TASK-5564 - Update data sources for CellBase 6.2#696

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jtarraga wants to merge 436 commits intodevelopfrom

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Commits on Jul 24, 2024

lib: fix minor sonnar issue, #TASK-5575, #TASK-5564
jtarraga
committed
lib: improve protein downloader by checking if data is already downloaded, #TASK-5575, #TASK-5564
jtarraga
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lib: improve variation downloader by checking if data is already downloaded, #TASK-5575, #TASK-5564
jtarraga
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lib: fix variation folder in downloader, #TASK-5575, #TASK-5564
jtarraga
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core: remove DISGENET, #TASK-5575, #TASK-5564
jtarraga
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lib: improve gene downloader, removing DISGENET, fixing sonnar issues, #TASK-5575, #TASK-5564
jtarraga
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lib: fix command line to execute Perl script, #TASK-5575, #TASK-5564
jtarraga
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Commits on Jul 25, 2024

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lib: fix the function to save status and message of the downloaded files; improve summary log and update downloader managers according to these changes, #TASK-5575, #TASK-5564
jtarraga
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Commits on Aug 10, 2024

Commits on Aug 13, 2024

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Commits on Aug 19, 2024

Merge branch 'release-6.2.x' into TASK-6515
pfurio
authored

Commits on Aug 20, 2024

Merge pull request #702 from opencb/TASK-6515
j-coll
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Commits on Sep 3, 2024

server: improve MetaWSServer for multiple species support, #TASK-6426, #TASK-5564
jtarraga
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Commits on Sep 4, 2024

cicd: Upload reference to develop branch in pull-request-approve to test-xetabase-workflow #TASK-6807
juanfeSanahuja
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Commits on Sep 9, 2024

cicd: Fix xetabase branch calculation #TASK-6807
juanfeSanahuja
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Commits on Sep 10, 2024

Commits on Sep 12, 2024

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Commits on Sep 16, 2024

SDLC: Prepare release 2.3.0 of Xetabase #TASK-6879
juanfeSanahuja
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Commits on Sep 17, 2024

Commits on Sep 19, 2024

Merge pull request #708 from opencb/TASK-6879
juanfeSanahuja
authored

Commits on Sep 20, 2024

Merge branch 'release-6.x.x' into TASK-5318
jtarraga
committed

Commits on Sep 26, 2024

Commits on Oct 11, 2024

Merge pull request #712 from opencb/TASK-7038
juanfeSanahuja
authored

Commits on Oct 15, 2024

Commits on Jan 8, 2025

cicd: added if github.event.review.state approved #TASK-7301
juanfeSanahuja
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Commits on Jan 16, 2025

Merge pull request #715 from opencb/TASK-7301
juanfeSanahuja
authored

Commits on Feb 3, 2025

config: update version
imedina
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Commits on Feb 18, 2025

Merge branch 'TASK-5564' of https://github.com/opencb/cellbase into TASK-5564
jtarraga
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Commits on Feb 19, 2025

Commits on Feb 20, 2025

Commits on Mar 5, 2025

lib: add _chunkIds in the collection conservation when loading data, #TASK-5564
jtarraga
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Commits on Mar 10, 2025

lib: remove hardcoded versions from the clinical variant builders, it is taken from the xxxVersion.json file, #TASK-7463
jtarraga
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Commits on Mar 27, 2025

Merge pull request #721 from opencb/TASK-7463
jtarraga
authored

Commits on Apr 8, 2025

Prepare release 5.8.5
juanfeSanahuja
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Commits on May 7, 2025

Commits on May 26, 2025

config: update all data sources
imedina
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Commits on May 28, 2025

Merge branch 'release-6.x.x' into TASK-5564
jtarraga
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Commits on May 29, 2025

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Commits on Jul 27, 2025

lib: add ChimerDB data (gene fusion) to gene annotation, #TASK-7830, #TASK-5564
jtarraga
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Commits on Jul 28, 2025

Commits on Jul 29, 2025

lib: update variant annotation calculator to take into account imprinted genes and gene fusions, #TASK-5564
jtarraga
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Commits on Aug 1, 2025

pom: add the profile default-config-test-local, #TASK-5564
jtarraga
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Commits on Aug 11, 2025

Commits on Aug 14, 2025

Delete Xetabase test #TASK-7883
juanfeSanahuja
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Commits on Sep 3, 2025

Merge pull request #735 from opencb/TASK-7883
juanfeSanahuja
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Commits on Sep 8, 2025

lib: download CIViC data, #TASK-7903, #TASK-5564
jtarraga
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Commits on Sep 9, 2025

lib: implement CivicIndexer, #TASK-7903, #TASK-5564
jtarraga
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Commits on Sep 10, 2025

Commits on Sep 11, 2025

lib: add the include value 'genomicContext', #TASK-7627, #TASK-7549
jtarraga
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Commits on Sep 12, 2025

Commits on Sep 16, 2025

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Commits on Sep 25, 2025

lib: improve CIViC indexer, #TASK-7903, #TASK-5564
jtarraga
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Commits on Oct 22, 2025

pom: Upgrade avro version from 1.9.1 to 1.11.4 #TASK-7809 #TASK-7962
j-coll
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Commits on Oct 30, 2025

cicd: Fix task name workflow #TASK-7549
juanfeSanahuja
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Commits on Oct 31, 2025

Commits on Nov 4, 2025

Commits on Nov 5, 2025

Commits on Nov 6, 2025

Merge branch 'release-6.x.x' into TASK-7809
j-coll
committed

Commits on Nov 12, 2025

Commits on Nov 18, 2025

lib: fix loader (PubMed), #TASK-6142, #TASK-5564
jtarraga
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Commits on Nov 24, 2025

server: add some admin/endpoints to API key management, TASK-7912, #TASK-5564
jtarraga
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Commits on Dec 9, 2025

lib: add DbSnpDownloader, and remove building and loading dbSNP data from the variantion processing, #TASK-5564
jtarraga
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Commits on Dec 12, 2025

lib: backwards compatibility, #TASK-5564
jtarraga
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Commits on Dec 16, 2025

Commits on Dec 17, 2025