08.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:08.296][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.298][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.300][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.307][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:53:08.309][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:53:08.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.312][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.314][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:53:08.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:53:08.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.321][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:53:08.323][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:53:08.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.327][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.329][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:53:08.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:53:08.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.335][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:53:08.337][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:53:08.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.339][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:53:08.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:53:08.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.348][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:53:08.351][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:53:08.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.354][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.356][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:53:08.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:53:08.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.362][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:08.364][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:08.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.367][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.369][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:08.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:08.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.377][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:53:08.378][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:08.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.382][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.384][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:53:08.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:08.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.389][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:08.390][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:08.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.392][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:08.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:08.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.399][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:53:08.401][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:53:08.403][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.404][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.407][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:53:08.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:53:08.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.414][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:53:08.416][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:53:08.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.420][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.422][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:53:08.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:53:08.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.429][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:53:08.431][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:53:08.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.435][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.437][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:53:08.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:53:08.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.464][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:08.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:08.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:08.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:08.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:08.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:08.546][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-07-05 20:53:08.547][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-07-05 20:53:08.549][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-07-05 20:53:08.572][biodb::testThat]
biodb.INFO [2024-07-05 20:53:08.573][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-07-05 20:53:08.575][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:53:08.577][biodb::testThat]
biodb.INFO [2024-07-05 20:53:08.610][biodb::testThat]
biodb.INFO [2024-07-05 20:53:08.612][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-07-05 20:53:08.613][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:53:08.614][biodb::testThat]
biodb.INFO [2024-07-05 20:53:08.626][biodb::testThat]
biodb.INFO [2024-07-05 20:53:08.627][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-07-05 20:53:08.628][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:53:08.630][biodb::testThat]
biodb.DEBUG[2024-07-05 20:53:08.633][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:08.638][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:53:08.639][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:53:08.642][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-07-05 20:53:09.128][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-07-05 20:53:09.694][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:53:09.703][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-07-05 20:53:09.710][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-07-05 20:53:09.731][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:53:09.734][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:53:09.736][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:09.739][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:09.741][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:09.743][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:09.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:09.748][ef$get] fields variable is a list.
biodb.INFO [2024-07-05 20:53:09.752][biodb::testThat]
biodb.INFO [2024-07-05 20:53:09.754][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-07-05 20:53:09.756][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:53:09.759][biodb::testThat]
biodb.ERROR[2024-07-05 20:53:09.799][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-07-05 20:53:09.848][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-07-05 20:53:09.886][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-05 20:53:09.890][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-05 20:53:09.894][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-05 20:53:09.896][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-05 20:53:09.898][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:09.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:09.903][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:09.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:09.907][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:09.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-05 20:53:09.977][biodb::testContext]
biodb.INFO [2024-07-05 20:53:09.980][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-05 20:53:09.983][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-07-05 20:53:09.986][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-05 20:53:09.989][biodb::testContext]
biodb.INFO [2024-07-05 20:53:09.995][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-05 20:53:10.000][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-05 20:53:10.011][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-05 20:53:10.014][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-05 20:53:10.018][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-05 20:53:10.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.029][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-05 20:53:10.032][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-05 20:53:10.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.041][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-05 20:53:10.043][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-05 20:53:10.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.051][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-05 20:53:10.054][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-05 20:53:10.056][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-05 20:53:10.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.063][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-05 20:53:10.066][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-05 20:53:10.069][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-05 20:53:10.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.076][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-05 20:53:10.078][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-05 20:53:10.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.086][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-05 20:53:10.089][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-05 20:53:10.091][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-05 20:53:10.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.099][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-05 20:53:10.102][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-05 20:53:10.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.110][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-05 20:53:10.112][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-05 20:53:10.114][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-05 20:53:10.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.122][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-05 20:53:10.124][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-05 20:53:10.126][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-05 20:53:10.128][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-05 20:53:10.130][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-05 20:53:10.133][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-05 20:53:10.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.139][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-05 20:53:10.141][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-05 20:53:10.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.148][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-05 20:53:10.150][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-05 20:53:10.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.156][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-05 20:53:10.159][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-05 20:53:10.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.166][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-05 20:53:10.168][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-05 20:53:10.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.173][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-05 20:53:10.174][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-05 20:53:10.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.179][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-05 20:53:10.182][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-05 20:53:10.191][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-05 20:53:10.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.200][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-05 20:53:10.203][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-05 20:53:10.206][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-05 20:53:10.