NEWS

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AnnotationHubData 1.29.0

NEW FEATURES

• 1.29.2 Added HIC as acceptable source type
• 1.29.1 Added CDF as acceptable source type

AnnotationHubData 1.25.0

SIGNIFICANT UPDATES

• 1.25.7 Update recipes to upload to azure. NonStandardOrgDb release recipe updated
• 1.25.6 Update recipes to upload to azure. TwoBit ensembl and release recipes for standard TxDb and OrgDb updated

NEW FEATURES

• 1.25.5 Add helper function to upload to azure

MODIFICATIONS

• 1.25.2 Changed makeAnnotationHubMetadata to point to Azure instead of AWS

AnnotationHubData 1.21.0

MODIFICATIONS

• 1.21.9 Add PNG as valid source type
• 1.21.4 Removed vignette for creating annotation hub package. Reference and refer to single vignette in AnnotationHub
• 1.21.3 Tags for database now combination of biocViews and meta$Tags. Also checks for valid AnnotationHub or AnnotationHubSoftware biocViews.
• 1.21.2 Add mtx.gz as valid source type

BUG CORRECTION

• 1.21.3 Fixed bug to run make*HubMetadata using "."

INTERNAL BUG CORRECTION

• 1.21.1 misplaced ! clause

REMOVED

• 1.21.5 Removed BioPax. url no longer valid. Resources were old and never used beyond first addition

AnnotationHubData 1.19.0

INTERNAL BUG CORRECTION

• 1.19.2 Update Metadata from Ensembl function to use GenomeInfoDb:::fetch_species_index_from_Ensembl_FTP instead of parsing the file path
• 1.19.1 misplaced ! clause

AnnotationHubData 1.17.0

MODIFICATIONS

• 1.17.3 add check for valid Title and Description in metadata file. It should not be empty or NA
• 1.17.2 add XML as valid source type
• 1.17.1 add GSEMatrix as valid source type

AnnotationHubData 1.15.0

MODIFICATIONS

• 1.15.13 Added "BLOB" as a valid source type
• 1.15.7 Added "MTX" as a valid source type
• 1.15.6 Expanded documentation to clarify that data can be hosted publically not strictly Bioconductor AWS
• 1.15.4 Added "XLS/XLSX" as valid source type

INTERNAL BUG CORRECTION

• 1.15.11 updated GencodeGFF recipes for potential future use (still would revisit this with another update to do like ensembl on the fly)
• 1.15.5 remove validity check that is wrong/outdated
• 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.

AnnotationHubData 1.13.0

NEW FEATURES

• Added ability to have multiple RDataPaths associated with single hub id for strongly associated files (like bam and its bai index file)
• DispatchClass are now validated against AnnotationHub::DispatchClassList() which contains currently available DispatchClass and brief description of loading process.

AnnotationHubData 1.11.0

MODIFICATIONS

• Removed scripts for Pazar DB as website no longer active
• Update from BiocInstaller to BiocManager

NEW FEATURES

• Species and taxonomyId are now validated against GenomeInfoDbData object

BUG FIX

• Fix TwoBit resource receipe. Converts DNA that is not A,C,T,G,N to N do to design of rtracklayer::export for TwoBit
• Fix bug with assignment of tags in annotationhub
• makeEpigenomeRoadMap recipe updated to account for XML bug that cannot handle http urls. updated to https

AnnotationHubData 1.10.0

MODIFICATIONS

• Moved readMetadataFromCsv back to AnnotationHubData.
• Use AnnotationHubData::makeAnnotationHubMetadata to validate metadata.csv
• readMetadataFromCsv is now internal function

AnnotationHubData 1.8.0

NEW FEATURES

• Instead of using dropbox or ftp to deliver contributed resources to Bioconductor Core, temporary access to Annotation-Contributor user on S3 is utilized.

MODIFICATIONS

• Modified readMetadataFromCsv; make RDataPath mandatory entry and if location_prefix is Bioconductor S3 bucket the Rdatapath must start with the package name

BUG FIXES

• Add garbage collection to fix twobit memory allocation error
• Fix files not deleting do to special characters in file names
• Import dbGetQuery from DBI
• Remove hard coded biocVersion in unit tests

AnnotationHubData 1.6.0

NEW FEATURES

• add makeStandardTxDbsToSqlite() recipe
• add 'ensembl' and 'MySQL' as possible SourceType values
• tidy and export makeStandard*ToAHMs and makeNCBIToOrgDbsToAHMs

MODIFICATIONS

• move currentMetadata
• tidy pushResources interface
• modified parsing of species name and genome in .ensemblMetadataFromUrl()
• modified standard OrgDb recipe
• enhance and clean vignette
• move 'Tags' check from readCsvFromMetadata() to makeAnnotationHubMetadata()
• remove dependency on xml2, curl, httr and probably other wheel reinventions, alter imports and suggests
• specify multiple 'Tags' as colon separated string instead of comma separated; avoids problems with read.csv()
• select data moved to GenomeInfoDbData package
• Added additional documentation instructions for core members to add contributed data to AnnotationHub
• rename files; remove old JSON test file no longer applicable
• pass 'install' argument down through recipe
• General code tidy; remove unused functions and comments; clarify checks

BUG FIXES

• readMetadataFromCsv() fills in DataProvider and Coordinate_1_based if missing
• fix bug introduced in checking 'release' in makeEnsemblTwoBit recipe
• makeAnnotationHubMetadata() now processes all inst/extdata/*.csv files
• fix subset and import bug in makeAnnotationHubMetadata()
• Fix bug in Rdatapath and sourceurl for makeEnsemblFasta.R

AnnotationHubData 1.4.0

NEW FEATURES

• add script to generate user-contributed resources
• makeEnsemblGtfToGRanges() no longer stores data in S3 but downloads and converts to GRanges on the fly
• add EnsemblFastaTwoBitToAHM unit test
• add man page for makeEnsemblTwoBitToAHM and ensemblFastaToTwoBitFile
• add makeAnnotationHubMetadata() helper

MODIFICATIONS

• move GSE62944-related code to ExperimentHub
• move old vignettes to inst/scripts; add 'Introduction to AnnotationHubData' vignette
• remove fasta and towbit files on the fly
• add 'uploadToS3' argument to pushResources() and runRecipes()
• move readMetadataFromCsv() from ExperimentHubData to AnnotationHubData
• add 'fileName' arg to readMetadataFromCsv(); don't warn when 'Tags' are provided
• specify length for args in readMetadataFromCsv()
• makeAnnotationHubMetadata() populates PreparerClass with package name
• add 'fileName' arg to makeAnnotationHubMetadata()

AnnotationHubData 1.2.0

NEW FEATURES

• add makeEnsemblTwoBit()
• add hubError(), hubError<- generics and methods
• create 'HubMetadata' class which 'AnnotationHubMetadata' inherits from

MODIFICATIONS

• export ensemblFastaToTwoBitFile()
• 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)
• 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
• 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.
• update makedbSNPVCF() to look in new clinvar location

BUG FIXES

• fix bugs in makedbSNPVCF() recipe related to genome and tags

AnnotationHubData 1.0.0

BUG FIXES

• ENSEMBL recipes discover gtf files on Windows.

AnnotationHubData 0.0.214

NEW FEATURES

• 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/"
• 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
• The user can refer to http://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/ for VCF file type formats