Pierrick Roger
| Snapshot Date: 2024-11-01 13:40 -0400 (Fri, 01 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_20 |
| git_last_commit: e6b963e |
| git_last_commit_date: 2024-10-29 11:04:35 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-02 12:03 -0400 (Sat, 02 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4500 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4505 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 202/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.12.0 (landing page) Pierrick Roger
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2024-11-01 20:41:52 -0400 (Fri, 01 Nov 2024) |
| EndedAt: 2024-11-01 20:47:22 -0400 (Fri, 01 Nov 2024) |
| EllapsedTime: 330.8 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_1.12.0.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 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 [2024-11-01 20:46:13.599][biodb::testContext]
biodb.INFO [2024-11-01 20:46:13.601][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-01 20:46:13.602][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-11-01 20:46:13.603][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-01 20:46:13.604][biodb::testContext]
biodb.INFO [2024-11-01 20:46:13.611][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-01 20:46:13.613][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-01 20:46:13.620][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-01 20:46:13.621][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-01 20:46:13.622][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-01 20:46:13.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.626][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-01 20:46:13.647][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-01 20:46:13.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.651][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-01 20:46:13.652][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-01 20:46:13.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.655][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-01 20:46:13.656][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-01 20:46:13.658][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-01 20:46:13.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.662][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-01 20:46:13.663][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-01 20:46:13.664][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-01 20:46:13.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.667][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-01 20:46:13.668][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-01 20:46:13.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.672][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-01 20:46:13.673][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-01 20:46:13.674][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-01 20:46:13.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.678][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-01 20:46:13.679][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-01 20:46:13.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.683][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-01 20:46:13.684][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-01 20:46:13.685][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-01 20:46:13.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.689][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-01 20:46:13.690][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-01 20:46:13.691][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-01 20:46:13.692][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-01 20:46:13.693][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-01 20:46:13.694][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-01 20:46:13.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.698][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-01 20:46:13.699][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-01 20:46:13.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.703][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-01 20:46:13.704][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-01 20:46:13.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.707][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-01 20:46:13.708][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-01 20:46:13.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.712][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-01 20:46:13.713][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-01 20:46:13.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.716][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[2024-11-01 20:46:13.717][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-01 20:46:13.718][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-01 20:46:13.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.722][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-01 20:46:13.723][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-01 20:46:13.727][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-01 20:46:13.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.729][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[2024-11-01 20:46:13.730][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-01 20:46:13.731][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-01 20:46:13.732][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-01 20:46:13.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.739][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-01 20:46:13.776][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:13.800][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-01 20:46:13.801][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.802][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:13.803][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.804][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:13.805][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:13.806][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:13.806][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-01 20:46:13.807][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:13.808][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.809][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-01 20:46:13.810][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:13.811][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:13.812][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.813][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-01 20:46:13.813][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-01 20:46:13.813][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-01 20:46:13.813][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-01 20:46:13.813][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-01 20:46:13.814][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:13.815][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:13.815][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:13.816][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:13.817][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:13.818][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:13.819][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:13.820][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:13.820][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:13.821][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:13.822][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:13.823][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:13.824][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-01 20:46:13.826][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:13.827][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-01 20:46:13.828][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.829][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:13.829][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.830][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:13.831][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:13.832][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:13.833][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-01 20:46:13.834][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:13.835][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.836][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-01 20:46:13.837][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:13.837][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:13.838][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.839][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-01 20:46:13.839][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-01 20:46:13.839][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-01 20:46:13.839][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-01 20:46:13.839][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-01 20:46:13.840][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:13.841][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:13.842][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:13.843][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:13.844][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:13.844][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:13.845][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:13.846][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:13.847][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:13.848][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:13.849][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:13.849][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:13.851][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-01 20:46:13.852][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.853][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-01 20:46:13.854][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.855][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:13.856][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.857][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:13.858][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:13.858][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:13.859][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-01 20:46:13.860][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:13.861][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:13.862][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-01 20:46:13.863][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:13.864][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:13.865][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.866][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:13.866][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:13.867][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:13.868][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:13.869][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:13.870][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:13.871][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:13.871][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:13.872][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:13.873][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:13.874][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:13.875][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:13.876][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:13.877][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-01 20:46:13.878][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.879][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-01 20:46:13.880][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.881][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:13.882][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.883][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:13.884][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:13.885][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:13.886][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-01 20:46:13.886][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:13.887][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:13.888][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-01 20:46:13.889][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:13.890][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:13.891][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:13.892][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:13.893][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:13.893][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:13.894][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:13.895][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:13.896][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:13.897][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:13.898][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:13.898][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:13.899][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:13.900][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:13.901][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:13.902][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:13.905][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-01 20:46:13.906][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.907][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[2024-11-01 20:46:13.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.927][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[2024-11-01 20:46:13.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.935][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[2024-11-01 20:46:13.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.938][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[2024-11-01 20:46:13.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.942][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[2024-11-01 20:46:13.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.946][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[2024-11-01 20:46:13.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.958][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[2024-11-01 20:46:13.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.970][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[2024-11-01 20:46:13.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:13.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:13.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:13.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:13.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:13.984][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-01 20:46:13.990][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-01 20:46:13.991][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-01 20:46:13.993][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-01 20:46:13.994][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-01 20:46:13.995][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-01 20:46:13.997][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-01 20:46:13.998][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-01 20:46:14.000][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-01 20:46:14.001][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-01 20:46:14.002][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-01 20:46:14.004][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-01 20:46:14.005][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-01 20:46:14.006][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-01 20:46:14.008][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-01 20:46:14.009][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-01 20:46:14.011][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-01 20:46:14.012][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-01 20:46:14.013][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-01 20:46:14.015][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-01 20:46:14.016][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-01 20:46:14.018][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-01 20:46:14.019][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-01 20:46:14.020][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-01 20:46:14.022][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-01 20:46:14.023][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-01 20:46:14.024][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-01 20:46:14.026][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-01 20:46:14.027][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-01 20:46:14.029][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-01 20:46:14.030][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-01 20:46:14.031][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-01 20:46:14.033][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-01 20:46:14.034][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-01 20:46:14.035][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-01 20:46:14.037][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-01 20:46:14.038][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-01 20:46:14.053][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-01 20:46:14.054][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-01 20:46:14.056][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-01 20:46:14.057][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-01 20:46:14.059][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-01 20:46:14.060][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-01 20:46:14.061][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-01 20:46:14.063][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-01 20:46:14.064][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-01 20:46:14.065][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-01 20:46:14.067][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-01 20:46:14.068][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-01 20:46:14.070][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-01 20:46:14.071][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-01 20:46:14.073][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-01 20:46:14.074][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-01 20:46:14.075][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-01 20:46:14.077][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-01 20:46:14.078][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-01 20:46:14.080][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-01 20:46:14.081][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-01 20:46:14.082][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-01 20:46:14.084][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-01 20:46:14.085][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-01 20:46:14.087][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-01 20:46:14.088][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-01 20:46:14.090][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-01 20:46:14.091][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-01 20:46:14.092][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-01 20:46:14.094][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-01 20:46:14.095][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-01 20:46:14.096][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-01 20:46:14.098][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-01 20:46:14.099][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-01 20:46:14.101][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-01 20:46:14.102][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-01 20:46:14.103][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-01 20:46:14.105][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-01 20:46:14.106][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-01 20:46:14.107][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-01 20:46:14.109][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-01 20:46:14.110][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-01 20:46:14.112][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-01 20:46:14.113][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-01 20:46:14.114][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-01 20:46:14.116][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-01 20:46:14.122][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-01 20:46:14.123][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-01 20:46:14.127][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-01 20:46:14.127][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.129][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:14.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:14.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.146][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[2024-11-01 20:46:14.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:14.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:14.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.164][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[2024-11-01 20:46:14.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:14.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:14.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:14.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:14.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:14.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:14.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:14.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.212][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[2024-11-01 20:46:14.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:14.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.224][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[2024-11-01 20:46:14.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.230][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[2024-11-01 20:46:14.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:14.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.235][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[2024-11-01 20:46:14.237][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-01 20:46:14.246][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-01 20:46:14.247][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:14.248][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-01 20:46:14.249][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:14.250][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:14.251][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:14.252][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:14.253][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:14.254][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-01 20:46:14.255][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-01 20:46:14.255][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:14.256][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:14.257][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-01 20:46:14.258][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:14.259][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-01 20:46:14.259][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-01 20:46:14.259][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-01 20:46:14.259][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-01 20:46:14.259][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-01 20:46:14.259][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-01 20:46:14.259][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-01 20:46:14.259][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-01 20:46:14.259][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-01 20:46:14.259][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-01 20:46:14.259][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-01 20:46:14.260][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:14.261][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-01 20:46:14.261][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-01 20:46:14.261][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-01 20:46:14.262][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-01 20:46:14.263][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:14.264][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:14.264][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:14.265][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:14.266][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:14.267][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:14.268][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:14.268][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-01 20:46:14.269][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:14.270][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:14.270][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:14.271][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-01 20:46:14.271][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-01 20:46:14.277][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-01 20:46:14.278][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-01 20:46:14.280][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-01 20:46:14.281][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-01 20:46:14.282][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-01 20:46:14.284][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-01 20:46:14.309][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-01 20:46:14.310][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-01 20:46:14.314][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-01 20:46:14.317][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-01 20:46:14.321][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-01 20:46:14.322][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-01 20:46:14.323][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-01 20:46:14.324][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-01 20:46:14.332][biodb::testThat]
biodb.INFO [2024-11-01 20:46:14.333][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-11-01 20:46:14.334][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:14.335][biodb::testThat]
biodb.TRACE[2024-11-01 20:46:14.338][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[2024-11-01 20:46:14.340][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:14.343][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:14.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:14.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:14.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:14.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:14.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:14.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:14.365][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:14.374][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.375][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.377][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.393][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:14.394][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:14.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.396][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.420][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:14.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:14.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.424][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:14.425][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:14.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.427][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.428][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:14.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:14.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.432][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:14.432][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:14.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.434][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:14.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:14.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.439][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.440][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.442][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.443][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.447][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:14.447][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:14.448][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.449][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.450][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:14.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:14.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.454][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:14.455][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.457][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.458][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:14.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.462][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:14.463][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:14.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.464][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:14.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:14.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.469][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:14.470][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:14.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.472][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:14.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:14.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.477][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:14.478][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:14.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.479][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.481][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:14.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:14.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.484][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:14.485][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:14.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.487][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.488][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:14.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:14.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:14.569][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-11-01 20:46:14.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:14.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:14.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:14.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:14.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.600][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.615][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-01 20:46:14.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-01 20:46:14.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.618][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-01 20:46:14.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-01 20:46:14.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.622][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-01 20:46:14.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-01 20:46:14.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.625][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-01 20:46:14.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-01 20:46:14.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.715][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.716][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.718][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:14.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:14.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.765][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.766][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.768][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:14.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.779][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:14.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:14.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:14.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:14.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:14.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:14.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.790][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:14.791][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:14.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.793][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:14.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:14.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.804][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:14.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:14.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.807][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:14.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:14.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.811][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:14.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:14.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.814][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:14.815][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:14.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.817][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.818][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:14.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:14.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.839][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.840][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.841][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:14.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:14.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:14.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:14.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:14.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:14.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:14.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.863][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:14.864][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:14.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.866][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:14.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:14.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.877][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:14.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:14.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.881][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:14.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:14.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.885][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:14.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:14.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.888][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:14.889][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:14.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.891][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.892][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:14.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:14.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.902][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-01 20:46:14.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:14.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.905][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-01 20:46:14.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:14.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.909][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-01 20:46:14.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:14.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.913][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-01 20:46:14.914][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:14.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.915][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.916][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-01 20:46:14.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:14.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.926][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:14.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:14.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.930][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:14.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:14.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.933][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:14.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:14.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.937][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:14.938][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:14.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.939][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.940][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:14.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:14.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.950][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:14.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:14.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.954][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:14.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:14.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.962][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:14.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:14.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.965][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:14.966][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:14.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.968][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.969][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:14.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:14.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.979][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.983][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.986][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.990][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.991][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.993][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:14.994][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:14.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:14.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.004][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:15.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:15.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:15.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:15.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:15.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:15.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.015][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:15.016][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:15.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.018][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:15.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:15.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.029][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:15.030][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:15.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.032][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.035][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:15.036][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:15.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.038][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.042][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:15.043][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:15.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.045][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.048][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:15.049][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:15.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.051][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.055][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:15.056][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:15.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.057][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.061][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:15.062][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:15.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.064][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.068][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:15.068][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:15.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.070][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.074][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:15.075][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:15.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.077][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.080][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-01 20:46:15.081][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:15.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.083][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.087][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:15.088][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:15.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.089][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.093][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:15.094][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:15.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.096][ef$get] fields variable is a list.
biodb.INFO [2024-11-01 20:46:15.102][biodb::testThat]
biodb.INFO [2024-11-01 20:46:15.103][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-11-01 20:46:15.104][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:15.104][biodb::testThat]
biodb.DEBUG[2024-11-01 20:46:15.117][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-11-01 20:46:15.124][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:15.128][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-11-01 20:46:15.130][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:15.131][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-11-01 20:46:15.132][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:15.154][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:15.160][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:15.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:15.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:15.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:15.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:15.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:15.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:15.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:15.172][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:15.173][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:15.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.175][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:15.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:15.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.195][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:15.196][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:15.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.198][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.199][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:15.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:15.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.202][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:15.203][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:15.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.205][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.206][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:15.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:15.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.210][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:15.211][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:15.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.213][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.214][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:15.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:15.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.217][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:15.218][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:15.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.220][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.221][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:15.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:15.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.225][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:15.226][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:15.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.228][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.229][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:15.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:15.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.233][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:15.234][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:15.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.235][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.236][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:15.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:15.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.240][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:15.241][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:15.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.243][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:15.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:15.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.248][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:15.249][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:15.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.250][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.252][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:15.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:15.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.255][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:15.256][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:15.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.258][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.259][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:15.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:15.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.263][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:15.264][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:15.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.265][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.266][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:15.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:15.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:15.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:15.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:15.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:15.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:15.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:15.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:15.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:15.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:15.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:15.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:15.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:15.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:15.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:15.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:15.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:15.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:15.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:15.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:15.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:15.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:15.305][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-11-01 20:46:15.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-11-01 20:46:15.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-11-01 20:46:15.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-11-01 20:46:15.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-11-01 20:46:15.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-11-01 20:46:15.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-11-01 20:46:15.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-01 20:46:15.323][biodb::testThat]
biodb.INFO [2024-11-01 20:46:15.324][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-11-01 20:46:15.325][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:15.325][biodb::testThat]
biodb.TRACE[2024-11-01 20:46:15.328][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:15.329][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:15.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.331][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:15.332][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-11-01 20:46:15.358][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:15.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:15.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:15.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:15.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.365][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:15.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:15.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:15.371][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-11-01 20:46:15.375][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-01 20:46:15.394][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:15.408][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-01 20:46:15.409][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:15.411][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-01 20:46:15.432][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[2024-11-01 20:46:15.435][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:15.436][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-01 20:46:15.437][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:15.438][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-01 20:46:15.440][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-11-01 20:46:15.450][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:15.451][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:15.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.452][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.453][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:15.454][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:15.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.456][ef$get] fields variable is a list.