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.215][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-05 20:53:10.219][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:10.221][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-05 20:53:10.223][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.225][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:10.227][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.228][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:10.230][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:10.231][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:53:10.233][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-05 20:53:10.235][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:10.237][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.239][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-05 20:53:10.242][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:10.244][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:10.247][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.250][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-05 20:53:10.250][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-05 20:53:10.250][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-05 20:53:10.250][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-05 20:53:10.250][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-05 20:53:10.252][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:53:10.254][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:10.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:10.258][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:10.260][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:10.262][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:10.264][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:10.267][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:10.269][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:10.271][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:10.273][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:10.275][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:10.277][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-05 20:53:10.281][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:10.283][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-05 20:53:10.286][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.288][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:10.290][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.292][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:10.293][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:10.295][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:53:10.297][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-05 20:53:10.299][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:10.301][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.302][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-05 20:53:10.304][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:10.307][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:10.309][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.311][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-05 20:53:10.311][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-05 20:53:10.311][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-05 20:53:10.311][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-05 20:53:10.311][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-05 20:53:10.313][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:53:10.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:10.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:10.319][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:10.322][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:10.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:10.326][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:10.328][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:10.330][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:10.332][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:10.726][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:10.728][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:10.731][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-05 20:53:10.734][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.736][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-05 20:53:10.738][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.740][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:10.742][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.744][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:10.746][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:10.748][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:53:10.751][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-05 20:53:10.754][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:10.756][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:10.759][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-05 20:53:10.762][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:10.764][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:10.766][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.768][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:10.770][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:53:10.772][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:10.774][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:10.775][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:10.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:10.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:10.779][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:10.780][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:10.781][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:10.782][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:10.783][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:10.785][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:10.787][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-05 20:53:10.789][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.790][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-05 20:53:10.791][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.792][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:10.793][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.794][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:10.795][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:10.796][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:53:10.797][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-05 20:53:10.798][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:10.799][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:10.800][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-05 20:53:10.801][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:10.803][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:10.804][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:10.806][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:10.808][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:53:10.809][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:10.811][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:10.813][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:10.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:10.816][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:10.817][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:10.819][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:10.821][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:10.822][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:10.824][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:10.826][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:10.829][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-05 20:53:10.831][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:10.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:10.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:10.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:10.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:10.967][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-05 20:53:10.969][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-05 20:53:10.971][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-05 20:53:10.972][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-05 20:53:10.974][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-05 20:53:10.976][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-05 20:53:10.978][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-05 20:53:10.980][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-05 20:53:10.983][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-05 20:53:10.986][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-05 20:53:10.988][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-05 20:53:10.992][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-05 20:53:10.995][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-05 20:53:11.000][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-05 20:53:11.005][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-05 20:53:11.009][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-05 20:53:11.013][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-05 20:53:11.015][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-05 20:53:11.017][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-05 20:53:11.043][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-05 20:53:11.047][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-05 20:53:11.050][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-05 20:53:11.053][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-05 20:53:11.055][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-05 20:53:11.058][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-05 20:53:11.062][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-05 20:53:11.066][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-05 20:53:11.070][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-05 20:53:11.073][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-05 20:53:11.077][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-05 20:53:11.081][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-05 20:53:11.084][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-05 20:53:11.086][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-05 20:53:11.090][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-05 20:53:11.093][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-05 20:53:11.096][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-05 20:53:11.099][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-05 20:53:11.103][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-05 20:53:11.106][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-05 20:53:11.109][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-05 20:53:11.112][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-05 20:53:11.116][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-05 20:53:11.119][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-05 20:53:11.123][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-05 20:53:11.127][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-05 20:53:11.130][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-05 20:53:11.133][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-05 20:53:11.136][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-05 20:53:11.140][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-05 20:53:11.144][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-05 20:53:11.148][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-05 20:53:11.152][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-05 20:53:11.156][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-05 20:53:11.160][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-05 20:53:11.164][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-05 20:53:11.168][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-05 20:53:11.173][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-05 20:53:11.178][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-05 20:53:11.181][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-05 20:53:11.184][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-05 20:53:11.186][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-05 20:53:11.188][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-05 20:53:11.190][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-05 20:53:11.192][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-05 20:53:11.194][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-05 20:53:11.197][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-05 20:53:11.200][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-05 20:53:11.202][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-05 20:53:11.205][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-05 20:53:11.209][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-05 20:53:11.211][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-05 20:53:11.214][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-05 20:53:11.217][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-05 20:53:11.220][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-05 20:53:11.223][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-05 20:53:11.226][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-05 20:53:11.230][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-05 20:53:11.234][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-05 20:53:11.238][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-05 20:53:11.240][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-05 20:53:11.242][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-05 20:53:11.243][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-05 20:53:11.245][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-05 20:53:11.248][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-05 20:53:11.251][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-05 20:53:11.253][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-05 20:53:11.255][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.258][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:11.