CHANGES IN VERSION 1.21.0 ------------------------ MODIFICATIONS o 1.21.9 Add PNG as valid source type o 1.21.4 Removed vignette for creating annotation hub package. Reference and refer to single vignette in AnnotationHub o 1.21.3 Tags for database now combination of biocViews and meta$Tags. Also checks for valid AnnotationHub or AnnotationHubSoftware biocViews. o 1.21.2 Add mtx.gz as valid source type BUG CORRECTION o 1.21.3 Fixed bug to run make*HubMetadata using "." INTERNAL BUG CORRECTION o 1.21.1 misplaced ! clause REMOVED o 1.21.5 Removed BioPax. url no longer valid. Resources were old and never used beyond first addition CHANGES IN VERSION 1.19.0 ------------------------ INTERNAL BUG CORRECTION o 1.19.2 Update Metadata from Ensembl function to use GenomeInfoDb:::fetch_species_index_from_Ensembl_FTP instead of parsing the file path o 1.19.1 misplaced ! clause CHANGES IN VERSION 1.17.0 ------------------------ MODIFICATIONS o 1.17.3 add check for valid Title and Description in metadata file. It should not be empty or NA o 1.17.2 add XML as valid source type o 1.17.1 add GSEMatrix as valid source type CHANGES IN VERSION 1.15.0 ------------------------ MODIFICATIONS o 1.15.13 Added "BLOB" as a valid source type o 1.15.7 Added "MTX" as a valid source type o 1.15.6 Expanded documentation to clarify that data can be hosted publically not strictly Bioconductor AWS o 1.15.4 Added "XLS/XLSX" as valid source type INTERNAL BUG CORRECTION o 1.15.11 updated GencodeGFF recipes for potential future use (still would revisit this with another update to do like ensembl on the fly) o 1.15.5 remove validity check that is wrong/outdated o 1.15.1 needToRerunNonStandardOrgDb added as helper function for when generating non standard org dbs. 1.15.3 added try catch in case aws buckets unreachable. CHANGES IN VERSION 1.13.0 ------------------------ NEW FEATURES o Added ability to have multiple RDataPaths associated with single hub id for strongly associated files (like bam and its bai index file) o DispatchClass are now validated against AnnotationHub::DispatchClassList() which contains currently available DispatchClass and brief description of loading process. CHANGES IN VERSION 1.11.0 ------------------------ MODIFICATIONS o Removed scripts for Pazar DB as website no longer active o Update from BiocInstaller to BiocManager NEW FEATURES o Species and taxonomyId are now validated against GenomeInfoDbData object BUG FIX o Fix TwoBit resource receipe. Converts DNA that is not A,C,T,G,N to N do to design of rtracklayer::export for TwoBit o Fix bug with assignment of tags in annotationhub o makeEpigenomeRoadMap recipe updated to account for XML bug that cannot handle http urls. updated to https CHANGES IN VERSION 1.10.0 ------------------------ MODIFICATIONS o Moved readMetadataFromCsv back to AnnotationHubData. o Use AnnotationHubData::makeAnnotationHubMetadata to validate metadata.csv o readMetadataFromCsv is now internal function CHANGES IN VERSION 1.8.0 ------------------------ NEW FEATURES o Instead of using dropbox or ftp to deliver contributed resources to Bioconductor Core, temporary access to Annotation-Contributor user on S3 is utilized. MODIFICATIONS o Modified readMetadataFromCsv; make RDataPath mandatory entry and if location_prefix is Bioconductor S3 bucket the Rdatapath must start with the package name BUG FIXES o Add garbage collection to fix twobit memory allocation error o Fix files not deleting do to special characters in file names o Import dbGetQuery from DBI o Remove hard coded biocVersion in unit tests CHANGES IN VERSION 1.6.0 ------------------------ NEW FEATURES o add makeStandardTxDbsToSqlite() recipe o add 'ensembl' and 'MySQL' as possible SourceType values o tidy and export makeStandard*ToAHMs and makeNCBIToOrgDbsToAHMs MODIFICATIONS o move currentMetadata o tidy