biodb.INFO [2024-11-01 20:46:15.459][biodb::testThat]
biodb.INFO [2024-11-01 20:46:15.460][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-11-01 20:46:15.461][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:15.462][biodb::testThat]
biodb.TRACE[2024-11-01 20:46:15.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:15.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:15.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:15.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:15.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:15.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:15.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:15.548][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[2024-11-01 20:46:15.551][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:15.552][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-01 20:46:15.554][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:15.555][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-11-01 20:46:15.568][biodb::testThat]
biodb.INFO [2024-11-01 20:46:15.569][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-11-01 20:46:15.570][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:15.571][biodb::testThat]
biodb.TRACE[2024-11-01 20:46:15.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:15.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:15.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.592][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:15.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:15.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:15.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:15.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:15.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:15.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:15.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:15.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:15.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:15.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.610][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-01 20:46:15.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-01 20:46:15.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.613][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-01 20:46:15.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-01 20:46:15.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.617][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-01 20:46:15.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-01 20:46:15.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.620][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-01 20:46:15.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-01 20:46:15.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.640][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:15.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:15.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.644][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:15.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:15.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.647][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:15.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:15.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:15.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:15.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:15.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:15.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:15.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:15.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.661][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-01 20:46:15.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-01 20:46:15.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.665][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-01 20:46:15.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-01 20:46:15.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.668][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-01 20:46:15.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-01 20:46:15.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:15.672][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-01 20:46:15.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-01 20:46:15.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:15.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-01 20:46:15.680][biodb::testThat]
biodb.INFO [2024-11-01 20:46:15.681][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-11-01 20:46:15.682][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:15.683][biodb::testThat]
biodb.INFO [2024-11-01 20:46:15.690][biodb::testThat]
biodb.INFO [2024-11-01 20:46:15.690][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-11-01 20:46:15.691][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:15.692][biodb::testThat]
biodb.INFO [2024-11-01 20:46:15.699][biodb::testThat]
biodb.INFO [2024-11-01 20:46:15.700][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-11-01 20:46:15.701][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:15.702][biodb::testThat]
biodb.DEBUG[2024-11-01 20:46:15.705][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-11-01 20:46:16.262][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-11-01 20:46:17.310][biodb::testThat]
biodb.INFO [2024-11-01 20:46:17.312][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-11-01 20:46:17.314][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:17.316][biodb::testThat]
biodb.DEBUG[2024-11-01 20:46:17.682][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[2024-11-01 20:46:18.052][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:18.055][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:18.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:18.059][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:18.061][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:18.064][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:18.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:18.068][ef$get] fields variable is a list.
biodb.INFO [2024-11-01 20:46:18.100][biodb::testThat]
biodb.INFO [2024-11-01 20:46:18.102][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-11-01 20:46:18.104][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:18.106][biodb::testThat]
biodb.TRACE[2024-11-01 20:46:18.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:18.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:18.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:18.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:18.139][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:18.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:18.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:18.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:18.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:18.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:18.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:18.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:18.321][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[2024-11-01 20:46:18.325][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:18.327][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-01 20:46:18.329][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:18.330][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-01 20:46:18.410][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[2024-11-01 20:46:18.414][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:18.416][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-01 20:46:18.417][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:18.418][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-11-01 20:46:18.431][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-01 20:46:18.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-01 20:46:18.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:18.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:18.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:18.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:18.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:18.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:18.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:18.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:18.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:18.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:18.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:18.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:18.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:18.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:18.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:18.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:18.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:18.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:18.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:18.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:18.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:18.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:18.465][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[2024-11-01 20:46:18.469][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:18.470][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-01 20:46:18.471][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:18.473][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-01 20:46:18.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:18.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:18.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:18.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:18.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:18.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:18.484][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.DEBUG[2024-11-01 20:46:18.485][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-11-01 20:46:18.540][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:18.542][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-11-01 20:46:18.543][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:18.544][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:18.545][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:18.546][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:18.547][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:18.548][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:18.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:18.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:18.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:18.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:18.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:18.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:18.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:18.561][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-11-01 20:46:18.564][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:18.565][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:18.566][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-11-01 20:46:18.899][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-11-01 20:46:19.237][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:19.241][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-11-01 20:46:19.265][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-11-01 20:46:19.269][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-11-01 20:46:19.271][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:19.273][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:19.275][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:19.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:19.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:19.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:19.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:19.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:19.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:19.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:19.293][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:19.294][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:19.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.297][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:19.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:19.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.302][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:19.303][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:19.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.305][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.307][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:19.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:19.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.311][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:19.312][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:19.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.313][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.315][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:19.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:19.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.319][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:19.320][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:19.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.322][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:19.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:19.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.327][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:19.328][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:19.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.329][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:19.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:19.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.334][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:19.335][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:19.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.337][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.338][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:19.339][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:19.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.347][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.351][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:19.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:19.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.355][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:19.356][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:19.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.358][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:19.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:19.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.363][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:19.364][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:19.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.365][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:19.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:19.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.370][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:19.371][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:19.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.373][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.374][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:19.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:19.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.378][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:19.379][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:19.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.381][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.382][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:19.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:19.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:19.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:19.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:19.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:19.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:19.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:19.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:19.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:19.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:19.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:19.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:19.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:19.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:19.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:19.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:19.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:19.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:19.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:19.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:19.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:19.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:19.422][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-11-01 20:46:19.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:19.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:19.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:19.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:19.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:19.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:19.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:19.443][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[2024-11-01 20:46:19.446][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:19.447][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-01 20:46:19.448][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:19.450][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-01 20:46:19.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:19.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:19.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:19.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:19.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:19.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:19.473][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[2024-11-01 20:46:19.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:19.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:19.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:19.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:19.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:19.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:19.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:19.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:19.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:19.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:19.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:19.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:19.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:19.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:19.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:19.493][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[2024-11-01 20:46:19.494][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-11-01 20:46:19.495][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:19.496][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-11-01 20:46:19.498][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:19.499][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:19.500][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:19.501][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:19.502][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:19.502][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:19.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:19.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:19.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:19.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:19.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:19.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:19.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:19.535][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-11-01 20:46:19.551][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:19.552][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:19.567][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-11-01 20:46:19.897][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-11-01 20:46:20.230][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:20.233][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-11-01 20:46:20.238][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-11-01 20:46:20.242][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-11-01 20:46:20.244][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:20.246][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:20.248][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:20.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:20.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:20.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:20.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:20.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:20.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:20.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:20.269][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:20.270][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:20.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.273][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:20.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:20.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.281][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:20.283][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:20.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.285][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.287][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:20.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:20.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.292][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:20.293][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:20.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.295][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.297][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:20.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:20.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.301][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:20.302][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:20.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.304][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:20.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:20.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.309][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:20.310][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:20.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.312][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.313][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:20.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:20.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.316][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:20.317][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:20.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.319][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.320][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:20.321][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:20.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.323][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.324][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:20.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:20.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.328][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:20.329][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:20.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.330][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:20.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:20.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.335][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:20.336][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:20.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.338][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:20.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:20.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.343][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:20.344][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:20.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.346][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.347][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:20.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:20.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.350][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:20.351][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:20.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.362][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.363][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:20.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:20.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:20.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:20.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:20.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:20.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:20.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:20.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:20.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:20.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:20.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:20.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:20.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:20.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:20.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:20.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:20.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:20.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:20.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:20.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:20.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:20.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:20.404][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-11-01 20:46:20.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:20.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:20.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:20.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:20.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:20.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:20.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:20.431][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[2024-11-01 20:46:20.433][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:20.435][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-01 20:46:20.436][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:20.437][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-01 20:46:20.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:20.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:20.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:20.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:20.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:20.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:20.448][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:20.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:20.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:20.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:20.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:20.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:20.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:20.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:20.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:20.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:20.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:20.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:20.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:20.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:20.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:20.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:20.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:20.469][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-11-01 20:46:20.470][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:20.471][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-11-01 20:46:20.472][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:20.473][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:20.474][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:20.475][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:20.476][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:20.477][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:20.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:20.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:20.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:20.485][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:20.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:20.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:20.488][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[2024-11-01 20:46:20.489][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-11-01 20:46:20.491][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:20.492][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:20.493][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-11-01 20:46:20.833][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-11-01 20:46:21.174][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:21.185][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-11-01 20:46:21.198][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-11-01 20:46:21.207][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-11-01 20:46:21.211][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:21.215][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:21.218][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:21.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:21.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:21.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:21.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:21.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:21.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:21.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:21.254][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:21.255][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:21.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.307][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:21.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:21.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.315][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:21.317][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:21.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.320][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.321][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:21.323][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:21.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.326][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.328][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:21.330][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:21.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.333][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.334][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:21.336][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:21.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.338][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.340][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:21.341][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:21.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.343][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.345][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:21.346][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:21.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.349][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.350][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:21.352][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:21.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.354][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.355][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:21.357][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:21.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.359][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:21.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:21.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.366][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:21.368][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:21.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.370][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.372][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:21.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:21.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.377][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:21.378][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:21.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.380][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:21.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:21.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:21.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:21.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:21.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:21.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:21.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:21.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:21.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:21.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:21.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:21.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:21.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:21.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:21.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:21.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:21.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:21.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:21.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:21.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:21.431][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-11-01 20:46:21.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:21.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:21.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:21.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:21.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:21.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:21.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:21.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:21.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:21.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:21.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:21.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:21.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:21.457][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:21.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:21.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:21.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:21.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:21.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:21.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:21.469][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-11-01 20:46:21.471][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:21.473][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-11-01 20:46:21.474][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:21.476][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:21.477][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:21.478][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:21.480][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:21.481][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:21.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:21.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:21.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:21.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:21.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:21.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:21.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:21.495][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-11-01 20:46:21.498][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:21.499][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:21.500][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-11-01 20:46:21.832][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-11-01 20:46:22.167][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:22.172][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-11-01 20:46:22.179][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-11-01 20:46:22.185][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-11-01 20:46:22.188][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:22.191][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:22.194][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:22.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:22.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:22.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:22.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:22.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:22.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:22.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:22.232][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:22.234][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:22.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.236][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:22.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:22.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.243][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:22.245][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:22.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.247][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.248][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:22.250][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:22.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.252][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.253][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:22.254][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:22.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.256][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.258][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:22.259][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:22.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.261][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.262][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:22.263][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:22.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.265][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.266][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:22.267][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:22.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.269][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.270][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:22.271][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:22.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.273][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.275][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:22.276][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:22.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.277][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:22.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:22.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.283][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:22.284][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:22.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.286][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.287][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:22.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:22.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.291][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:22.292][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:22.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.294][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:22.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:22.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:22.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:22.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:22.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:22.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:22.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:22.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:22.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:22.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:22.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:22.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:22.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:22.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:22.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:22.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:22.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:22.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:22.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:22.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:22.335][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-11-01 20:46:22.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:22.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:22.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:22.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:22.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:22.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:22.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:22.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:22.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:22.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:22.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:22.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:22.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:22.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:22.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:22.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:22.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:22.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:22.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:22.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:22.366][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-11-01 20:46:22.367][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:22.368][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-11-01 20:46:22.370][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:22.371][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:22.372][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:22.373][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:22.374][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:22.375][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:22.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:22.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:22.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:22.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:22.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:22.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:22.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:22.388][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-11-01 20:46:22.391][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:22.392][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:22.393][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-11-01 20:46:22.725][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-11-01 20:46:23.061][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:23.064][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-11-01 20:46:23.083][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-11-01 20:46:23.088][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-11-01 20:46:23.090][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:23.093][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:23.095][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:23.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:23.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:23.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:23.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:23.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:23.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:23.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:23.116][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:23.117][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:23.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.120][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:23.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:23.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.126][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:23.127][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:23.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.129][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.131][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:23.132][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:23.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.134][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.135][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:23.137][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:23.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.138][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.140][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:23.141][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:23.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.143][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.144][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:23.145][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:23.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.147][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.148][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:23.149][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:23.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.151][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.152][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:23.153][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:23.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.155][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.156][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:23.157][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:23.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.159][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.161][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:23.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:23.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.165][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:23.166][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:23.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.168][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.169][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:23.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:23.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.173][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:23.174][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:23.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.176][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:23.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:23.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:23.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:23.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:23.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:23.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:23.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:23.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:23.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:23.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:23.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:23.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:23.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:23.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:23.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:23.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:23.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:23.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:23.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:23.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:23.216][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-11-01 20:46:23.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:23.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:23.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:23.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:23.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:23.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:23.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:23.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:23.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:23.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:23.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:23.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:23.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:23.237][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:23.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:23.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:23.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:23.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:23.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:23.246][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[2024-11-01 20:46:23.247][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-11-01 20:46:23.248][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:23.250][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-11-01 20:46:23.251][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:23.252][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:23.253][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:23.254][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:23.255][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:23.256][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:23.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:23.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:23.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:23.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:23.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:23.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:23.268][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[2024-11-01 20:46:23.275][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-11-01 20:46:23.278][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:23.279][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:23.280][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-11-01 20:46:23.612][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-11-01 20:46:23.945][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:23.949][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-11-01 20:46:23.957][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-11-01 20:46:23.963][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-11-01 20:46:23.966][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:23.969][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:23.972][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:23.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:23.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:23.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:23.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:23.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:23.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:23.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:23.998][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:24.000][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:24.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.003][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:24.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:24.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.010][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:24.012][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:24.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.014][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.016][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:24.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:24.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.021][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:24.023][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:24.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.025][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.026][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:24.