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:11.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:11.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:11.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:11.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:11.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:11.450][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-05 20:53:11.453][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-05 20:53:11.457][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:11.459][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-05 20:53:11.461][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:11.463][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:11.465][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:11.467][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:11.469][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:11.470][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-05 20:53:11.472][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-05 20:53:11.474][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:11.475][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:11.477][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-05 20:53:11.478][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:11.480][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-05 20:53:11.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-05 20:53:11.480][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-05 20:53:11.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-05 20:53:11.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-05 20:53:11.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-05 20:53:11.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-05 20:53:11.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-05 20:53:11.480][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-05 20:53:11.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-05 20:53:11.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-05 20:53:11.482][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:11.483][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-05 20:53:11.483][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-05 20:53:11.483][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-05 20:53:11.485][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-05 20:53:11.487][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:11.488][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:11.489][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:11.491][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:11.492][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:11.492][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:11.493][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:53:11.493][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-05 20:53:11.494][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:11.495][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:11.496][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:11.497][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-05 20:53:11.497][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-05 20:53:11.498][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-05 20:53:11.501][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-05 20:53:11.504][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-05 20:53:11.506][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-05 20:53:11.509][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-05 20:53:11.511][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-05 20:53:11.520][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-05 20:53:11.524][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-05 20:53:11.527][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-05 20:53:11.531][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-05 20:53:11.533][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-05 20:53:11.536][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-05 20:53:11.539][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-05 20:53:11.541][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-05 20:53:11.544][biodb::testThat]
biodb.INFO [2024-07-05 20:53:11.546][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-07-05 20:53:11.547][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:53:11.548][biodb::testThat]
biodb.DEBUG[2024-07-05 20:53:11.555][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-05 20:53:11.563][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:11.566][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-05 20:53:11.568][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:11.571][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-05 20:53:11.579][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:11.586][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:53:11.589][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:53:11.593][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-05 20:53:12.008][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-05 20:53:12.497][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:53:12.502][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-07-05 20:53:12.509][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-07-05 20:53:12.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:12.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:12.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:12.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:12.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:12.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:12.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:12.530][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:12.533][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:53:12.534][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:53:12.536][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-05 20:53:12.994][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-05 20:53:13.430][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:53:13.434][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-07-05 20:53:13.439][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-07-05 20:53:13.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:13.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:13.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:13.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:13.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:13.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:13.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:13.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:13.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:13.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:13.607][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:13.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:13.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:13.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:13.622][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:13.630][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:13.633][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-07-05 20:53:13.635][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:13.638][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-07-05 20:53:13.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:13.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:13.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:13.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:13.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:13.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:13.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:13.664][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:13.672][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:13.675][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-07-05 20:53:13.677][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:13.680][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-07-05 20:53:13.684][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:13.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:13.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:13.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:13.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:13.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:13.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:13.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:13.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:13.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:13.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:13.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:13.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:13.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:13.741][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:13.746][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:13.748][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-07-05 20:53:13.751][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:13.754][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-07-05 20:53:13.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:13.759][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:13.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:13.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:13.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:13.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:13.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:13.777][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:13.782][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:13.784][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-07-05 20:53:13.786][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:13.788][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-07-05 20:53:13.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:13.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:13.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:13.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:13.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:13.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:13.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:13.815][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:13.824][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:53:13.827][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:53:13.832][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-05 20:53:14.284][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-05 20:53:14.719][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:53:14.723][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-07-05 20:53:14.731][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-07-05 20:53:14.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:14.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:14.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:14.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:14.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:14.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:14.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-05 20:53:14.773][biodb::testThat]