pushResources interface o modified parsing of species name and genome in .ensemblMetadataFromUrl() o modified standard OrgDb recipe o enhance and clean vignette o move 'Tags' check from readCsvFromMetadata() to makeAnnotationHubMetadata() o remove dependency on xml2, curl, httr and probably other wheel reinventions, alter imports and suggests o specify multiple 'Tags' as colon separated string instead of comma separated; avoids problems with read.csv() o select data moved to GenomeInfoDbData package o Added additional documentation instructions for core members to add contributed data to AnnotationHub o rename files; remove old JSON test file no longer applicable o pass 'install' argument down through recipe o General code tidy; remove unused functions and comments; clarify checks BUG FIXES o readMetadataFromCsv() fills in DataProvider and Coordinate_1_based if missing o fix bug introduced in checking 'release' in makeEnsemblTwoBit recipe o makeAnnotationHubMetadata() now processes all inst/extdata/*.csv files o fix subset and import bug in makeAnnotationHubMetadata() o Fix bug in Rdatapath and sourceurl for makeEnsemblFasta.R CHANGES IN VERSION 1.4.0 ------------------------ NEW FEATURES o add script to generate user-contributed resources o makeEnsemblGtfToGRanges() no longer stores data in S3 but downloads and converts to GRanges on the fly o add EnsemblFastaTwoBitToAHM unit test o add man page for makeEnsemblTwoBitToAHM and ensemblFastaToTwoBitFile o add makeAnnotationHubMetadata() helper MODIFICATIONS o move GSE62944-related code to ExperimentHub o move old vignettes to inst/scripts; add 'Introduction to AnnotationHubData' vignette o remove fasta and towbit files on the fly o add 'uploadToS3' argument to pushResources() and runRecipes() o move readMetadataFromCsv() from ExperimentHubData to AnnotationHubData o add 'fileName' arg to readMetadataFromCsv(); don't warn when 'Tags' are provided o specify length for args in readMetadataFromCsv() o makeAnnotationHubMetadata() populates PreparerClass with package name o add 'fileName' arg to makeAnnotationHubMetadata() CHANGES IN VERSION 1.2.0 ------------------------ NEW FEATURES o add makeEnsemblTwoBit() o add hubError(), hubError<- generics and methods o create 'HubMetadata' class which 'AnnotationHubMetadata' inherits from MODIFICATIONS o export ensemblFastaToTwoBitFile() o modifications due to changes in httr::HEAD(): - AFAICT httr::HEAD() >= 1.1.0 accepts https only, not ftp - use xml2 instead of XML for parsing (httr >= 1.1.0 dependency change) o work on recipes: - clean up ChEA and Gencode - don't export tracksToUpdate(); was broken and not used - reorg man pages; combine Ensembl Fasta and TwoBit on single man page o work on updateResources(): - push data to S3 before inserting metadata in db - isolate pushResources() and pushMetadata() from updateResources() - NOTE: Epigenome unit test is failing due to bad url. If not fixed by the host the recipe will need to change. o update makedbSNPVCF() to look in new clinvar location BUG FIXES o fix bugs in makedbSNPVCF() recipe related to genome and tags CHANGES IN VERSION 1.0.0 ------------------------ BUG FIXES o ENSEMBL recipes discover gtf files on Windows. CHANGES IN VERSION 0.0.214 -------------------------- NEW FEATURES o Have added vcf files from the following genome builds for humans "human_9606/VCF/clinical_vcf_set/", "human_9606_b141_GRCh37p13/VCF/", "human_9606_b142_GRCh37p13/VCF/", "human_9606_b142_GRCh37p13/VCF/clinical_vcf_set/" o For each genome build, where available, the following VCF file formats are available a) all.vcf.gz b) all_papu.vcf.gz c) common_all.vcf.gz d) clinvar.vcf.gz e) clinvar_papu f) common_and_clinical g) common_no_known_medical_impact o The user can refer to http://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/ for VCF file type formats