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TASK-5564 - Update data sources for CellBase 6.x - #696

Merged

jtarraga merged 307 commits into

release-6.x.xfrom

TASK-5564

Jan 23, 2026

Merged

TASK-5564 - Update data sources for CellBase 6.x#696
jtarraga merged 307 commits into
release-6.x.xfrom
TASK-5564

This pull request is big! We're only showing the most recent 250 commits

Commits on Apr 18, 2024
Commits on Apr 19, 2024
- lib: update gene downloader (specially for ensembl data), and improve log messages, #TASK-5564
  jtarraga
  committed
  55afe6b
- Merge branch 'TASK-5564' into TASK-5387
  jtarraga
  committed
  d81b68f
Commits on Apr 22, 2024
Commits on Apr 23, 2024
Commits on Apr 24, 2024
Commits on Apr 25, 2024
Commits on Apr 26, 2024
Commits on Apr 29, 2024
Commits on May 7, 2024
Commits on May 8, 2024
- core: fix PGS section in the configuration file, #TASK-5406, #TASK-5387
  jtarraga
  committed
  a25b9c1
- app: add PGS_DATA (polygenic scores) as valid data in the CellBase builder, #TASK-5407, #TASK-5387
  jtarraga
  committed
  df05c91
Commits on May 10, 2024
Commits on May 11, 2024
- lib: include SpliceAI/MMSplice in the configuration file, and create the splice score downloader to create the splice score version files, #TASK-5575, #TASK-5564
  jtarraga
  committed
  57c6f6f
- lib: remove deprecated functions, #TASK-5575, #TASK-5564
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  c131459
Commits on May 15, 2024
Commits on May 16, 2024
- lib: improve gene downloader by taking into account the manually downloaded files and creating the data source version files, #TASK-5575, #TASK-5564
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  committed
  a8a047c
Commits on May 17, 2024
- lib: update gene builder (Ensembl/RefSeq) according to last changes, #TASK-5576, #TASK-5564
  jtarraga
  committed
  100d6f3
- Merge branch 'TASK-5564' into TASK-5387
  jtarraga
  committed
  1852f3e
Commits on May 18, 2024
- lib: refactor PGS builder to solve the RocksDB issue, #TASK-5407, #TASK-5387
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  committed
  910ffd3
Commits on May 20, 2024
- lib: improve PGS builder by speeding-up RocksDB, #TASK-5407, #TASK-5387
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  committed
  3939ac3
Commits on May 27, 2024
Commits on Jun 22, 2024
- Merge branch 'develop' into TASK-5564
  imedina
  committed
  4d965d7
Commits on Jun 23, 2024
- lib: add hpo filter to GeneQuery
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  committed
  fc65d14
Commits on Jul 2, 2024
- Many improvements and fixes:
  imedina
  committed
  84ad97b
- * Add new ensembl_canonical.pl
  imedina
  committed
  aaec065
- Merge branch 'TASK-5564' of https://github.com/opencb/cellbase into TASK-5564
  jtarraga
  committed
  dad180d
- lib: use DockerUtils to execute Perl script from docker image, #TASK-5775, #TASK-5564
  jtarraga
  committed
  694b81d
Commits on Jul 3, 2024
- test: update JUnit tests, #TASK-5564
  jtarraga
  committed
  c8e719a
- cicd: update task.yml to deploy cellbase-builder docker, #TASK-5564
  jtarraga
  committed
  19efdf4
Commits on Jul 4, 2024
- build: create the MiRTarBase parser for .xlsx files, #TASK-5576, #TASK-5564
  jtarraga
  committed
  fcbb680
- Builder improvements and several data cleaning
  imedina
  committed
  10a579a
- Merge branch 'TASK-5564' of github.com:opencb/cellbase into TASK-5564
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  committed
  87d95e8
- Gene downloader fixes
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  committed
  c6bcbdd
Commits on Jul 5, 2024
- Add VariationDownloader
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  0a6a84f
- Add VariationDownloader
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  committed
  3dcad47
Commits on Jul 8, 2024
- app: update Dockerfile for cellbase-builder in order to allow the script ensembl_canonical.pl to create sub-folders, #TASK-5575, #TASK-5564
  jtarraga
  committed
  5eb33ae
- Merge branch 'TASK-5564' of https://github.com/opencb/cellbase into TASK-5564
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  committed
  f44dcc5
Commits on Jul 9, 2024
- lib: add variation to the EtlCommons dataVersionFilenamesMap, #TASK-5575, #TASK-5564
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  committed
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Commits on Jul 22, 2024
- Merge branch 'develop' into TASK-5564