biodb.INFO [2024-07-05 20:53:14.775][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-07-05 20:53:14.777][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:53:14.779][biodb::testThat]
biodb.DEBUG[2024-07-05 20:53:14.784][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:14.789][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:53:14.791][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:53:14.797][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-05 20:53:15.237][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-05 20:53:15.699][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:53:15.704][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-07-05 20:53:15.710][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-07-05 20:53:15.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:15.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:15.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:15.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:15.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:15.756][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:15.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:15.767][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:15.773][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:53:15.775][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:53:15.777][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-05 20:53:16.232][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-05 20:53:16.657][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:53:16.661][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-07-05 20:53:16.675][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-07-05 20:53:16.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:16.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:16.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:16.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:16.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:16.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-05 20:53:16.702][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-05 20:53:16.705][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-05 20:53:16.707][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-05 20:53:16.709][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-05 20:53:16.711][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:16.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:16.714][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:16.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:16.717][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-05 20:53:16.728][biodb::testContext]
biodb.INFO [2024-07-05 20:53:16.730][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-05 20:53:16.732][biodb::testContext] Test context - Test web services
biodb.INFO [2024-07-05 20:53:16.733][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-05 20:53:16.734][biodb::testContext]
biodb.INFO [2024-07-05 20:53:16.737][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-05 20:53:16.739][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-05 20:53:16.746][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-05 20:53:16.749][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-05 20:53:16.752][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-05 20:53:16.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.762][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-05 20:53:16.764][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-05 20:53:16.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.772][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-05 20:53:16.774][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-05 20:53:16.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.782][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-05 20:53:16.784][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-05 20:53:16.787][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-05 20:53:16.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.792][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-05 20:53:16.793][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-05 20:53:16.794][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-05 20:53:16.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.798][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-05 20:53:16.799][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-05 20:53:16.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.814][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-05 20:53:16.818][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-05 20:53:16.821][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-05 20:53:16.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.828][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-05 20:53:16.831][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-05 20:53:16.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.838][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-05 20:53:16.840][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-05 20:53:16.842][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-05 20:53:16.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.848][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-05 20:53:16.849][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-05 20:53:16.851][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-05 20:53:16.853][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-05 20:53:16.854][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-05 20:53:16.856][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-05 20:53:16.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.862][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-05 20:53:16.864][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-05 20:53:16.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.871][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-05 20:53:16.874][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-05 20:53:16.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.884][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-05 20:53:16.886][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-05 20:53:16.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.895][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-05 20:53:16.897][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-05 20:53:16.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.903][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-05 20:53:16.905][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-05 20:53:16.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.911][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-05 20:53:16.913][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-05 20:53:16.919][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-05 20:53:16.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.930][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-05 20:53:16.931][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-05 20:53:16.933][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-05 20:53:16.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:16.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:16.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:16.940][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-05 20:53:16.945][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:16.947][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-05 20:53:16.950][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:16.952][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:16.955][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:16.957][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:16.960][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:16.962][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:53:16.964][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-05 20:53:16.966][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:16.968][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:16.970][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-05 20:53:16.971][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:16.973][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:17.009][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.023][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-05 20:53:17.023][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-05 20:53:17.023][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-05 20:53:17.023][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-05 20:53:17.023][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-05 20:53:17.025][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:53:17.027][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:17.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:17.031][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:17.033][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:17.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:17.036][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:17.038][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:17.040][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:17.041][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:17.043][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:17.045][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:17.047][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-05 20:53:17.052][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:17.055][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-05 20:53:17.058][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.060][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:17.062][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.064][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:17.066][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:17.068][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:53:17.069][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-05 20:53:17.071][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:17.073][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.074][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-05 20:53:17.076][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:17.078][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:17.080][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.082][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-05 20:53:17.082][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-05 20:53:17.082][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-05 20:53:17.082][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-05 20:53:17.082][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-05 20:53:17.083][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:53:17.085][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:17.086][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:17.088][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:17.