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:24.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.031][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:24.032][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:24.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.033][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:24.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:24.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.038][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:24.039][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:24.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.041][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.042][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:24.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:24.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.046][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:24.047][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:24.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.049][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.050][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:24.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:24.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.054][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:24.055][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:24.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.057][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.058][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:24.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:24.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.062][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:24.063][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:24.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.064][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:24.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:24.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.069][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:24.070][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:24.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.072][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:24.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:24.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.077][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:24.078][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:24.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.080][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.081][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:24.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:24.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.085][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:24.086][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:24.087][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.087][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.089][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:24.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:24.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:24.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:24.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:24.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:24.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:24.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:24.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:24.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:24.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:24.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:24.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:24.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:24.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:24.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:24.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:24.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:24.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:24.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:24.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:24.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:24.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:24.129][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-11-01 20:46:24.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:24.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:24.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:24.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:24.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:24.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:24.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:24.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:24.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:24.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:24.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:24.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:24.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:24.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:24.162][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-11-01 20:46:24.162][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:24.164][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-11-01 20:46:24.165][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:24.166][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:24.167][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:24.168][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:24.169][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:24.170][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:24.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:24.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:24.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:24.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:24.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:24.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:24.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:24.182][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-11-01 20:46:24.185][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:24.186][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:24.187][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-11-01 20:46:24.520][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-11-01 20:46:24.851][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:24.854][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-11-01 20:46:24.860][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-11-01 20:46:24.864][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-11-01 20:46:24.867][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:24.869][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:24.871][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:24.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:24.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:24.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:24.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:24.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:24.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:24.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:24.892][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:24.894][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:24.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.897][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:24.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:24.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.905][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:24.906][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:24.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.908][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.910][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:24.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:24.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.915][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:24.916][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:24.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.918][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.920][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:24.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:24.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.925][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:24.926][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:24.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.928][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:24.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:24.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.933][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:24.934][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:24.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.936][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:24.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:24.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.941][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:24.942][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:24.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.944][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.945][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:24.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:24.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.949][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:24.950][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:24.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.952][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.953][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:24.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:24.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.957][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:24.958][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:24.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.960][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:24.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:24.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.965][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:24.966][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:24.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.968][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.969][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:24.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:24.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.973][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:24.974][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:24.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.976][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.977][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:24.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:24.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.982][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:24.983][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:24.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.985][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.986][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:24.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:24.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:24.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:24.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:24.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:24.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:24.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:24.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:24.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:24.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:25.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:25.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:25.036][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-11-01 20:46:25.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:25.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:25.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:25.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:25.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:25.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:25.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:25.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:25.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:25.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:25.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:25.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:25.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:25.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:25.057][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-11-01 20:46:25.058][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:25.060][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-11-01 20:46:25.061][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:25.062][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:25.063][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:25.064][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:25.065][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:25.066][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:25.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:25.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:25.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:25.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:25.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:25.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:25.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:25.078][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-11-01 20:46:25.080][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:25.081][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:25.082][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-11-01 20:46:25.415][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-11-01 20:46:25.749][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-11-01 20:46:25.752][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-11-01 20:46:25.754][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-11-01 20:46:25.759][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-11-01 20:46:25.763][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-11-01 20:46:25.765][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:25.767][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:25.769][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:25.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:25.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:25.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:25.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:25.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:25.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:25.786][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:25.789][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.791][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.794][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.802][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:25.803][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:25.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.805][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.807][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:25.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:25.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.812][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:25.813][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:25.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.815][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.816][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:25.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:25.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.820][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:25.822][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:25.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.823][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.825][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:25.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:25.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.828][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:25.829][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:25.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.831][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.832][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:25.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:25.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.836][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:25.837][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:25.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.839][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.840][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:25.841][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:25.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.843][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.844][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:25.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:25.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.847][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:25.848][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:25.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.850][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:25.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:25.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.864][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:25.865][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:25.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.867][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:25.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:25.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.901][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:25.902][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:25.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.904][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.906][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:25.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:25.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.910][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:25.911][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:25.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.913][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.915][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:25.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:25.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:25.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:25.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:25.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:25.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:25.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:25.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:25.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:25.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:25.959][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-11-01 20:46:25.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:25.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:25.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:25.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:25.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:25.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:25.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:25.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:25.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:25.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:25.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:25.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:25.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:25.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:25.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:25.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:25.983][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-11-01 20:46:25.984][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:25.985][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-11-01 20:46:25.987][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:25.988][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:25.989][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:25.990][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:25.991][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:25.992][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:25.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:25.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:25.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:26.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:26.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:26.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:26.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:26.005][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-11-01 20:46:26.008][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:26.009][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:26.011][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-11-01 20:46:26.344][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-11-01 20:46:26.675][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:26.679][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-11-01 20:46:26.683][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-11-01 20:46:26.687][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-11-01 20:46:26.689][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:26.691][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:26.692][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:26.695][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:26.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:26.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:26.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:26.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:26.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:26.707][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:26.711][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:26.712][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:26.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.714][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:26.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:26.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.722][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:26.723][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:26.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.726][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.727][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:26.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:26.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.732][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:26.734][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:26.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.736][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.738][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:26.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:26.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.743][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:26.744][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:26.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.746][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:26.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:26.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.757][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:26.763][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:26.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.764][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.766][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:26.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:26.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.770][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:26.771][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:26.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.773][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.774][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:26.775][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:26.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.777][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.778][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:26.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:26.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.782][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:26.783][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:26.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.785][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:26.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:26.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.790][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:26.791][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:26.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.793][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:26.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:26.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.799][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:26.800][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:26.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.802][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.803][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:26.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:26.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.807][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:26.808][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:26.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.810][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.811][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:26.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:26.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:26.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:26.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:26.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:26.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:26.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:26.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:26.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:26.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:26.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:26.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:26.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:26.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:26.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:26.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:26.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:26.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:26.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:26.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:26.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:26.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:26.854][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-11-01 20:46:26.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:26.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:26.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:26.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:26.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:26.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:26.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:26.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:26.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:26.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:26.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:26.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:26.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:26.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:26.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:26.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:26.877][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-11-01 20:46:26.878][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:26.879][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-11-01 20:46:26.880][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:26.881][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:26.882][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:26.883][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:26.884][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:26.885][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:26.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:26.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:26.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:26.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:26.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:26.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:26.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:26.898][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-11-01 20:46:26.901][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:26.902][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:26.903][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-11-01 20:46:27.235][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-11-01 20:46:27.566][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:27.569][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-11-01 20:46:27.572][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-11-01 20:46:27.575][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-11-01 20:46:27.576][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:27.577][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:27.578][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:27.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:27.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:27.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:27.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:27.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:27.589][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:27.590][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:27.598][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:27.604][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:27.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.606][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:27.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:27.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.612][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:27.613][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:27.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.615][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.616][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:27.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:27.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.621][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:27.622][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:27.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.624][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.625][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:27.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:27.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.629][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:27.630][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:27.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.632][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:27.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:27.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.637][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:27.638][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:27.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.640][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:27.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:27.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.645][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:27.646][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:27.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.648][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.649][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:27.650][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:27.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.652][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.653][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:27.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:27.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.657][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:27.658][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:27.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.660][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:27.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:27.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.665][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:27.666][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:27.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.668][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.670][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:27.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:27.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.674][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:27.675][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:27.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.676][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.678][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:27.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:27.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.682][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:27.683][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:27.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.684][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.686][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:27.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:27.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:27.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:27.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:27.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:27.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:27.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:27.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:27.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:27.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:27.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:27.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:27.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:27.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:27.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:27.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:27.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:27.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:27.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:27.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:27.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:27.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:27.728][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-11-01 20:46:27.729][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:27.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:27.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:27.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:27.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:27.736][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:27.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:27.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:27.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:27.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:27.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:27.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:27.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:27.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:27.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:27.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:27.750][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-11-01 20:46:27.751][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:27.752][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-11-01 20:46:27.754][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:27.755][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:27.756][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:27.757][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:27.758][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:27.759][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:27.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:27.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:27.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:27.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:27.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:27.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:27.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:27.778][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-11-01 20:46:27.780][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:27.781][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:27.783][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-11-01 20:46:28.112][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-11-01 20:46:28.444][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:28.447][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-11-01 20:46:28.450][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-11-01 20:46:28.453][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-11-01 20:46:28.454][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:28.456][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:28.457][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:28.459][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:28.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:28.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:28.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:28.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:28.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:28.468][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:28.471][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:28.472][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:28.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.474][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:28.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:28.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.479][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:28.480][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:28.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.482][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.484][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:28.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:28.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.488][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:28.489][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:28.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.491][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.492][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:28.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:28.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.496][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:28.497][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:28.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.499][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.501][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:28.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:28.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.504][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:28.506][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:28.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.507][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.509][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:28.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:28.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.513][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:28.514][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:28.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.515][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.517][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:28.518][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:28.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.520][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.521][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:28.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:28.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.525][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:28.526][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:28.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.527][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:28.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:28.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.533][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:28.534][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:28.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.536][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.537][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:28.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:28.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.541][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:28.542][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:28.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.544][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.545][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:28.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:28.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.549][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:28.550][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:28.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.552][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.553][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:28.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:28.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:28.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:28.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:28.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:28.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:28.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:28.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:28.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:28.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:28.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:28.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:28.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:28.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:28.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:28.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:28.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:28.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:28.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:28.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:28.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:28.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:28.593][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-11-01 20:46:28.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:28.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:28.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:28.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:28.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:28.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:28.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:28.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:28.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:28.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:28.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:28.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:28.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:28.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:28.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:28.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:28.663][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-11-01 20:46:28.664][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:28.665][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-11-01 20:46:28.667][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:28.668][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:28.669][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:28.670][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:28.671][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:28.672][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:28.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:28.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:28.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:28.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:28.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:28.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:28.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:28.685][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-11-01 20:46:28.688][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:28.689][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:28.691][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-11-01 20:46:29.021][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-11-01 20:46:29.354][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:29.358][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-11-01 20:46:29.364][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-11-01 20:46:29.368][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-11-01 20:46:29.370][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:29.373][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:29.375][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:29.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:29.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:29.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:29.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:29.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:29.392][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:29.394][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.TRACE[2024-11-01 20:46:29.398][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:29.399][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:29.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.402][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:29.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:29.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.410][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:29.412][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:29.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.414][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.416][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:29.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:29.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.421][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:29.422][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:29.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.424][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.426][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:29.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:29.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.430][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:29.432][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:29.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.434][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:29.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:29.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.439][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:29.440][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:29.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.442][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.443][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:29.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:29.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.447][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:29.448][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:29.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.450][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.451][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:29.452][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:29.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.454][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.456][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:29.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:29.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.459][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:29.461][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:29.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.462][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:29.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:29.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.467][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:29.468][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:29.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.470][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:29.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:29.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.476][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:29.477][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:29.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.479][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.480][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:29.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:29.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.484][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:29.485][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:29.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.487][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.488][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:29.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:29.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:29.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:29.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:29.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:29.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:29.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:29.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:29.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:29.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:29.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:29.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:29.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:29.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:29.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:29.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:29.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:29.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:29.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:29.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:29.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:29.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:29.542][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-11-01 20:46:29.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:29.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:29.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:29.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:29.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:29.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:29.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:29.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:29.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:29.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:29.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:29.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:29.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:29.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:29.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:29.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:29.565][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-11-01 20:46:29.567][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:29.568][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-11-01 20:46:29.569][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:29.571][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:29.572][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:29.573][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:29.574][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:29.575][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:29.