v1.0.7

Introduce several updates and bugfixes:

• Modification of the submission process to allow for alternative job clustering applications
• Improved versioning. When a check script discovers a new release, it will update the release tag for the corresponding data source. However, this can cause conflict if the downstream scripts were not triggered/failed, leading to a release tag that is not corresponding to the current version of the data. Thus, check scripts will update a tag called NEW-[DATASOURCE] where [DATASOURCE] is the name of the data source. a Prd script will then take that NEW-[DATASOURCE] tag value to update the [DATASOURCE] tag value which will represent the version of the data in the database. If the NEW-[DATASOURCE] and the [DATASOURCE] tag differs, no new update will be triggered until that version of the data is processed.
• Complete removal of rmj_ scripts: This rewriting simplifies the code base, centralize the batch jobs processing and allow for alternative job clustering applications.
• Separate the installation script in two for easier reusability
• Separate protein sequence alignment and protein domain sequence alignment as two distinct processes, allowing more flexibility for users
• Create a prd_chembl
• Correct issue in singularity definition in which the uninstall of a package would trigger a crash
• Add clustalw in the singularity definition
• Drug names with double quotes or anti slash were triggering a failure. Those cases are now handled
• Removed ALFA files that are not provided by NCBI anymore
• Change paths for ALFA scripts to reflect changes in rmj_scripts
• Update path for GTEX as web location changed
• Allow GTEX to be triggered automatically. (was manual before)

What's Changed

• Create SECURITY.md by @jdesaphy in #3
• Patch config 1 by @jdesaphy in #5
• Patch api 1 by @jdesaphy in #7
• Feature reviewer quickstart by @jdesaphy in #9
• Patch biorj variant by @jdesaphy in #11
• Patch omim by @jdesaphy in #13
• Update BioRelsEXT by @jdesaphy in #19
• Bio rels ext by @jdesaphy in #27
• Patch chembl drugbank by @jdesaphy in #29
• Apply the check to all array_combine calls by @jdesaphy in #30
• Patch license docs by @jdesaphy in #31
• Add images by @jdesaphy in #32
• Improve docs and README by @jdesaphy in #34
• Update dockerfile by @jdesaphy in #35
• Ft job status by @jdesaphy in #37
• Ft job submission by @jdesaphy in #38

Full Changelog: v1.0.6...v1.0.7

v1.0.6

What's Changed

• Patch pubmed restart by @jdesaphy in #23
• Patch uniprot isoform by @jdesaphy in #24
• Patch chembl drug name by @jdesaphy in #25
• Correct issue with isoform id shift by @jdesaphy in #26

List of modifications:

• dl_pubmed was currently restarting from the prd_pubmed last successful date. However, in the initial run, this can lead to redownloading and reprocessing the whole pubmed IF it takes more than 3 days to process it initially. Therefore, we switch from prd_pubmed to db_pubmed_info last successful date to avoid that.
• A typo was introduced in CONFIG_JOB for db_pubmed_info for the conflict jobs.
• Critical hot fix: Isoform sequences were not processed in the system. The grep on the isoform pointer file and the processing of its results was not allowing for isoforms. The fix introduce an array instead of a string, which is then iterated over to process all isoforms
• Hot fix: Drug synonyms containing double quotes were processed during the \COPY in postgres incorrectly. This resulted in the removal of those double quotes, which in some situation led to being considered as duplicated, triggering a failProcess.
• Patch: Removed trailing spaces in synonyms.
• Patch: During the process of ChEMBL variant information, a shift in the isoform identifier was leading to missed mapping against uniprot protein isoforms. This patch correct the shift.

Full Changelog: v1.0.5...v1.0.6

v1.0.5

Modify source sequence starting position and correct typo in public schema

v1.0.4

What's Changed

• Avoid inserting existing records by @jdesaphy in #20
• Update list sources by @jdesaphy in #21
• Patch update container by @jdesaphy in #22

Full Changelog: v1.0.2...v1.0.4

v1.0.3

What's Changed

• Patch omim by @jdesaphy in #12
• Add length to transcript by @jdesaphy in #14
• Feat alfa process by @jdesaphy in #15
• Patch disease conflict by @jdesaphy in #16
• Add missing set up of PROCESS_CONTROL directories by @jdesaphy in #17
• Patch uniprot pname by @jdesaphy in #18
• Update container by @jdesaphy in #22
• Update source list by @jdesaphy in #21

Full Changelog: v1.0.1...v1.0.3

v1.0.2

What's Changed

• Patch omim by @jdesaphy in #12
• Add length to transcript by @jdesaphy in #14
• Feat alfa process by @jdesaphy in #15
• Patch disease conflict by @jdesaphy in #16
• Add missing set up of PROCESS_CONTROL directories by @jdesaphy in #17
• Patch uniprot pname by @jdesaphy in #18

Full Changelog: v1.0.1...v1.0.2

v1.0.1

What's Changed

• Patch biorj variant by @jdesaphy in #10

Full Changelog: v1.0.0...v1.0.1

code_ocean release

vX

disabled db_gene_syn and db_orthologs. change python version

v1.0.0

What's Changed

• Patch config 1 by @jdesaphy in #4
• Patch api 1 by @jdesaphy in #6
• Feature reviewer quickstart by @jdesaphy in #8

Full Changelog: v1.0...v1.0.0