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:17.091][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:17.092][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:17.094][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:17.096][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:17.098][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:17.100][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:17.102][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:17.105][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-05 20:53:17.112][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.115][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-05 20:53:17.117][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.120][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:17.121][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.123][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:17.125][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:17.126][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:53:17.128][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-05 20:53:17.129][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:17.131][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:17.132][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-05 20:53:17.134][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:17.135][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:17.137][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.138][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:17.139][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:53:17.141][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:17.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:17.143][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:17.145][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:17.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:17.148][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:17.151][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:17.154][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:17.155][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:17.157][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:17.159][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:17.163][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-05 20:53:17.169][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.172][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-05 20:53:17.174][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.176][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:17.179][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.181][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:17.183][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:17.185][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:53:17.186][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-05 20:53:17.189][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:17.191][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:17.192][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-05 20:53:17.194][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:17.195][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:17.197][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.199][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:17.201][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:53:17.202][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:17.203][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:17.204][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:17.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:17.207][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:17.208][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:17.209][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:17.211][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:17.212][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:17.213][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:17.216][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:17.220][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-05 20:53:17.222][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.373][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-05 20:53:17.376][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-05 20:53:17.379][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-05 20:53:17.382][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-05 20:53:17.385][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-05 20:53:17.388][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-05 20:53:17.391][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-05 20:53:17.395][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-05 20:53:17.398][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-05 20:53:17.400][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-05 20:53:17.402][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-05 20:53:17.404][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-05 20:53:17.406][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-05 20:53:17.408][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-05 20:53:17.409][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-05 20:53:17.412][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-05 20:53:17.415][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-05 20:53:17.418][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-05 20:53:17.420][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-05 20:53:17.422][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-05 20:53:17.425][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-05 20:53:17.428][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-05 20:53:17.431][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-05 20:53:17.433][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-05 20:53:17.436][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-05 20:53:17.438][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-05 20:53:17.440][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-05 20:53:17.441][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-05 20:53:17.443][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-05 20:53:17.444][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-05 20:53:17.445][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-05 20:53:17.446][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-05 20:53:17.449][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-05 20:53:17.452][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-05 20:53:17.457][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-05 20:53:17.460][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-05 20:53:17.463][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-05 20:53:17.465][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-05 20:53:17.467][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-05 20:53:17.470][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-05 20:53:17.471][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-05 20:53:17.473][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-05 20:53:17.476][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-05 20:53:17.478][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-05 20:53:17.482][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-05 20:53:17.486][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-05 20:53:17.490][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-05 20:53:17.495][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-05 20:53:17.500][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-05 20:53:17.503][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-05 20:53:17.505][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-05 20:53:17.508][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-05 20:53:17.511][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-05 20:53:17.513][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-05 20:53:17.516][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-05 20:53:17.518][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-05 20:53:17.521][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-05 20:53:17.523][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-05 20:53:17.526][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-05 20:53:17.529][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-05 20:53:17.531][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-05 20:53:17.534][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-05 20:53:17.535][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-05 20:53:17.537][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-05 20:53:17.538][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-05 20:53:17.540][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-05 20:53:17.541][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-05 20:53:17.543][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-05 20:53:17.544][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-05 20:53:17.545][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-05 20:53:17.547][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-05 20:53:17.549][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-05 20:53:17.551][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-05 20:53:17.553][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-05 20:53:17.557][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-05 20:53:17.559][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-05 20:53:17.561][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-05 20:53:17.563][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-05 20:53:17.566][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-05 20:53:17.568][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-05 20:53:17.570][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-05 20:53:17.572][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-05 20:53:17.573][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-05 20:53:17.575][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-05 20:53:17.577][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-05 20:53:17.578][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-05 20:53:17.579][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.581][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:17.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:17.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:17.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:17.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:17.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:17.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:17.760][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-05 20:53:17.762][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-05 20:53:17.766][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:17.767][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-05 20:53:17.769][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.771][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:17.773][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.775][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:17.776][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.778][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-05 20:53:17.779][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-05 20:53:17.781][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:17.782][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.784][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-05 20:53:17.785][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:17.787][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-05 20:53:17.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-05 20:53:17.787][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-05 20:53:17.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-05 20:53:17.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-05 20:53:17.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-05 20:53:17.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-05 20:53:17.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-05 20:53:17.787][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-05 20:53:17.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-05 20:53:17.787][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-05 20:53:17.789][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:17.790][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-05 20:53:17.790][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-05 20:53:17.790][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-05 20:53:17.791][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-05 20:53:17.792][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:17.793][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:17.794][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:17.795][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:17.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:17.798][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:17.799][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:53:17.799][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-05 20:53:17.800][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:17.801][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:17.802][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:17.802][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-05 20:53:17.802][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-05 20:53:17.804][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-05 20:53:17.807][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-05 20:53:17.809][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-05 20:53:17.812][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-05 20:53:17.815][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-05 20:53:17.818][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-05 20:53:17.825][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-05 20:53:17.827][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-05 20:53:17.829][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-05 20:53:17.832][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-05 20:53:17.834][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-05 20:53:17.836][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-05 20:53:17.837][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-05 20:53:17.839][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-05 20:53:17.841][biodb::testThat]