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:29.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:29.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:29.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:29.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:29.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:29.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:29.588][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-11-01 20:46:29.591][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:29.592][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:29.594][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-11-01 20:46:29.924][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-11-01 20:46:30.259][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:30.264][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-11-01 20:46:30.271][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-11-01 20:46:30.276][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-11-01 20:46:30.279][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:30.281][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:30.284][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:30.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:30.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:30.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:30.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:30.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:30.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:30.305][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:30.309][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:30.310][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:30.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.313][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:30.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:30.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.321][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:30.322][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:30.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.325][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.327][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:30.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:30.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.332][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:30.333][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:30.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.335][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.336][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:30.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:30.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.341][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:30.342][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:30.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.344][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.345][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:30.346][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:30.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.348][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.349][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:30.350][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:30.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.352][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.353][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:30.354][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:30.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.356][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.357][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:30.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:30.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.361][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:30.362][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:30.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.364][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:30.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:30.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.369][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:30.370][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:30.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.372][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.373][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:30.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:30.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.377][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:30.378][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:30.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.380][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.381][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:30.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:30.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.385][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:30.385][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:30.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.387][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:30.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:30.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:30.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:30.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:30.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:30.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:30.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:30.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:30.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:30.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:30.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:30.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:30.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:30.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:30.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:30.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:30.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:30.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:30.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:30.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:30.439][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-11-01 20:46:30.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:30.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:30.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:30.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:30.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:30.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:30.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:30.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:30.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:30.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:30.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:30.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:30.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:30.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:30.461][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:30.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:30.463][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-11-01 20:46:30.464][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:30.465][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-11-01 20:46:30.467][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:30.468][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:30.469][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:30.470][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:30.471][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:30.472][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:30.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:30.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:30.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:30.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:30.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:30.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:30.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:30.485][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-11-01 20:46:30.488][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:30.489][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:30.490][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-11-01 20:46:30.822][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-11-01 20:46:31.156][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:31.161][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-11-01 20:46:31.168][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-11-01 20:46:31.173][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-11-01 20:46:31.176][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:31.178][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:31.181][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:31.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:31.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:31.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:31.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:31.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:31.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:31.202][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.TRACE[2024-11-01 20:46:31.206][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:31.207][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:31.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.210][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:31.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:31.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.218][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:31.220][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:31.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.222][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.224][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:31.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:31.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.229][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:31.230][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:31.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.232][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.234][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:31.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:31.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.238][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:31.239][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:31.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.241][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.243][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:31.244][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:31.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.245][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.247][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:31.248][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:31.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.250][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.251][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:31.252][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:31.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.254][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.255][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:31.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:31.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.259][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:31.260][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:31.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.262][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:31.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:31.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.267][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:31.268][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:31.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.270][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:31.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:31.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.288][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:31.289][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:31.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.290][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.292][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:31.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:31.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.296][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:31.297][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:31.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.299][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:31.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:31.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:31.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:31.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:31.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:31.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:31.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:31.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:31.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:31.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:31.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:31.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:31.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:31.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:31.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:31.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:31.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:31.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:31.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:31.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:31.341][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-11-01 20:46:31.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:31.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:31.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:31.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:31.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:31.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:31.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:31.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:31.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:31.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:31.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:31.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:31.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:31.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:31.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:31.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:31.394][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-11-01 20:46:31.396][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:31.400][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-11-01 20:46:31.402][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:31.403][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:31.405][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:31.406][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:31.408][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:31.409][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:31.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:31.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:31.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:31.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:31.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:31.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:31.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:31.431][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-11-01 20:46:31.435][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:31.437][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:31.439][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-11-01 20:46:31.773][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-11-01 20:46:32.107][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:32.113][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-11-01 20:46:32.120][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-11-01 20:46:32.125][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-11-01 20:46:32.128][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:32.131][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:32.134][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:32.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:32.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:32.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:32.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:32.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:32.153][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:32.155][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:32.165][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:32.167][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:32.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.169][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:32.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:32.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.177][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:32.178][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:32.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.181][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.182][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:32.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:32.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.187][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:32.188][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:32.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.190][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.192][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:32.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:32.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.196][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:32.197][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:32.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.199][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:32.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:32.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.205][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:32.206][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:32.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.208][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.209][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:32.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:32.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.255][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:32.257][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:32.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.259][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.261][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:32.263][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:32.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.266][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.267][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:32.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:32.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.274][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:32.275][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:32.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.278][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:32.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:32.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.285][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:32.286][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:32.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.288][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.290][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:32.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:32.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.295][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:32.297][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:32.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.299][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.301][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:32.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:32.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.306][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:32.307][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:32.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.310][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.311][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:32.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:32.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:32.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:32.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:32.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:32.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:32.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:32.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:32.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:32.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:32.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:32.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:32.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:32.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:32.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:32.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:32.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:32.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:32.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:32.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:32.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:32.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:32.357][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-11-01 20:46:32.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:32.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:32.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:32.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:32.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:32.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:32.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:32.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:32.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:32.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:32.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:32.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:32.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:32.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:32.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:32.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:32.379][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-11-01 20:46:32.380][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:32.381][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-11-01 20:46:32.382][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:32.383][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:32.384][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:32.385][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:32.386][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:32.387][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:32.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:32.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:32.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:32.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:32.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:32.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:32.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:32.399][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-11-01 20:46:32.402][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:32.403][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:32.404][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-11-01 20:46:32.733][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-11-01 20:46:33.069][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:33.074][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-11-01 20:46:33.080][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-11-01 20:46:33.085][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-11-01 20:46:33.088][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:33.090][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:33.093][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:33.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:33.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:33.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:33.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:33.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:33.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:33.113][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:33.117][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:33.119][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:33.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.122][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:33.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:33.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.140][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:33.141][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:33.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.143][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.145][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:33.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:33.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.149][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:33.150][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:33.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.152][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.153][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:33.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:33.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.157][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:33.159][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:33.159][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.160][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.162][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:33.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:33.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.165][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:33.166][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:33.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.168][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.169][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:33.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:33.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.173][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:33.174][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:33.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.176][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.177][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:33.178][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:33.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.180][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.181][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:33.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:33.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.185][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:33.186][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:33.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.187][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:33.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:33.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.192][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:33.193][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:33.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.195][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.196][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:33.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:33.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.200][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:33.201][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:33.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.203][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.204][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:33.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:33.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.208][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:33.209][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:33.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.211][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.212][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:33.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:33.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:33.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:33.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:33.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:33.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:33.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:33.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:33.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:33.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:33.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:33.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:33.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:33.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:33.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:33.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:33.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:33.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:33.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:33.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:33.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:33.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:33.253][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-11-01 20:46:33.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:33.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:33.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:33.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:33.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:33.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:33.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:33.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:33.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:33.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:33.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:33.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:33.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:33.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:33.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:33.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:33.274][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-11-01 20:46:33.275][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:33.277][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-11-01 20:46:33.278][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:33.279][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:33.280][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:33.281][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:33.282][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:33.283][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:33.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:33.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:33.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:33.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:33.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:33.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:33.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:33.295][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-11-01 20:46:33.298][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:33.299][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:33.300][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-11-01 20:46:33.630][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-11-01 20:46:33.973][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:33.977][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-11-01 20:46:33.985][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-11-01 20:46:33.990][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-11-01 20:46:33.993][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:33.996][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:33.999][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:34.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:34.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:34.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:34.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:34.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:34.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:34.021][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:34.025][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:34.026][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:34.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.029][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:34.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:34.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.037][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:34.039][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:34.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.041][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.043][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:34.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:34.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.048][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:34.049][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:34.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.051][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.052][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:34.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:34.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.057][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:34.058][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:34.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.060][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:34.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:34.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.065][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:34.066][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:34.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.068][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:34.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:34.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.073][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:34.074][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:34.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.075][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.077][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:34.078][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:34.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.079][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.080][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:34.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:34.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.084][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:34.085][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:34.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.087][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:34.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:34.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.092][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:34.093][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:34.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.094][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.096][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:34.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:34.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.099][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:34.100][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:34.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.102][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.103][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:34.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:34.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.107][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:34.108][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:34.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.110][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.111][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:34.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:34.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:34.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:34.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:34.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:34.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:34.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:34.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:34.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:34.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:34.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:34.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:34.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:34.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:34.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:34.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:34.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:34.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:34.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:34.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:34.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:34.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:34.152][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-11-01 20:46:34.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:34.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:34.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:34.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:34.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:34.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:34.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:34.164][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:34.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:34.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:34.170][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:34.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:34.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:34.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:34.180][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-11-01 20:46:34.181][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:34.183][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-11-01 20:46:34.184][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:34.185][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:34.186][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:34.187][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:34.188][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:34.189][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:34.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:34.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:34.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:34.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:34.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:34.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:34.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:34.201][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-11-01 20:46:34.204][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:34.205][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:34.206][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-11-01 20:46:34.538][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-11-01 20:46:34.871][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:34.875][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-11-01 20:46:34.881][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-11-01 20:46:34.885][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-11-01 20:46:34.887][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:34.889][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:34.891][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:34.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:34.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:34.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:34.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:34.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:34.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:34.909][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.TRACE[2024-11-01 20:46:34.912][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:34.914][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:34.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.917][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:34.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:34.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.925][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:34.926][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:34.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.929][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.931][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:34.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:34.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.936][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:34.937][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:34.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.939][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.940][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:34.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:34.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.945][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:34.946][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:34.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.948][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:34.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:34.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.953][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:34.954][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:34.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.956][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:34.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:34.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.961][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:34.962][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:34.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.964][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.966][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:34.967][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:34.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.968][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.970][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:34.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:34.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.974][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:34.975][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:34.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.977][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:34.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:34.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.982][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:34.983][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:34.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.985][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.987][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:34.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:34.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.991][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:34.992][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:34.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.994][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.995][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:34.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:34.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:34.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:34.999][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:35.000][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:35.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.002][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.003][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:35.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:35.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:35.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:35.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:35.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:35.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:35.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:35.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:35.059][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-11-01 20:46:35.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:35.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:35.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:35.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:35.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:35.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:35.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:35.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:35.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:35.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:35.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:35.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:35.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:35.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:35.083][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-11-01 20:46:35.084][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:35.085][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-11-01 20:46:35.087][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:35.088][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:35.089][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:35.090][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:35.091][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:35.092][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:35.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:35.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:35.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:35.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:35.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:35.103][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:35.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:35.105][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-11-01 20:46:35.108][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:35.109][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:35.111][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-11-01 20:46:35.441][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-11-01 20:46:35.773][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:35.778][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-11-01 20:46:35.785][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-11-01 20:46:35.791][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-11-01 20:46:35.794][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:35.797][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:35.799][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:35.803][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:35.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:35.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:35.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:35.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:35.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:35.821][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:35.825][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.827][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.830][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.838][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:35.840][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:35.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.842][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.844][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:35.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:35.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.849][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:35.850][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:35.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.852][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.854][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:35.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:35.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.858][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:35.859][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:35.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.861][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.863][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:35.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:35.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.867][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:35.868][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:35.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.870][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:35.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:35.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.875][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:35.877][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:35.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.878][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.880][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:35.881][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:35.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.883][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.884][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:35.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:35.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.888][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:35.889][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:35.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.891][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:35.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:35.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.897][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:35.898][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:35.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.900][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:35.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:35.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.905][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:35.906][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:35.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.908][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.909][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:35.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:35.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.913][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:35.914][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:35.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.916][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.925][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:35.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:35.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:35.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:35.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:35.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:35.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:35.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:35.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:35.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:35.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:35.975][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-11-01 20:46:35.