biodb.INFO [2024-07-05 20:53:17.843][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-07-05 20:53:17.844][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:53:17.846][biodb::testThat]
biodb.DEBUG[2024-07-05 20:53:17.852][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-05 20:53:17.859][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:17.861][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-05 20:53:17.863][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:17.865][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-05 20:53:17.871][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:17.877][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:53:17.879][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:53:17.881][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-05 20:53:18.330][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-05 20:53:18.785][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:53:18.802][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-07-05 20:53:18.812][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-07-05 20:53:18.833][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-05 20:53:18.836][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-05 20:53:18.839][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-05 20:53:18.841][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-05 20:53:18.844][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:18.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:18.848][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:18.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:18.852][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:18.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-05 20:53:18.862][biodb::testContext]
biodb.INFO [2024-07-05 20:53:18.864][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-05 20:53:18.867][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-07-05 20:53:18.869][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-05 20:53:18.871][biodb::testContext]
biodb.INFO [2024-07-05 20:53:18.876][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-05 20:53:18.881][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-05 20:53:18.889][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-05 20:53:18.891][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-05 20:53:18.892][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-05 20:53:18.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:18.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:18.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:18.900][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-05 20:53:18.902][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-05 20:53:18.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:18.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:18.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:18.909][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-05 20:53:18.912][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-05 20:53:18.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:18.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:18.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:18.919][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-05 20:53:18.921][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-05 20:53:18.923][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-05 20:53:18.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:18.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:18.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:18.930][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-05 20:53:18.931][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-05 20:53:18.933][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-05 20:53:18.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:18.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:18.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:18.938][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-05 20:53:18.940][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-05 20:53:18.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:18.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:18.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:18.946][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-05 20:53:18.947][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-05 20:53:18.949][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-05 20:53:18.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:18.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:18.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:18.955][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-05 20:53:18.957][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-05 20:53:18.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:18.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:18.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:18.963][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-05 20:53:18.964][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-05 20:53:18.965][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-05 20:53:18.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:18.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:18.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:18.971][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-05 20:53:18.973][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-05 20:53:18.974][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-05 20:53:18.976][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-05 20:53:18.978][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-05 20:53:18.980][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-05 20:53:18.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:18.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:18.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:18.987][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-05 20:53:18.989][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-05 20:53:18.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:18.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:18.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:18.994][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-05 20:53:18.996][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-05 20:53:18.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:18.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:18.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:18.999][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-05 20:53:19.000][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-05 20:53:19.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.004][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-05 20:53:19.005][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-05 20:53:19.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.009][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-05 20:53:19.010][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-05 20:53:19.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.014][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-05 20:53:19.016][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-05 20:53:19.021][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-05 20:53:19.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.028][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-05 20:53:19.030][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-05 20:53:19.032][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-05 20:53:19.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.039][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-05 20:53:19.043][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:19.044][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-05 20:53:19.045][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.047][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:19.048][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.049][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.051][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:19.052][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.053][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-05 20:53:19.054][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:19.055][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.056][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-05 20:53:19.057][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:19.059][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:19.061][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.063][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-05 20:53:19.063][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-05 20:53:19.063][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-05 20:53:19.063][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-05 20:53:19.063][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-05 20:53:19.065][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:53:19.067][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:19.069][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:19.070][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:19.072][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:19.073][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:19.075][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.077][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:19.079][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:19.080][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:19.082][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:19.083][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:19.085][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-05 20:53:19.089][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:19.090][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-05 20:53:19.092][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.094][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:19.096][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.097][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.098][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:19.112][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.115][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-05 20:53:19.117][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:19.120][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.122][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-05 20:53:19.124][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:19.127][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:19.129][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.131][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-05 20:53:19.131][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-05 20:53:19.131][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-05 20:53:19.131][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-05 20:53:19.131][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-05 20:53:19.134][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:53:19.136][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:19.