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:35.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:35.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:35.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:35.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:35.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:35.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:35.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:35.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:35.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:35.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:35.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:35.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:35.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:35.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:35.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:35.999][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-11-01 20:46:36.000][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:36.002][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-11-01 20:46:36.003][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:36.004][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:36.005][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:36.006][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:36.007][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:36.008][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:36.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:36.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:36.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:36.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:36.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:36.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:36.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:36.022][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-11-01 20:46:36.025][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:36.026][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:36.027][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-11-01 20:46:36.359][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-11-01 20:46:36.692][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:36.694][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-11-01 20:46:36.698][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-11-01 20:46:36.701][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-11-01 20:46:36.703][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:36.704][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:36.706][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:36.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:36.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:36.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:36.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:36.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:36.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:36.719][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.TRACE[2024-11-01 20:46:36.722][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:36.723][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:36.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.726][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:36.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:36.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.732][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:36.733][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:36.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.735][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.737][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:36.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:36.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.742][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:36.743][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:36.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.745][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.747][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:36.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:36.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.751][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:36.752][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:36.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.754][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:36.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:36.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.759][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:36.760][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:36.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.762][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:36.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:36.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.766][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:36.767][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:36.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.769][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.770][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:36.771][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:36.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.773][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.775][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:36.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:36.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.791][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:36.792][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:36.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.794][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:36.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:36.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.799][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:36.800][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:36.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.802][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:36.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:36.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.808][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:36.809][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:36.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.811][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.812][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:36.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:36.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.816][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:36.817][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:36.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.819][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.820][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:36.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:36.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:36.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:36.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:36.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:36.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:36.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:36.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:36.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:36.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:36.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:36.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:36.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:36.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:36.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:36.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:36.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:36.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:36.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:36.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:36.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:36.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:36.894][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-11-01 20:46:36.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:36.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:36.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:36.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:36.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:36.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:36.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:36.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:36.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:36.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:36.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:36.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:36.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:36.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:36.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:36.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:36.932][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-11-01 20:46:36.933][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:36.936][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-11-01 20:46:36.938][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:36.939][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:36.941][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:36.942][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:36.943][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:36.945][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:36.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:36.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:36.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:36.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:36.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:36.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:36.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:36.966][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-11-01 20:46:36.970][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:36.972][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:36.974][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-11-01 20:46:37.307][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-11-01 20:46:37.640][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:37.643][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-11-01 20:46:37.648][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-11-01 20:46:37.651][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-11-01 20:46:37.653][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:37.655][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:37.657][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:37.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:37.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:37.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:37.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:37.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:37.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:37.671][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:37.675][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:37.676][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:37.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.679][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:37.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:37.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.686][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:37.687][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:37.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.690][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.692][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:37.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:37.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.697][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:37.721][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:37.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.725][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.727][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:37.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:37.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.733][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:37.735][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:37.736][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.737][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:37.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:37.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.745][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:37.746][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:37.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.749][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.751][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:37.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:37.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.756][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:37.757][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:37.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.760][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.761][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:37.763][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:37.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.765][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.766][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:37.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:37.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.771][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:37.772][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:37.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.774][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:37.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:37.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.778][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:37.779][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:37.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.781][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:37.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:37.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.786][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:37.787][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:37.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.789][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.790][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:37.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:37.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.794][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:37.795][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:37.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.796][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.797][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:37.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:37.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:37.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:37.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:37.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:37.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:37.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:37.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:37.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:37.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:37.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:37.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:37.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:37.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:37.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:37.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:37.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:37.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:37.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:37.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:37.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:37.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:37.837][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-11-01 20:46:37.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:37.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:37.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:37.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:37.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:37.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:37.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:37.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:37.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:37.866][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-01 20:46:37.869][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:37.870][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:37.872][private$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[2024-11-01 20:46:38.365][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[2024-11-01 20:46:38.839][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:38.843][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-11-01 20:46:38.849][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-11-01 20:46:38.855][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:38.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:38.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:38.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:38.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:38.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:38.869][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.TRACE[2024-11-01 20:46:38.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:38.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:38.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:38.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:38.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:38.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:38.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:38.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:38.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:38.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:38.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:38.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:38.923][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:38.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:38.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:38.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:38.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:38.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:38.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:38.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:38.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:38.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:38.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:38.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:38.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:38.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:38.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:38.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:38.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:38.968][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:38.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:38.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:38.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:38.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:38.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:38.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:38.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:38.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:38.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:38.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:38.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:38.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:38.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:38.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:38.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:38.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:38.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:38.998][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.TRACE[2024-11-01 20:46:38.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.028][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:39.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.051][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:39.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.073][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:39.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.101][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:39.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.123][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:39.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.145][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:39.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.167][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:39.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.189][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:39.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.211][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[2024-11-01 20:46:39.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.220][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.233][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:39.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.255][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.TRACE[2024-11-01 20:46:39.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.283][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.TRACE[2024-11-01 20:46:39.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.305][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.306][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[2024-11-01 20:46:39.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.328][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.TRACE[2024-11-01 20:46:39.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.350][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.TRACE[2024-11-01 20:46:39.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.363][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:39.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:39.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:39.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:39.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:39.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:39.372][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.TRACE[2024-11-01 20:46:39.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:39.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:39.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:39.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:39.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:39.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:39.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:39.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:39.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:39.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:39.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:39.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:39.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:39.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:39.451][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[2024-11-01 20:46:39.454][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:39.455][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:39.457][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-01 20:46:39.785][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-01 20:46:40.116][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:40.120][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-11-01 20:46:40.126][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-11-01 20:46:40.132][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-01 20:46:40.137][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:40.139][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:40.142][private$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[2024-11-01 20:46:40.477][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[2024-11-01 20:46:40.808][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:40.811][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-11-01 20:46:40.815][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-11-01 20:46:40.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:40.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:40.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:40.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:40.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:40.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:40.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:40.829][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-11-01 20:46:40.830][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:40.832][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-11-01 20:46:40.833][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:40.834][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:40.836][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:40.837][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:40.838][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:40.839][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:40.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:40.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:40.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:40.849][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:40.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:40.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:40.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:40.853][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-11-01 20:46:40.856][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:40.857][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:40.859][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-11-01 20:46:41.188][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-11-01 20:46:41.519][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:41.522][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-11-01 20:46:41.525][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-11-01 20:46:41.528][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-11-01 20:46:41.529][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:41.530][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:41.532][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:41.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:41.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:41.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:41.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:41.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:41.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:41.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:41.546][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:41.547][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:41.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.549][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:41.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:41.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.555][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:41.556][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:41.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.558][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.559][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:41.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:41.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.564][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:41.565][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:41.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.567][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.568][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:41.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:41.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.573][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:41.574][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:41.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.576][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:41.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:41.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.581][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:41.582][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:41.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.584][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.585][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:41.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:41.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.589][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:41.590][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:41.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.592][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.593][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:41.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:41.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.597][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:41.598][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:41.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.600][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.601][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:41.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:41.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.605][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.606][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.608][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.631][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:41.632][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:41.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.634][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:41.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:41.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.639][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:41.640][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:41.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.642][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.644][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:41.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:41.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.648][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:41.649][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:41.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.651][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.652][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:41.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:41.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:41.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:41.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:41.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:41.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:41.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:41.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:41.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:41.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:41.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:41.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:41.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:41.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:41.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:41.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:41.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:41.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:41.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:41.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:41.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:41.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:41.695][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-11-01 20:46:41.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:41.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:41.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:41.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:41.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:41.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:41.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:41.717][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.TRACE[2024-11-01 20:46:41.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:41.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:41.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:41.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:41.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:41.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:41.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:41.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:41.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:41.738][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:41.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:41.740][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-11-01 20:46:41.741][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:41.743][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-11-01 20:46:41.744][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:41.745][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:41.746][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:41.747][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:41.748][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:41.749][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:41.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:41.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:41.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:41.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:41.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:41.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:41.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:41.763][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-11-01 20:46:41.766][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:41.767][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:41.768][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-11-01 20:46:42.099][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-11-01 20:46:42.432][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:42.434][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-11-01 20:46:42.437][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-11-01 20:46:42.439][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-11-01 20:46:42.441][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:42.442][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:42.443][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:42.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:42.455][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:42.456][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:42.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.470][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:42.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:42.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.476][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:42.477][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:42.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.480][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.481][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:42.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:42.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.485][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:42.486][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:42.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.488][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.490][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:42.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:42.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.494][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:42.495][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:42.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.497][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:42.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:42.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.502][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:42.503][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:42.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.505][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:42.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:42.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.510][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:42.511][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:42.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.513][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.515][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:42.516][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:42.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.518][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.519][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:42.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:42.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.523][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.524][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.526][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.531][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:42.532][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:42.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.534][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.535][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:42.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:42.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.539][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:42.540][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:42.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.542][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.544][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:42.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:42.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.548][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:42.549][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:42.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.550][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.552][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:42.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:42.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:42.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:42.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:42.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:42.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:42.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:42.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:42.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:42.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:42.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:42.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:42.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:42.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:42.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:42.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:42.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:42.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:42.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:42.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:42.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:42.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.595][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-11-01 20:46:42.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.626][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[2024-11-01 20:46:42.629][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:42.631][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-01 20:46:42.632][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:42.633][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-01 20:46:42.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.652][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:42.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.674][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.675][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[2024-11-01 20:46:42.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.704][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.705][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:42.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.736][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:42.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.766][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:42.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.789][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:42.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.811][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[2024-11-01 20:46:42.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.839][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:42.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.861][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.TRACE[2024-11-01 20:46:42.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.883][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.TRACE[2024-11-01 20:46:42.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.904][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:42.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.926][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:42.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.948][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:42.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.969][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.969][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.TRACE[2024-11-01 20:46:42.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:42.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:42.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:42.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:42.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:42.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:42.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:42.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:42.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:42.996][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:42.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:42.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.019][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.040][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[2024-11-01 20:46:43.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.062][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.083][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.105][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.134][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[2024-11-01 20:46:43.137][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:43.138][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-01 20:46:43.140][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:43.141][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-01 20:46:43.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.153][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.185][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.216][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.230][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.247][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.268][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.277][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[2024-11-01 20:46:43.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.300][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.322][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.TRACE[2024-11-01 20:46:43.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.335][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.344][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.363][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.372][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.TRACE[2024-11-01 20:46:43.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.394][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.TRACE[2024-11-01 20:46:43.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.415][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.437][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.TRACE[2024-11-01 20:46:43.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.459][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.TRACE[2024-11-01 20:46:43.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.481][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[2024-11-01 20:46:43.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.502][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.TRACE[2024-11-01 20:46:43.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.529][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.530][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.TRACE[2024-11-01 20:46:43.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.552][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.574][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.618][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.649][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:43.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:43.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.685][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-01 20:46:43.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-01 20:46:43.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-01 20:46:43.702][biodb::testThat]
biodb.INFO [2024-11-01 20:46:43.704][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-11-01 20:46:43.705][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:43.706][biodb::testThat]
biodb.TRACE[2024-11-01 20:46:43.713][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-01 20:46:43.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-01 20:46:43.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:43.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:43.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:43.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:43.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:43.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:43.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:43.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:43.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:43.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:43.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:43.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:43.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:43.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:43.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:43.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:43.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:43.756][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[2024-11-01 20:46:43.761][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[2024-11-01 20:46:43.787][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:43.789][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:43.793][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-01 20:46:44.126][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-01 20:46:44.458][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:44.463][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-11-01 20:46:44.473][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-11-01 20:46:44.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:44.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:44.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:44.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:44.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:44.500][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:44.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:44.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:44.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:44.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:44.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:44.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:44.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:44.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:44.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:44.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:44.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:44.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:44.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:44.525][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-01 20:46:44.529][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:44.530][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:44.532][private$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[2024-11-01 20:46:44.866][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[2024-11-01 20:46:45.199][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:45.204][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-11-01 20:46:45.212][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-11-01 20:46:45.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:45.221][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:45.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:45.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:45.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:45.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:45.238][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.TRACE[2024-11-01 20:46:45.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:45.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:45.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:45.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:45.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:45.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:45.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:45.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:45.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:45.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:45.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:45.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:45.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:45.272][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:45.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:45.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:45.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:45.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:45.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:45.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:45.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:45.287][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-01 20:46:45.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:45.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:45.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:45.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:45.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:45.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:45.298][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.TRACE[2024-11-01 20:46:45.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.307][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:45.308][private$selectFields]
biodb.TRACE[2024-11-01 20:46:45.309][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:45.310][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:45.311][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:45.312][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.313][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.315][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.316][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.317][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.319][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.320][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:45.321][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:45.321][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.323][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.324][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.325][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:45.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.349][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-01 20:46:45.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:45.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:45.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:45.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:45.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:45.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:45.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:45.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.384][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:45.384][private$selectFields]
biodb.TRACE[2024-11-01 20:46:45.385][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:45.386][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:45.387][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:45.388][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.389][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.391][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.392][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.393][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.395][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.396][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:45.397][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:45.398][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.399][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.400][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.401][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:45.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.414][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-01 20:46:45.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:45.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:45.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:45.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:45.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:45.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:45.424][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:45.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.433][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:45.434][private$selectFields]
biodb.TRACE[2024-11-01 20:46:45.435][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:45.436][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:45.436][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:45.437][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.438][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.440][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.441][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.442][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.444][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.445][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:45.446][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:45.447][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.448][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.450][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.451][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:45.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:45.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.464][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-01 20:46:45.465][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-01 20:46:45.466][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-01 20:46:45.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:45.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:45.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:45.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:45.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:45.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:45.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:45.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:45.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:45.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:45.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:45.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:45.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:45.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:45.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:45.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:45.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:45.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:45.567][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[2024-11-01 20:46:45.571][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:45.571][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:45.573][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-01 20:46:45.903][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-01 20:46:46.233][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:46.237][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-11-01 20:46:46.245][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-11-01 20:46:46.251][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-01 20:46:46.258][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:46.260][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:46.264][private$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[2024-11-01 20:46:46.603][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[2024-11-01 20:46:46.936][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:46.940][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-11-01 20:46:46.947][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-11-01 20:46:46.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:46.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:46.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:46.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:46.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:46.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:46.973][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:46.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:46.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:46.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:46.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:46.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:46.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:46.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:46.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:46.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:46.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:46.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:46.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:46.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:46.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:46.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.004][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.007][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:47.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:47.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.030][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:47.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:47.081][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-01 20:46:47.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.115][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:47.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.124][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.125][private$selectFields]
biodb.TRACE[2024-11-01 20:46:47.126][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:47.127][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:47.128][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.129][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.130][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.131][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.132][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.133][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.135][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.136][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.137][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.138][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.139][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.141][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.142][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:47.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.155][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-01 20:46:47.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:47.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.206][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.207][private$selectFields]
biodb.TRACE[2024-11-01 20:46:47.208][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:47.209][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:47.210][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.211][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.212][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.214][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.215][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.216][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.218][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.219][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.236][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.237][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.238][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.240][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.241][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:47.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.254][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-01 20:46:47.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.263][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.TRACE[2024-11-01 20:46:47.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.272][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.273][private$selectFields]
biodb.TRACE[2024-11-01 20:46:47.274][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:47.275][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:47.275][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.276][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.277][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.279][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.280][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.281][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.283][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.284][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.285][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.286][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.287][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.288][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.289][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:47.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.302][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-01 20:46:47.303][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-01 20:46:47.304][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-01 20:46:47.312][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-01 20:46:47.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-01 20:46:47.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-01 20:46:47.319][biodb::testThat]
biodb.INFO [2024-11-01 20:46:47.320][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-11-01 20:46:47.321][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:47.322][biodb::testThat]
biodb.TRACE[2024-11-01 20:46:47.325][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-01 20:46:47.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-01 20:46:47.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:47.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:47.359][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[2024-11-01 20:46:47.363][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:47.364][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-01 20:46:47.365][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:47.367][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-01 20:46:47.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.378][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:47.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:47.392][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[2024-11-01 20:46:47.395][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:47.396][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-01 20:46:47.397][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:47.398][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-01 20:46:47.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.417][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:47.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:47.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.438][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.TRACE[2024-11-01 20:46:47.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:47.450][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-01 20:46:47.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.460][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:47.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.469][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.470][private$selectFields]
biodb.TRACE[2024-11-01 20:46:47.471][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:47.472][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:47.473][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.474][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.475][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.477][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.478][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.479][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.480][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.481][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.482][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.483][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.484][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.486][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.487][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:47.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.500][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-01 20:46:47.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:47.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.520][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.521][private$selectFields]
biodb.TRACE[2024-11-01 20:46:47.521][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:47.522][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:47.523][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.524][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.525][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.527][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.528][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.529][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.531][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.532][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.533][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.534][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.535][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.537][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.538][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:47.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.552][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-01 20:46:47.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.562][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:47.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.571][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.578][private$selectFields]
biodb.TRACE[2024-11-01 20:46:47.579][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:47.580][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:47.582][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.583][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.584][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.585][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.586][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.587][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.589][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.590][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.591][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.592][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.593][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.595][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.596][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:47.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.608][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-01 20:46:47.609][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-01 20:46:47.610][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-01 20:46:47.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:47.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:47.647][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[2024-11-01 20:46:47.651][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:47.652][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-01 20:46:47.653][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:47.655][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-01 20:46:47.658][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[2024-11-01 20:46:47.661][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:47.662][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-01 20:46:47.664][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:47.665][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-01 20:46:47.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.676][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:47.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:47.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.698][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[2024-11-01 20:46:47.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:47.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.720][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:47.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:47.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:47.733][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-01 20:46:47.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.744][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:47.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.760][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.761][private$selectFields]
biodb.TRACE[2024-11-01 20:46:47.762][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:47.763][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:47.764][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.765][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.766][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.768][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.769][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.770][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.772][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.772][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.773][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.774][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.775][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.777][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.778][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:47.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.790][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-01 20:46:47.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.798][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.799][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:47.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.809][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.810][private$selectFields]
biodb.TRACE[2024-11-01 20:46:47.811][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:47.812][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:47.812][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.813][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.814][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.816][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.817][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.818][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.820][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.821][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.822][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.823][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.824][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.826][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.827][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:47.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.840][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-01 20:46:47.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.850][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[2024-11-01 20:46:47.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.859][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.860][private$selectFields]
biodb.TRACE[2024-11-01 20:46:47.860][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:47.861][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:47.862][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.863][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.864][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.866][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.867][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.868][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.870][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.871][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.872][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:47.873][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.874][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.876][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.877][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:47.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:47.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.890][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-01 20:46:47.891][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-01 20:46:47.892][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-01 20:46:47.900][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-01 20:46:47.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-01 20:46:47.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-01 20:46:47.907][biodb::testThat]
biodb.INFO [2024-11-01 20:46:47.908][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-11-01 20:46:47.909][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:47.910][biodb::testThat]
biodb.TRACE[2024-11-01 20:46:47.913][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-01 20:46:47.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-01 20:46:47.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:47.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:47.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:47.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:47.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:47.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:47.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:47.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:47.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:47.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:47.989][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.DEBUG[2024-11-01 20:46:47.995][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[2024-11-01 20:46:48.001][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:48.003][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-01 20:46:48.004][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:48.006][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-01 20:46:48.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:48.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:48.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:48.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:48.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:48.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:48.020][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:48.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:48.038][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[2024-11-01 20:46:48.042][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:48.043][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-01 20:46:48.045][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:48.046][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-01 20:46:48.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:48.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:48.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:48.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:48.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:48.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:48.061][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.TRACE[2024-11-01 20:46:48.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:48.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:48.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:48.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:48.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:48.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:48.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:48.090][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:48.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:48.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:48.107][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-01 20:46:48.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:48.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:48.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:48.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:48.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:48.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:48.122][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:48.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.134][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.136][private$selectFields]
biodb.TRACE[2024-11-01 20:46:48.137][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:48.138][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:48.139][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.141][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.142][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.143][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.144][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.145][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.147][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.149][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.150][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.151][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.152][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.154][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.156][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.157][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:48.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.207][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-01 20:46:48.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:48.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:48.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:48.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:48.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:48.216][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:48.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:48.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.226][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.227][private$selectFields]
biodb.TRACE[2024-11-01 20:46:48.227][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:48.228][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:48.229][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.230][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.231][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.233][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.234][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.235][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.236][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.237][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.238][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.239][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.240][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.242][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.242][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:48.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.254][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-01 20:46:48.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:48.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:48.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:48.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:48.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:48.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:48.263][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.TRACE[2024-11-01 20:46:48.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.272][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.273][private$selectFields]
biodb.TRACE[2024-11-01 20:46:48.273][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:48.274][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:48.275][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.276][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.277][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.279][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.280][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.281][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.282][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.283][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.284][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.285][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.286][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.288][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.288][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:48.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.301][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-01 20:46:48.302][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-01 20:46:48.303][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-01 20:46:48.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:48.342][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:48.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:48.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:48.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:48.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:48.350][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:48.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:48.353][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[2024-11-01 20:46:48.357][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:48.358][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-01 20:46:48.359][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:48.360][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-01 20:46:48.370][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[2024-11-01 20:46:48.374][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:48.375][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-01 20:46:48.376][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:48.378][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-01 20:46:48.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:48.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:48.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:48.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:48.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:48.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:48.390][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.TRACE[2024-11-01 20:46:48.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:48.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:48.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:48.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:48.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:48.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:48.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:48.412][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.TRACE[2024-11-01 20:46:48.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:48.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:48.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:48.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:48.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:48.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:48.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:48.434][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:48.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:48.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:48.447][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-01 20:46:48.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:48.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:48.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:48.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:48.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:48.457][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:48.458][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:48.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.467][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.468][private$selectFields]
biodb.TRACE[2024-11-01 20:46:48.469][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:48.470][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:48.470][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.471][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.472][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.474][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.475][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.476][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.478][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.479][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.480][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.481][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.482][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.484][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.485][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:48.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.498][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-01 20:46:48.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:48.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:48.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:48.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:48.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:48.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:48.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:48.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.518][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.519][private$selectFields]
biodb.TRACE[2024-11-01 20:46:48.520][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:48.521][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:48.522][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.522][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.524][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.525][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.526][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.527][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.529][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.530][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.531][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.532][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.533][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.535][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.536][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:48.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.556][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-01 20:46:48.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:48.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:48.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:48.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:48.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:48.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:48.567][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.TRACE[2024-11-01 20:46:48.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.576][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.577][private$selectFields]
biodb.TRACE[2024-11-01 20:46:48.578][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-01 20:46:48.579][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-01 20:46:48.580][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.581][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.582][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.584][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.585][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.586][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.587][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.588][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.589][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-01 20:46:48.590][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.591][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.593][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.594][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-01 20:46:48.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:48.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:48.607][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-01 20:46:48.608][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-01 20:46:48.609][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-01 20:46:48.627][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-01 20:46:48.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-01 20:46:48.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:48.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-01 20:46:48.634][biodb::testThat]
biodb.INFO [2024-11-01 20:46:48.635][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-11-01 20:46:48.636][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:48.637][biodb::testThat]
biodb.DEBUG[2024-11-01 20:46:48.639][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-11-01 20:46:48.640][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:46:48.642][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-11-01 20:46:48.643][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:46:48.644][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:48.645][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:48.646][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:48.647][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:48.648][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:48.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:48.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:48.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:48.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:48.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:48.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:48.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:48.661][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-11-01 20:46:48.663][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:48.664][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:48.666][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-11-01 20:46:49.000][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-11-01 20:46:49.366][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:49.368][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-11-01 20:46:49.372][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-11-01 20:46:49.375][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-11-01 20:46:49.376][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:49.377][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:46:49.379][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:49.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:49.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:49.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:49.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:49.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:49.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:49.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:46:49.393][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:49.394][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:49.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.396][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:49.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:49.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.402][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:49.403][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:49.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.405][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.406][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:49.407][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:49.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.409][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.411][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:49.418][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:49.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.425][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.427][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:49.428][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:49.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.430][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.431][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:49.432][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:49.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.434][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.435][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:49.436][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:49.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.438][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.440][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:49.441][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:49.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.443][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.444][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:49.445][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:49.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.447][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.448][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:49.449][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:49.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.451][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.452][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:49.453][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:49.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.455][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:49.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:49.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:49.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:49.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:49.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:49.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:49.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:49.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:49.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:49.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:49.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:49.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:49.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:49.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:49.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:49.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:49.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:49.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:49.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:49.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:49.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:49.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:49.495][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-11-01 20:46:49.496][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-11-01 20:46:49.504][biodb::testThat]
biodb.INFO [2024-11-01 20:46:49.505][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-11-01 20:46:49.506][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:49.507][biodb::testThat]
biodb.DEBUG[2024-11-01 20:46:49.515][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-11-01 20:46:49.517][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-11-01 20:46:49.518][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-11-01 20:46:49.519][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-11-01 20:46:49.521][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-11-01 20:46:49.522][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:46:49.523][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:46:49.524][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:49.525][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:46:49.526][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:46:49.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:49.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:49.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:49.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:49.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:49.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:49.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:49.540][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-11-01 20:46:49.543][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:49.544][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:49.545][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-11-01 20:46:49.879][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-11-01 20:46:50.212][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:50.216][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-11-01 20:46:50.221][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-11-01 20:46:50.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:50.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:50.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:50.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:50.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:50.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:50.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:50.241][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-11-01 20:46:50.246][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:50.247][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:50.250][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-11-01 20:46:50.584][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-11-01 20:46:50.916][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:50.919][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-11-01 20:46:50.922][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-11-01 20:46:50.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:50.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:50.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:50.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:50.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:50.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:50.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:50.949][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-11-01 20:46:50.953][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:50.954][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:50.955][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-11-01 20:46:51.288][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-11-01 20:46:51.620][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:51.623][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-11-01 20:46:51.626][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-11-01 20:46:51.629][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-11-01 20:46:51.630][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:46:51.632][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-11-01 20:46:51.633][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-11-01 20:46:51.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:51.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:51.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:51.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:51.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:51.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:51.644][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:51.646][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.648][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.649][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.655][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:51.656][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:51.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.658][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.659][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:51.660][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:51.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.662][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.663][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:51.664][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:51.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.666][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.668][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:51.669][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:51.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.670][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.672][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:51.673][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:51.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.675][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.676][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:51.677][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:51.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.679][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.680][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:51.681][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:51.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.683][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.684][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:51.685][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:51.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.687][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.688][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:51.689][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:51.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.691][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.692][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:51.694][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:51.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.695][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.709][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:51.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:51.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:51.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:51.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:51.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:51.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:51.734][FUN] Functions in observer BiodbConfig: [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[2024-11-01 20:46:51.736][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.737][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.739][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.745][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:51.746][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:51.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.748][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.749][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:51.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:51.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.753][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:51.754][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:51.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.756][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.757][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:51.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:51.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.761][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:51.763][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:51.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.764][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.766][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:51.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:51.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.770][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:51.771][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:51.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.773][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:51.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:51.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.778][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:51.779][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:51.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.793][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.794][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:51.