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:19.140][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:19.141][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:19.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:19.143][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.145][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:19.146][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:19.146][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:19.147][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:19.149][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:19.151][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-05 20:53:19.154][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.156][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-05 20:53:19.158][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.159][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:19.160][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.161][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.162][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:19.163][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.164][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-05 20:53:19.165][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:19.166][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:19.168][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-05 20:53:19.169][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:19.171][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:19.172][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.174][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:19.175][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:53:19.177][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:19.178][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:19.180][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:19.182][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:19.183][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:19.185][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.187][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:19.188][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:19.190][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:19.191][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:19.193][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:19.195][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-05 20:53:19.199][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.200][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-05 20:53:19.201][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.203][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:19.204][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.206][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.207][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:19.209][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.210][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-05 20:53:19.212][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:19.213][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:19.215][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-05 20:53:19.216][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:19.218][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:19.220][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.221][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:19.223][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-05 20:53:19.224][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:19.226][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:19.227][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:19.229][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:19.230][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:19.232][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.233][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:19.235][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:19.236][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:19.237][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:19.239][self$setPropertyValue]
biodb.DEBUG[2024-07-05 20:53:19.241][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-05 20:53:19.243][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.343][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-05 20:53:19.345][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-05 20:53:19.358][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-05 20:53:19.359][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-05 20:53:19.361][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-05 20:53:19.362][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-05 20:53:19.364][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-05 20:53:19.365][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-05 20:53:19.367][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-05 20:53:19.368][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-05 20:53:19.370][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-05 20:53:19.372][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-05 20:53:19.375][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-05 20:53:19.377][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-05 20:53:19.380][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-05 20:53:19.382][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-05 20:53:19.385][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-05 20:53:19.387][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-05 20:53:19.388][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-05 20:53:19.391][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-05 20:53:19.393][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-05 20:53:19.396][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-05 20:53:19.398][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-05 20:53:19.400][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-05 20:53:19.402][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-05 20:53:19.403][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-05 20:53:19.405][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-05 20:53:19.406][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-05 20:53:19.407][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-05 20:53:19.409][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-05 20:53:19.411][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-05 20:53:19.413][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-05 20:53:19.414][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-05 20:53:19.415][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-05 20:53:19.417][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-05 20:53:19.418][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-05 20:53:19.419][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-05 20:53:19.421][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-05 20:53:19.423][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-05 20:53:19.425][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-05 20:53:19.427][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-05 20:53:19.430][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-05 20:53:19.433][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-05 20:53:19.434][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-05 20:53:19.436][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-05 20:53:19.438][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-05 20:53:19.440][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-05 20:53:19.442][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-05 20:53:19.443][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-05 20:53:19.445][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-05 20:53:19.446][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-05 20:53:19.447][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-05 20:53:19.449][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-05 20:53:19.450][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-05 20:53:19.452][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-05 20:53:19.455][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-05 20:53:19.458][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-05 20:53:19.460][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-05 20:53:19.462][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-05 20:53:19.465][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-05 20:53:19.467][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-05 20:53:19.469][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-05 20:53:19.471][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-05 20:53:19.474][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-05 20:53:19.476][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-05 20:53:19.478][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-05 20:53:19.481][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-05 20:53:19.484][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-05 20:53:19.488][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-05 20:53:19.490][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-05 20:53:19.491][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-05 20:53:19.493][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-05 20:53:19.495][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-05 20:53:19.496][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-05 20:53:19.498][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-05 20:53:19.500][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-05 20:53:19.503][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-05 20:53:19.505][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-05 20:53:19.508][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-05 20:53:19.510][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-05 20:53:19.513][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-05 20:53:19.515][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-05 20:53:19.518][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-05 20:53:19.521][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-05 20:53:19.524][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-05 20:53:19.526][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-05 20:53:19.527][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.529][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-05 20:53:19.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.707][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-05 20:53:19.710][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-05 20:53:19.714][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:19.717][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.719][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.721][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-05 20:53:19.723][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.725][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.727][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.730][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-05 20:53:19.732][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-05 20:53:19.735][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-05 20:53:19.737][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.738][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-05 20:53:19.740][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-05 20:53:19.741][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-05 20:53:19.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-05 20:53:19.741][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-05 20:53:19.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-05 20:53:19.