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:51.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.799][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:51.800][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:51.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.802][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.803][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:51.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:51.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.807][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:51.808][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:51.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.810][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:51.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:51.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.816][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:51.817][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:51.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.819][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:51.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:51.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.824][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:51.825][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:51.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.827][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.829][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:51.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:51.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.833][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:51.834][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:51.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.836][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.837][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:51.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:51.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:51.869][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:51.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:51.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:51.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:51.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:51.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:51.878][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.TRACE[2024-11-01 20:46:51.881][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.882][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.884][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.889][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:51.890][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:51.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.892][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.893][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:46:51.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:46:51.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.897][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:51.898][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:51.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.900][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.901][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:46:51.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:46:51.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.905][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:51.907][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:51.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.908][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:46:51.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:46:51.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.914][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:51.915][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:51.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.917][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.918][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:46:51.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:46:51.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.922][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:51.923][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:51.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.925][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.927][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:51.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:46:51.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.931][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:51.932][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:51.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.934][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.935][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:46:51.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:46:51.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.939][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:51.940][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:51.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.942][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:51.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:51.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.948][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:51.949][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:51.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.951][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:51.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:51.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.956][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:51.957][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:51.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.959][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.967][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:46:51.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:46:51.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.972][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:51.973][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:51.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.975][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.976][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:46:51.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:46:51.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:46:51.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:51.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:51.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:51.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:51.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:52.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:52.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:52.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:52.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:52.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:52.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:52.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:52.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:52.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:52.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:52.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:52.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:52.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:52.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:52.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:52.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:52.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:52.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:52.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:52.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:52.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:52.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:52.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:52.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:52.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:52.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:52.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:52.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:52.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:52.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:52.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:52.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:52.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:52.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:52.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:52.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:52.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:52.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:52.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:52.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:52.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:52.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:46:52.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:46:52.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:52.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:46:52.044][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-11-01 20:46:52.045][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-11-01 20:46:52.046][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-11-01 20:46:52.059][biodb::testThat]
biodb.INFO [2024-11-01 20:46:52.060][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-11-01 20:46:52.061][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:52.062][biodb::testThat]
biodb.INFO [2024-11-01 20:46:52.086][biodb::testThat]
biodb.INFO [2024-11-01 20:46:52.087][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-11-01 20:46:52.088][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:52.089][biodb::testThat]
biodb.INFO [2024-11-01 20:46:52.097][biodb::testThat]
biodb.INFO [2024-11-01 20:46:52.098][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-11-01 20:46:52.099][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:52.100][biodb::testThat]
biodb.DEBUG[2024-11-01 20:46:52.102][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[2024-11-01 20:46:52.106][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:52.107][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:52.109][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-11-01 20:46:52.524][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-11-01 20:46:52.996][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:53.001][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-11-01 20:46:53.009][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-11-01 20:46:53.034][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:46:53.036][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:46:53.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:53.048][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:46:53.055][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:53.057][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:46:53.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:46:53.060][ef$get] fields variable is a list.
biodb.INFO [2024-11-01 20:46:53.062][biodb::testThat]
biodb.INFO [2024-11-01 20:46:53.063][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-11-01 20:46:53.065][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:53.066][biodb::testThat]
biodb.ERROR[2024-11-01 20:46:53.082][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-11-01 20:46:53.099][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-11-01 20:46:53.111][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-01 20:46:53.112][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-01 20:46:53.113][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-01 20:46:53.114][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-01 20:46:53.114][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.116][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.118][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-01 20:46:53.128][biodb::testContext]
biodb.INFO [2024-11-01 20:46:53.129][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-01 20:46:53.129][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-11-01 20:46:53.130][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-01 20:46:53.131][biodb::testContext]
biodb.INFO [2024-11-01 20:46:53.133][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-01 20:46:53.135][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-01 20:46:53.138][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-01 20:46:53.139][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-01 20:46:53.140][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-01 20:46:53.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.143][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[2024-11-01 20:46:53.144][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-01 20:46:53.145][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-01 20:46:53.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.148][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-01 20:46:53.149][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-01 20:46:53.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.152][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-01 20:46:53.153][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-01 20:46:53.154][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-01 20:46:53.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.164][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-01 20:46:53.165][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-01 20:46:53.166][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-01 20:46:53.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.169][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[2024-11-01 20:46:53.170][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-01 20:46:53.171][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-01 20:46:53.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.174][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-01 20:46:53.175][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-01 20:46:53.176][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-01 20:46:53.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.180][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-01 20:46:53.181][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-01 20:46:53.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.185][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-01 20:46:53.186][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-01 20:46:53.187][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-01 20:46:53.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.191][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-01 20:46:53.192][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-01 20:46:53.193][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-01 20:46:53.194][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-01 20:46:53.195][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-01 20:46:53.197][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-01 20:46:53.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.200][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-01 20:46:53.201][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-01 20:46:53.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.205][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-01 20:46:53.206][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-01 20:46:53.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.210][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-01 20:46:53.211][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-01 20:46:53.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.214][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[2024-11-01 20:46:53.215][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-01 20:46:53.216][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-01 20:46:53.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.219][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-01 20:46:53.220][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-01 20:46:53.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.224][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-01 20:46:53.225][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-01 20:46:53.248][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-01 20:46:53.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.253][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-01 20:46:53.254][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-01 20:46:53.255][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-01 20:46:53.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.258][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[2024-11-01 20:46:53.259][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-01 20:46:53.261][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:53.279][self$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[2024-11-01 20:46:53.281][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.282][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:53.283][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.283][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.284][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:53.285][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.286][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-01 20:46:53.287][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:53.288][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.289][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-01 20:46:53.290][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:53.291][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:53.292][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.293][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-01 20:46:53.293][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-01 20:46:53.293][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-01 20:46:53.293][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-01 20:46:53.293][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-01 20:46:53.294][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:53.295][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:53.296][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:53.297][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:53.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:53.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:53.300][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.301][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:53.302][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:53.302][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:53.303][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:53.304][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:53.305][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-01 20:46:53.307][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:53.308][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-01 20:46:53.309][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.310][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:53.311][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.312][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.313][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:53.314][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.315][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-01 20:46:53.316][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:53.317][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.318][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-01 20:46:53.319][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:53.320][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:53.321][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.322][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-01 20:46:53.322][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-01 20:46:53.322][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-01 20:46:53.322][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-01 20:46:53.322][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-01 20:46:53.323][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:53.324][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:53.324][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:53.325][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:53.326][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:53.327][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:53.328][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.329][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:53.330][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:53.331][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:53.332][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:53.333][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:53.334][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-01 20:46:53.336][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.336][self$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[2024-11-01 20:46:53.337][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.338][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:53.339][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.340][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.341][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:53.342][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.343][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-01 20:46:53.344][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:53.345][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:53.346][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-01 20:46:53.347][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:53.348][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:53.349][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.349][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:53.350][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:53.351][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:53.352][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:53.353][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:53.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:53.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:53.355][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.356][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:53.357][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:53.358][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:53.359][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:53.360][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:53.361][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-01 20:46:53.363][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.363][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-01 20:46:53.364][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.365][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:53.366][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.367][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.368][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:53.369][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.370][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-01 20:46:53.371][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:53.372][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:53.373][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-01 20:46:53.373][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:53.374][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:53.375][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.376][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:53.377][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:53.378][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:53.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:53.380][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:53.381][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:53.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:53.382][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.383][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:53.384][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:53.385][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:53.386][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:53.387][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:53.388][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-01 20:46:53.389][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.390][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[2024-11-01 20:46:53.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.394][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[2024-11-01 20:46:53.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.575][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[2024-11-01 20:46:53.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.591][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[2024-11-01 20:46:53.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.599][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.DEBUG[2024-11-01 20:46:53.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.607][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.DEBUG[2024-11-01 20:46:53.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.611][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[2024-11-01 20:46:53.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.615][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[2024-11-01 20:46:53.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.626][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[2024-11-01 20:46:53.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.631][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-01 20:46:53.632][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-01 20:46:53.634][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-01 20:46:53.635][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-01 20:46:53.636][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-01 20:46:53.637][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-01 20:46:53.638][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-01 20:46:53.640][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-01 20:46:53.641][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-01 20:46:53.642][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-01 20:46:53.643][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-01 20:46:53.645][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-01 20:46:53.646][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-01 20:46:53.647][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-01 20:46:53.648][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-01 20:46:53.649][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-01 20:46:53.651][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-01 20:46:53.652][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-01 20:46:53.653][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-01 20:46:53.654][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-01 20:46:53.655][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-01 20:46:53.657][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-01 20:46:53.658][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-01 20:46:53.659][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-01 20:46:53.660][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-01 20:46:53.662][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-01 20:46:53.663][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-01 20:46:53.664][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-01 20:46:53.665][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-01 20:46:53.666][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-01 20:46:53.668][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-01 20:46:53.669][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-01 20:46:53.670][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-01 20:46:53.671][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-01 20:46:53.672][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-01 20:46:53.674][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-01 20:46:53.675][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-01 20:46:53.676][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-01 20:46:53.677][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-01 20:46:53.679][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-01 20:46:53.680][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-01 20:46:53.681][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-01 20:46:53.682][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-01 20:46:53.683][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-01 20:46:53.685][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-01 20:46:53.686][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-01 20:46:53.687][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-01 20:46:53.689][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-01 20:46:53.690][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-01 20:46:53.691][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-01 20:46:53.692][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-01 20:46:53.694][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-01 20:46:53.695][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-01 20:46:53.696][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-01 20:46:53.697][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-01 20:46:53.699][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-01 20:46:53.700][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-01 20:46:53.701][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-01 20:46:53.703][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-01 20:46:53.704][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-01 20:46:53.705][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-01 20:46:53.706][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-01 20:46:53.708][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-01 20:46:53.709][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-01 20:46:53.710][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-01 20:46:53.711][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-01 20:46:53.713][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-01 20:46:53.714][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-01 20:46:53.715][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-01 20:46:53.716][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-01 20:46:53.722][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-01 20:46:53.723][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-01 20:46:53.724][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-01 20:46:53.725][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-01 20:46:53.727][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-01 20:46:53.728][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-01 20:46:53.729][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-01 20:46:53.730][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-01 20:46:53.732][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-01 20:46:53.733][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-01 20:46:53.734][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-01 20:46:53.735][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-01 20:46:53.736][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-01 20:46:53.738][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-01 20:46:53.739][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-01 20:46:53.740][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-01 20:46:53.741][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.742][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.749][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[2024-11-01 20:46:53.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.759][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[2024-11-01 20:46:53.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.770][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[2024-11-01 20:46:53.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.776][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[2024-11-01 20:46:53.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.797][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[2024-11-01 20:46:53.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.803][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[2024-11-01 20:46:53.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.808][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[2024-11-01 20:46:53.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.813][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[2024-11-01 20:46:53.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:53.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.824][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[2024-11-01 20:46:53.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.830][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.DEBUG[2024-11-01 20:46:53.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:53.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:53.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:53.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:53.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:53.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:53.835][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.DEBUG[2024-11-01 20:46:53.837][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-01 20:46:53.838][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-01 20:46:53.840][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:53.841][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.842][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.842][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:53.843][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.844][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.845][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.846][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-01 20:46:53.847][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-01 20:46:53.848][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:53.849][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.850][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-01 20:46:53.851][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:53.851][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-01 20:46:53.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-01 20:46:53.851][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-01 20:46:53.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-01 20:46:53.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-01 20:46:53.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-01 20:46:53.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-01 20:46:53.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-01 20:46:53.851][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-01 20:46:53.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-01 20:46:53.851][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-01 20:46:53.852][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:53.853][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-01 20:46:53.853][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-01 20:46:53.853][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-01 20:46:53.854][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-01 20:46:53.855][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:53.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:53.857][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:53.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:53.858][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:53.859][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:53.860][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:53.860][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-01 20:46:53.861][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:53.862][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:53.863][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:53.864][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-01 20:46:53.864][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-01 20:46:53.865][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-01 20:46:53.870][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-01 20:46:53.871][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-01 20:46:53.873][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-01 20:46:53.874][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-01 20:46:53.875][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-01 20:46:53.878][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-01 20:46:53.879][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-01 20:46:53.880][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-01 20:46:53.882][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-01 20:46:53.883][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-01 20:46:53.883][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-01 20:46:53.885][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-01 20:46:53.885][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-01 20:46:53.887][biodb::testThat]
biodb.INFO [2024-11-01 20:46:53.888][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-11-01 20:46:53.888][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:53.889][biodb::testThat]
biodb.DEBUG[2024-11-01 20:46:53.892][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-01 20:46:53.896][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:53.896][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:53.898][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-11-01 20:46:54.223][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-11-01 20:46:54.706][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:54.710][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-11-01 20:46:54.717][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-11-01 20:46:54.725][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[2024-11-01 20:46:54.732][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:54.734][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:54.737][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-01 20:46:55.077][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-01 20:46:55.413][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:55.417][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-11-01 20:46:55.424][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-11-01 20:46:55.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:55.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:55.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:55.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:55.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:55.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:55.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:55.449][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-01 20:46:55.455][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:55.457][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:55.460][private$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[2024-11-01 20:46:55.791][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[2024-11-01 20:46:56.124][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:56.127][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-11-01 20:46:56.133][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-11-01 20:46:56.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:56.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:56.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:56.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:56.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:56.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:56.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:56.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:56.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:56.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:56.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:56.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:56.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:56.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:56.191][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[2024-11-01 20:46:56.194][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:56.196][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-01 20:46:56.197][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:56.198][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-01 20:46:56.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:56.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:56.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:56.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:56.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:56.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:56.208][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[2024-11-01 20:46:56.209][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[2024-11-01 20:46:56.212][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:56.213][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-01 20:46:56.214][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:56.215][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-01 20:46:56.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:56.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:56.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:56.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:56.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:56.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:56.225][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[2024-11-01 20:46:56.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:56.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:56.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:56.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:56.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:56.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:56.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:56.250][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[2024-11-01 20:46:56.253][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:56.254][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-01 20:46:56.255][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:56.256][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-01 20:46:56.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:56.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:56.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:56.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:56.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:56.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:56.265][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[2024-11-01 20:46:56.267][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[2024-11-01 20:46:56.269][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:56.270][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-01 20:46:56.272][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:56.273][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-01 20:46:56.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:56.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:56.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:56.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:56.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:56.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:56.282][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[2024-11-01 20:46:56.283][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[2024-11-01 20:46:56.286][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:56.287][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:56.288][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-01 20:46:56.624][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-01 20:46:56.958][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:56.962][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-11-01 20:46:56.970][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-11-01 20:46:56.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:56.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:56.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:56.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:56.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:56.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:56.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-01 20:46:57.014][biodb::testThat]
biodb.INFO [2024-11-01 20:46:57.016][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-11-01 20:46:57.018][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:57.020][biodb::testThat]
biodb.DEBUG[2024-11-01 20:46:57.026][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-01 20:46:57.032][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:57.034][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:57.037][private$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[2024-11-01 20:46:57.372][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[2024-11-01 20:46:57.709][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:57.713][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-11-01 20:46:57.721][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-11-01 20:46:57.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:57.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:57.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:57.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:57.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:57.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:57.742][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[2024-11-01 20:46:57.749][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[2024-11-01 20:46:57.755][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:57.756][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:57.759][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-01 20:46:58.094][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-01 20:46:58.432][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:58.436][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-11-01 20:46:58.444][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-11-01 20:46:58.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:46:58.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-01 20:46:58.477][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-01 20:46:58.480][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-01 20:46:58.481][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-01 20:46:58.483][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-01 20:46:58.484][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.487][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.490][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-01 20:46:58.496][biodb::testContext]
biodb.INFO [2024-11-01 20:46:58.497][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-01 20:46:58.498][biodb::testContext] Test context - Test web services
biodb.INFO [2024-11-01 20:46:58.500][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-01 20:46:58.501][biodb::testContext]