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-05 20:53:19.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-05 20:53:19.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-05 20:53:19.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-05 20:53:19.741][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-05 20:53:19.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-05 20:53:19.741][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-05 20:53:19.742][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-05 20:53:19.743][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-05 20:53:19.743][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-05 20:53:19.743][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-05 20:53:19.744][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-05 20:53:19.745][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:19.746][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:19.747][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-05 20:53:19.749][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-05 20:53:19.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-05 20:53:19.751][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-05 20:53:19.752][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:53:19.752][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-05 20:53:19.753][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-05 20:53:19.754][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-05 20:53:19.755][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-05 20:53:19.756][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-05 20:53:19.756][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-05 20:53:19.758][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-05 20:53:19.760][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-05 20:53:19.762][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-05 20:53:19.764][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-05 20:53:19.766][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-05 20:53:19.767][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-05 20:53:19.772][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-05 20:53:19.773][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-05 20:53:19.775][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-05 20:53:19.778][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-05 20:53:19.780][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-05 20:53:19.781][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-05 20:53:19.783][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-05 20:53:19.784][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-05 20:53:19.787][biodb::testThat]
biodb.INFO [2024-07-05 20:53:19.789][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-07-05 20:53:19.791][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-05 20:53:19.793][biodb::testThat]
biodb.DEBUG[2024-07-05 20:53:19.801][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-05 20:53:19.809][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:19.813][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-05 20:53:19.815][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:19.818][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-05 20:53:19.824][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-05 20:53:19.829][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-05 20:53:19.832][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-07-05 20:53:19.835][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-05 20:53:19.838][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-07-05 20:53:19.844][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-07-05 20:53:19.846][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-05 20:53:19.849][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-07-05 20:53:19.852][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-05 20:53:19.853][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-05 20:53:19.855][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-05 20:53:19.856][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-05 20:53:19.858][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-05 20:53:19.859][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-05 20:53:19.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:19.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:19.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:19.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:19.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:19.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:19.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-05 20:53:19.904][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-07-05 20:53:19.909][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-05 20:53:19.911][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-05 20:53:19.913][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-07-05 20:53:20.342][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-07-05 20:53:21.492][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-05 20:53:21.496][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-07-05 20:53:21.503][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-07-05 20:53:21.506][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-07-05 20:53:21.508][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-05 20:53:21.509][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-05 20:53:21.510][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-05 20:53:21.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-05 20:53:21.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:21.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:21.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:21.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:21.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:21.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-05 20:53:21.532][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:21.534][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:21.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.537][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:21.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:21.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.547][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:53:21.549][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:53:21.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.552][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.554][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-05 20:53:21.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-05 20:53:21.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.559][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:53:21.560][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:53:21.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.563][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.566][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-05 20:53:21.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-05 20:53:21.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.573][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-05 20:53:21.574][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-05 20:53:21.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.577][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.580][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-05 20:53:21.581][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-05 20:53:21.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.584][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.587][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:21.588][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:21.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.591][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.593][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:21.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-05 20:53:21.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.598][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:53:21.600][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:21.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.602][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.605][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-05 20:53:21.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-05 20:53:21.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.611][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:21.612][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:21.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.615][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:21.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-05 20:53:21.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.623][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:53:21.624][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:53:21.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.627][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-05 20:53:21.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-05 20:53:21.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.636][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:53:21.638][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:53:21.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.641][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.644][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-05 20:53:21.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-05 20:53:21.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.651][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:53:21.653][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:53:21.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.656][ef$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.658][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-05 20:53:21.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-05 20:53:21.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:21.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:21.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:21.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:21.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:21.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:21.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-05 20:53:21.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-05 20:53:21.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:21.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:21.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:21.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:21.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:21.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:21.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:21.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:21.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:21.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:21.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-05 20:53:21.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-05 20:53:21.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-05 20:53:21.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-05 20:53:21.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-05 20:53:21.735][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-07-05 20:53:21.748][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-05 20:53:21.751][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-05 20:53:21.753][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-05 20:53:21.754][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-05 20:53:21.755][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-05 20:53:21.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-05 20:53:21.758][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-05 20:53:21.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-05 20:53:21.760][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-05 20:53:21.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 387 ]
>
> proc.time()
user system elapsed
29.238 1.350 76.677
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.108 | 0.053 | 1.836 | |
| ChebiEntry | 0.163 | 0.000 | 0.162 | |