biodb.INFO [2024-11-01 20:46:58.503][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-01 20:46:58.505][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-01 20:46:58.510][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-01 20:46:58.511][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-01 20:46:58.512][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-01 20:46:58.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.520][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-01 20:46:58.530][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-01 20:46:58.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.534][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-01 20:46:58.535][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-01 20:46:58.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.538][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-01 20:46:58.539][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-01 20:46:58.540][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-01 20:46:58.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.543][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-01 20:46:58.544][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-01 20:46:58.544][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-01 20:46:58.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.548][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-01 20:46:58.549][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-01 20:46:58.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.552][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-01 20:46:58.553][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-01 20:46:58.554][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-01 20:46:58.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.557][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-01 20:46:58.558][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-01 20:46:58.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.561][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-01 20:46:58.562][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-01 20:46:58.563][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-01 20:46:58.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.566][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-01 20:46:58.567][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-01 20:46:58.568][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-01 20:46:58.569][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-01 20:46:58.570][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-01 20:46:58.571][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-01 20:46:58.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.574][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-01 20:46:58.575][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-01 20:46:58.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.578][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-01 20:46:58.579][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-01 20:46:58.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.582][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-01 20:46:58.583][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-01 20:46:58.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.586][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-01 20:46:58.587][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-01 20:46:58.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.590][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-01 20:46:58.591][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-01 20:46:58.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.595][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-01 20:46:58.595][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-01 20:46:58.599][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-01 20:46:58.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.602][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-01 20:46:58.603][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-01 20:46:58.604][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-01 20:46:58.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.607][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-01 20:46:58.609][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:58.609][self$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[2024-11-01 20:46:58.610][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.611][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:58.612][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.613][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:58.614][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:58.615][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:58.616][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-01 20:46:58.616][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:58.617][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.618][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-01 20:46:58.619][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:58.620][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:58.621][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.622][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-01 20:46:58.622][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-01 20:46:58.622][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-01 20:46:58.622][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-01 20:46:58.622][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-01 20:46:58.623][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:58.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:58.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:58.625][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:58.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:58.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:58.628][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:58.628][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:58.629][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:58.630][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:58.631][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:58.632][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:58.633][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-01 20:46:58.634][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:58.635][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-01 20:46:58.636][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.637][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:58.638][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.639][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:58.640][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:58.641][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:58.641][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-01 20:46:58.642][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:58.643][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.644][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-01 20:46:58.645][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:58.646][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:58.647][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.648][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-01 20:46:58.648][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-01 20:46:58.648][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-01 20:46:58.648][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-01 20:46:58.648][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-01 20:46:58.649][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:58.650][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:58.650][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:58.651][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:58.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:58.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:58.654][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:58.655][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:58.656][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:58.656][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:58.657][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:58.658][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:58.659][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-01 20:46:58.661][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.662][self$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[2024-11-01 20:46:58.663][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.664][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:58.664][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.665][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:58.666][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:58.667][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:58.668][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-01 20:46:58.669][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:58.670][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:58.671][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-01 20:46:58.672][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:58.673][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:58.673][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.674][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:58.675][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:58.676][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:58.677][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:58.682][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:58.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:58.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:58.684][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:58.685][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:58.686][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:58.687][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:58.688][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:58.688][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:58.689][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-01 20:46:58.691][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.692][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-01 20:46:58.693][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.694][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:58.694][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.695][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:58.696][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:58.697][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:58.698][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-01 20:46:58.699][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:58.700][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:58.701][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-01 20:46:58.702][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:58.702][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:58.703][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:58.704][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:58.705][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:58.706][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:58.707][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:58.708][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:58.708][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:58.709][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:58.710][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:58.711][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:58.712][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:58.713][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:58.713][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:58.714][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:58.715][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-01 20:46:58.716][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.717][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[2024-11-01 20:46:58.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.725][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.DEBUG[2024-11-01 20:46:58.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.729][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[2024-11-01 20:46:58.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.740][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.DEBUG[2024-11-01 20:46:58.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.752][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.DEBUG[2024-11-01 20:46:58.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.756][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[2024-11-01 20:46:58.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.779][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[2024-11-01 20:46:58.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.783][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[2024-11-01 20:46:58.784][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-01 20:46:58.785][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-01 20:46:58.787][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-01 20:46:58.788][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-01 20:46:58.789][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-01 20:46:58.790][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-01 20:46:58.792][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-01 20:46:58.793][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-01 20:46:58.794][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-01 20:46:58.795][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-01 20:46:58.797][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-01 20:46:58.798][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-01 20:46:58.799][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-01 20:46:58.800][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-01 20:46:58.802][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-01 20:46:58.803][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-01 20:46:58.804][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-01 20:46:58.805][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-01 20:46:58.807][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-01 20:46:58.808][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-01 20:46:58.809][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-01 20:46:58.811][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-01 20:46:58.812][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-01 20:46:58.813][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-01 20:46:58.814][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-01 20:46:58.816][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-01 20:46:58.817][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-01 20:46:58.818][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-01 20:46:58.819][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-01 20:46:58.821][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-01 20:46:58.822][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-01 20:46:58.823][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-01 20:46:58.828][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-01 20:46:58.829][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-01 20:46:58.831][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-01 20:46:58.832][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-01 20:46:58.833][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-01 20:46:58.834][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-01 20:46:58.836][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-01 20:46:58.837][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-01 20:46:58.838][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-01 20:46:58.839][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-01 20:46:58.840][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-01 20:46:58.842][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-01 20:46:58.843][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-01 20:46:58.844][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-01 20:46:58.845][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-01 20:46:58.847][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-01 20:46:58.848][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-01 20:46:58.849][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-01 20:46:58.850][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-01 20:46:58.851][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-01 20:46:58.853][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-01 20:46:58.854][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-01 20:46:58.855][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-01 20:46:58.856][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-01 20:46:58.858][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-01 20:46:58.859][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-01 20:46:58.860][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-01 20:46:58.861][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-01 20:46:58.862][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-01 20:46:58.864][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-01 20:46:58.865][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-01 20:46:58.866][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-01 20:46:58.867][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-01 20:46:58.868][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-01 20:46:58.870][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-01 20:46:58.871][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-01 20:46:58.872][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-01 20:46:58.873][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-01 20:46:58.874][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-01 20:46:58.876][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-01 20:46:58.877][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-01 20:46:58.878][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-01 20:46:58.879][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-01 20:46:58.881][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-01 20:46:58.882][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-01 20:46:58.883][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-01 20:46:58.884][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-01 20:46:58.885][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-01 20:46:58.887][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-01 20:46:58.888][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-01 20:46:58.889][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-01 20:46:58.890][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-01 20:46:58.892][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-01 20:46:58.893][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-01 20:46:58.893][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.895][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.896][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.DEBUG[2024-11-01 20:46:58.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.901][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[2024-11-01 20:46:58.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.907][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[2024-11-01 20:46:58.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.917][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[2024-11-01 20:46:58.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.928][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[2024-11-01 20:46:58.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.956][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.DEBUG[2024-11-01 20:46:58.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.989][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.DEBUG[2024-11-01 20:46:58.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:58.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:58.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:58.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:58.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:58.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:58.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:58.995][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-01 20:46:58.997][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-01 20:46:58.998][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:58.999][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-01 20:46:59.000][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.001][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:59.002][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.003][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:59.004][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.005][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-01 20:46:59.005][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-01 20:46:59.006][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:59.007][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.008][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-01 20:46:59.009][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:59.010][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-01 20:46:59.010][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-01 20:46:59.010][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-01 20:46:59.010][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-01 20:46:59.010][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-01 20:46:59.010][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-01 20:46:59.010][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-01 20:46:59.010][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-01 20:46:59.010][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-01 20:46:59.010][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-01 20:46:59.010][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-01 20:46:59.011][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:59.012][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-01 20:46:59.012][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-01 20:46:59.012][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-01 20:46:59.013][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-01 20:46:59.014][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:59.014][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:59.015][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:59.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:59.017][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:59.018][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:59.018][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:46:59.018][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-01 20:46:59.019][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:59.020][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:59.021][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.022][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-01 20:46:59.022][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-01 20:46:59.023][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-01 20:46:59.024][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-01 20:46:59.026][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-01 20:46:59.027][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-01 20:46:59.028][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-01 20:46:59.030][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-01 20:46:59.033][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-01 20:46:59.034][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-01 20:46:59.035][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-01 20:46:59.036][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-01 20:46:59.037][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-01 20:46:59.038][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-01 20:46:59.039][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-01 20:46:59.040][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-01 20:46:59.041][biodb::testThat]
biodb.INFO [2024-11-01 20:46:59.042][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-11-01 20:46:59.043][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:46:59.043][biodb::testThat]
biodb.DEBUG[2024-11-01 20:46:59.046][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-01 20:46:59.049][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:46:59.050][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-01 20:46:59.051][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:46:59.053][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-01 20:46:59.056][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-01 20:46:59.058][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:46:59.059][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:46:59.061][private$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[2024-11-01 20:46:59.395][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[2024-11-01 20:46:59.728][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:46:59.732][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-11-01 20:46:59.740][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-11-01 20:46:59.756][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-01 20:46:59.759][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-01 20:46:59.761][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-01 20:46:59.763][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-01 20:46:59.764][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:46:59.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:46:59.768][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:46:59.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:46:59.772][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.773][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.INFO [2024-11-01 20:46:59.779][biodb::testContext]
biodb.INFO [2024-11-01 20:46:59.781][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-01 20:46:59.782][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-11-01 20:46:59.784][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-01 20:46:59.785][biodb::testContext]
biodb.INFO [2024-11-01 20:46:59.788][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-01 20:46:59.791][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-01 20:46:59.796][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-01 20:46:59.797][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-01 20:46:59.798][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-01 20:46:59.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:59.803][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-01 20:46:59.804][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-01 20:46:59.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.807][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.DEBUG[2024-11-01 20:46:59.808][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-01 20:46:59.809][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-01 20:46:59.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:59.813][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-01 20:46:59.814][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-01 20:46:59.815][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-01 20:46:59.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.818][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[2024-11-01 20:46:59.819][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-01 20:46:59.820][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-01 20:46:59.821][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-01 20:46:59.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:59.824][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-01 20:46:59.825][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-01 20:46:59.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.838][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[2024-11-01 20:46:59.839][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-01 20:46:59.840][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-01 20:46:59.841][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-01 20:46:59.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:59.844][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-01 20:46:59.845][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-01 20:46:59.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:59.849][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-01 20:46:59.850][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-01 20:46:59.851][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-01 20:46:59.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:59.854][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-01 20:46:59.855][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-01 20:46:59.856][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-01 20:46:59.857][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-01 20:46:59.858][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-01 20:46:59.859][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-01 20:46:59.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.862][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.DEBUG[2024-11-01 20:46:59.862][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-01 20:46:59.864][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-01 20:46:59.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:59.867][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-01 20:46:59.868][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-01 20:46:59.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:59.871][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-01 20:46:59.872][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-01 20:46:59.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:59.876][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-01 20:46:59.877][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-01 20:46:59.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.879][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.DEBUG[2024-11-01 20:46:59.880][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-01 20:46:59.881][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-01 20:46:59.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:59.884][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-01 20:46:59.885][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-01 20:46:59.888][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-01 20:46:59.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:59.892][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-01 20:46:59.893][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-01 20:46:59.894][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-01 20:46:59.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:46:59.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:46:59.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:46:59.897][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-01 20:46:59.899][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:59.900][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-01 20:46:59.901][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.902][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:59.903][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.904][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:59.904][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:59.905][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:59.906][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-01 20:46:59.907][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:59.908][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.909][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-01 20:46:59.910][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:59.911][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:59.912][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.913][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-01 20:46:59.913][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-01 20:46:59.913][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-01 20:46:59.913][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-01 20:46:59.913][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-01 20:46:59.914][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:59.915][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:59.916][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:59.916][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:59.917][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:59.918][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:59.919][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:59.920][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:59.921][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:59.922][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:59.923][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:59.924][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:59.925][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-01 20:46:59.926][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:59.927][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-01 20:46:59.928][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.929][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:59.930][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.931][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:59.932][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:59.933][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:59.934][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-01 20:46:59.935][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:59.936][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.937][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-01 20:46:59.938][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:59.938][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:59.939][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.940][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-01 20:46:59.940][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-01 20:46:59.940][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-01 20:46:59.940][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-01 20:46:59.940][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-01 20:46:59.941][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:59.942][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:59.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:59.944][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:59.945][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:59.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:59.947][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:59.947][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:59.948][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:59.949][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:59.950][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:59.951][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:59.952][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-01 20:46:59.954][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.955][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-01 20:46:59.956][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.957][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:59.958][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.959][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:59.960][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:59.961][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:59.962][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-01 20:46:59.963][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:59.964][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:59.965][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-01 20:46:59.966][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:46:59.967][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:59.968][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.969][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:59.970][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:46:59.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:59.971][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:59.972][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:46:59.973][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:46:59.974][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:46:59.975][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:46:59.976][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:59.977][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:46:59.978][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:46:59.979][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:59.980][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:46:59.981][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-01 20:46:59.983][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.984][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-01 20:46:59.985][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.986][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:46:59.987][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:46:59.988][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:46:59.988][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:59.989][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-01 20:46:59.990][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-01 20:46:59.991][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:46:59.998][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:46:59.999][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-01 20:46:59.999][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:47:00.000][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:47:00.001][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-01 20:47:00.002][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:47:00.003][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-01 20:47:00.004][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:47:00.005][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:47:00.006][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:47:00.007][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:47:00.008][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:47:00.008][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:47:00.009][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:47:00.010][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:47:00.011][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:47:00.012][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-01 20:47:00.013][self$setPropertyValue]
biodb.DEBUG[2024-11-01 20:47:00.014][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-01 20:47:00.015][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.024][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.DEBUG[2024-11-01 20:47:00.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.029][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.DEBUG[2024-11-01 20:47:00.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.037][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[2024-11-01 20:47:00.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.049][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[2024-11-01 20:47:00.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.074][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[2024-11-01 20:47:00.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.087][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-01 20:47:00.089][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-01 20:47:00.090][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-01 20:47:00.091][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-01 20:47:00.093][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-01 20:47:00.094][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-01 20:47:00.095][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-01 20:47:00.096][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-01 20:47:00.098][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-01 20:47:00.099][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-01 20:47:00.100][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-01 20:47:00.102][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-01 20:47:00.103][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-01 20:47:00.104][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-01 20:47:00.105][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-01 20:47:00.107][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-01 20:47:00.108][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-01 20:47:00.110][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-01 20:47:00.111][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-01 20:47:00.112][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-01 20:47:00.114][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-01 20:47:00.115][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-01 20:47:00.116][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-01 20:47:00.118][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-01 20:47:00.119][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-01 20:47:00.120][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-01 20:47:00.122][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-01 20:47:00.123][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-01 20:47:00.125][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-01 20:47:00.126][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-01 20:47:00.127][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-01 20:47:00.129][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-01 20:47:00.130][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-01 20:47:00.131][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-01 20:47:00.133][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-01 20:47:00.134][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-01 20:47:00.136][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-01 20:47:00.137][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-01 20:47:00.138][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-01 20:47:00.140][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-01 20:47:00.141][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-01 20:47:00.142][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-01 20:47:00.144][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-01 20:47:00.145][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-01 20:47:00.146][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-01 20:47:00.154][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-01 20:47:00.155][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-01 20:47:00.157][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-01 20:47:00.158][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-01 20:47:00.159][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-01 20:47:00.160][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-01 20:47:00.162][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-01 20:47:00.163][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-01 20:47:00.164][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-01 20:47:00.165][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-01 20:47:00.167][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-01 20:47:00.168][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-01 20:47:00.169][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-01 20:47:00.170][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-01 20:47:00.172][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-01 20:47:00.173][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-01 20:47:00.174][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-01 20:47:00.175][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-01 20:47:00.177][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-01 20:47:00.178][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-01 20:47:00.179][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-01 20:47:00.180][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-01 20:47:00.181][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-01 20:47:00.183][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-01 20:47:00.184][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-01 20:47:00.185][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-01 20:47:00.186][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-01 20:47:00.188][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-01 20:47:00.189][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-01 20:47:00.190][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-01 20:47:00.191][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-01 20:47:00.192][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-01 20:47:00.194][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-01 20:47:00.195][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-01 20:47:00.196][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-01 20:47:00.197][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-01 20:47:00.199][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-01 20:47:00.200][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-01 20:47:00.201][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-01 20:47:00.203][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-01 20:47:00.203][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-01 20:47:00.204][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.206][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.207][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.DEBUG[2024-11-01 20:47:00.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.212][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[2024-11-01 20:47:00.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.234][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[2024-11-01 20:47:00.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.259][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[2024-11-01 20:47:00.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.280][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[2024-11-01 20:47:00.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.287][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[2024-11-01 20:47:00.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.306][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.DEBUG[2024-11-01 20:47:00.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-01 20:47:00.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-01 20:47:00.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.335][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[2024-11-01 20:47:00.337][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-01 20:47:00.339][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-01 20:47:00.341][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-01 20:47:00.342][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-01 20:47:00.343][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-01 20:47:00.344][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-01 20:47:00.345][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-01 20:47:00.346][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-01 20:47:00.347][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-01 20:47:00.348][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-01 20:47:00.349][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-01 20:47:00.350][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-01 20:47:00.351][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-01 20:47:00.352][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-01 20:47:00.353][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-01 20:47:00.354][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-01 20:47:00.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-01 20:47:00.354][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-01 20:47:00.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-01 20:47:00.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-01 20:47:00.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-01 20:47:00.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-01 20:47:00.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-01 20:47:00.354][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-01 20:47:00.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-01 20:47:00.354][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-01 20:47:00.355][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-01 20:47:00.356][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-01 20:47:00.356][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-01 20:47:00.356][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-01 20:47:00.356][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-01 20:47:00.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:47:00.358][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:47:00.359][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-01 20:47:00.360][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-01 20:47:00.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-01 20:47:00.362][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-01 20:47:00.363][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:47:00.363][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-01 20:47:00.364][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-01 20:47:00.365][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-01 20:47:00.366][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-01 20:47:00.367][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-01 20:47:00.367][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-01 20:47:00.368][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-01 20:47:00.370][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-01 20:47:00.371][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-01 20:47:00.373][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-01 20:47:00.374][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-01 20:47:00.376][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-01 20:47:00.379][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-01 20:47:00.380][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-01 20:47:00.381][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-01 20:47:00.383][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-01 20:47:00.384][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-01 20:47:00.385][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-01 20:47:00.386][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-01 20:47:00.387][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-01 20:47:00.388][biodb::testThat]
biodb.INFO [2024-11-01 20:47:00.389][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-11-01 20:47:00.390][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-01 20:47:00.391][biodb::testThat]
biodb.DEBUG[2024-11-01 20:47:00.395][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-01 20:47:00.399][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:47:00.400][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-01 20:47:00.401][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:47:00.402][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-01 20:47:00.406][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[2024-11-01 20:47:00.409][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-01 20:47:00.410][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-11-01 20:47:00.411][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-01 20:47:00.413][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-11-01 20:47:00.417][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-11-01 20:47:00.418][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-01 20:47:00.420][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-11-01 20:47:00.421][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-01 20:47:00.422][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-01 20:47:00.423][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-01 20:47:00.424][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-01 20:47:00.425][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-01 20:47:00.426][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-01 20:47:00.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:47:00.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:00.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:00.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:00.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:00.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:00.437][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[2024-11-01 20:47:00.439][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-11-01 20:47:00.441][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-01 20:47:00.442][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-01 20:47:00.443][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-11-01 20:47:00.776][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-11-01 20:47:01.816][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-01 20:47:01.819][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-11-01 20:47:01.823][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-11-01 20:47:01.825][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-11-01 20:47:01.827][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-01 20:47:01.828][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-01 20:47:01.830][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-01 20:47:01.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-01 20:47:01.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:01.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:01.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:01.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:01.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:01.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-01 20:47:01.846][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:47:01.847][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:47:01.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.849][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:47:01.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:47:01.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.855][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:47:01.856][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:47:01.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.858][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.860][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-01 20:47:01.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-01 20:47:01.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.864][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:47:01.865][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:47:01.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.867][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.868][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-01 20:47:01.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-01 20:47:01.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.883][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-01 20:47:01.884][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-01 20:47:01.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.886][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.887][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-01 20:47:01.888][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-01 20:47:01.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.890][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.891][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:47:01.892][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:47:01.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.894][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.896][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:47:01.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-01 20:47:01.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.900][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:47:01.901][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:47:01.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.902][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.904][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-01 20:47:01.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-01 20:47:01.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.908][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:47:01.909][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:47:01.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.911][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:47:01.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-01 20:47:01.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.916][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:47:01.917][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:47:01.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.919][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.920][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-01 20:47:01.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-01 20:47:01.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.924][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:47:01.925][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:47:01.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.927][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.928][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-01 20:47:01.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-01 20:47:01.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.932][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:47:01.933][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:47:01.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.935][ef$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.936][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-01 20:47:01.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-01 20:47:01.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:47:01.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:47:01.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:47:01.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:47:01.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:47:01.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:47:01.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-01 20:47:01.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-01 20:47:01.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:47:01.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:47:01.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:47:01.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:47:01.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:47:01.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:47:01.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:47:01.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:47:01.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:47:01.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:47:01.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-01 20:47:01.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-01 20:47:01.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-01 20:47:01.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-01 20:47:01.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-01 20:47:01.978][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-11-01 20:47:01.981][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-01 20:47:01.982][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-01 20:47:01.983][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-01 20:47:01.984][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-01 20:47:01.985][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-01 20:47:01.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-01 20:47:01.987][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-01 20:47:01.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-01 20:47:01.988][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-01 20:47:01.989][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
21.720 1.394 50.096
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 0.875 | 0.077 | 2.624 | |
| ChebiEntry | 0.132 | 0.006 | 0.138 | |