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  committed
  510819c
Commits on Jul 23, 2024
Commits on Jul 24, 2024
Commits on Jul 25, 2024
Commits on Jul 26, 2024
Commits on Jul 29, 2024
- lib: fix protein builder, #TASK-5576, #TASK-5564
  jtarraga
  committed
  039aa81
- lib: fix gene downloader for RefSeq files, #TASK-5575, #TASK-5564
  jtarraga
  committed
  7f77dec
Commits on Jul 31, 2024
Commits on Aug 1, 2024
Commits on Aug 2, 2024
Commits on Aug 5, 2024
Commits on Aug 6, 2024
Commits on Aug 7, 2024
Commits on Aug 8, 2024
Commits on Aug 9, 2024
- 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
  committed
  1f3572c
Commits on Aug 10, 2024
- Merge branch 'develop' into TASK-5564
  jtarraga
  committed
  6056655
- core: add dbSNP in config file (removed after merging), #TASK-5564
  jtarraga
  committed
  a8d6368
Commits on Aug 13, 2024
Commits on Aug 14, 2024
- server: fix meta/health for multiple species, #TASK-6426, #TASK-5564
  jtarraga
  committed
  22770de
Commits on Sep 3, 2024
- server: improve MetaWSServer for multiple species support, #TASK-6426, #TASK-5564
  jtarraga
  committed
  4cffc55
Commits on Sep 12, 2024
- lib: limit WriteBatch for number of items, #TASK-5407, #TASK-5387
  jtarraga
  committed
  2889192
Commits on Oct 1, 2024
- lib: improve PGS builder, #TASK-5407, #TASK-5387
  jtarraga
  committed
  8c8a4ea
- lib: fix sonnar issues, #TASK-5407, #TASK-5387
  jtarraga
  committed
  28a57ba
Commits on Feb 3, 2025
- config: update version
  imedina
  committed
  a49783e
Commits on Feb 18, 2025
- Merge branch 'TASK-5564' of https://github.com/opencb/cellbase into TASK-5564
  jtarraga
  committed
  76d849a
Commits on Feb 20, 2025
- lib: update MiRTarBase indexer to take into account the new format (CSV file), #TASK-5564
  jtarraga
  committed
  2a0eb28
- lib: fix checkstyle and sonnar issues, #TASK-5564
  jtarraga
  committed
  f5edb1f
Commits on Mar 5, 2025
- lib: add _chunkIds in the collection conservation when loading data, #TASK-5564
  jtarraga
  committed
  e65068d
Commits on May 26, 2025
- config: update all data sources
  imedina
  committed
  f45c2fc
Commits on May 28, 2025
- Merge branch 'release-6.x.x' into TASK-5564
  jtarraga
  committed
  32a1323
Commits on Jun 2, 2025
Commits on Jun 4, 2025
Commits on Jun 5, 2025
- lib: add more gnomAD 4.1 constraint scores, #TASK-5576, #TASK-5564
  jtarraga
  committed
  e3f80b5
Commits on Jun 10, 2025
Commits on Jun 25, 2025
Commits on Jul 7, 2025
- Merge branch 'release-6.x.x' into TASK-5564
  jtarraga
  committed
  a5590e9
- Merge branch 'TASK-5564' into TASK-5387
  jtarraga
  committed
  85c1dc6
Commits on Jul 8, 2025
- Merge branch 'TASK-5387' into TASK-5388
  jtarraga
  committed
  f981f22
- pom: upgrade biodata and java-commons-lib dependencies, #TASK-5564
  jtarraga
  committed
  18dddab
Commits on Jul 27, 2025
- lib: add ChimerDB data (gene fusion) to gene annotation, #TASK-7830, #TASK-5564
  jtarraga
  committed
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Commits on Jul 28, 2025
- lib: update according to biodata changes, #TASK-7830, #TASK-5564
  jtarraga
  committed
  7757e70
- lib: update according to biodata changes, #TASK-7745, #TASK-7830, #TASK-5564
  jtarraga
  committed
  12b699a
Commits on Jul 29, 2025
- lib: update variant annotation calculator to take into account imprinted genes and gene fusions, #TASK-5564
  jtarraga
  committed
  1165ee7
Commits on Aug 1, 2025
- pom: add the profile default-config-test-local, #TASK-5564
  jtarraga
  committed
  129051a
Commits on Aug 5, 2025
- lib: download ChimerKB, ChimerPub and ChimerSeq from ChimerDB, #TASK-7830, #TASK-5564
  jtarraga
  committed
  71e1352
- lib: download and build ChimerPub and ChimerSeq data from ChimerDB for gene annotation, #TASK-7830, #TASK-5564
  jtarraga
  committed
  f9c6e7e
Commits on Aug 11, 2025
- lib: update according to biodata changes, #TASK-7745, #TASK-7830, #TASK-5564
  jtarraga
  committed
  b147775
- lib: update according to biodata changes, and add mongodb-indexes, #TASK-7830, #TASK-5564
  jtarraga
  committed
  0d82f3b
Commits on Sep 8, 2025
- lib: download CIViC data, #TASK-7903, #TASK-5564
  jtarraga
  committed
  4858472
Commits on Sep 9, 2025
- lib: implement CivicIndexer, #TASK-7903, #TASK-5564
  jtarraga
  committed
  1b26b90
Commits on Sep 12, 2025
- lib: improve CIViC indexer, #TASK-7903, #TASK-5564
  jtarraga
  committed
  5e6d98c
- lib: add CIViC additional properties in evidence entries, #TASK-7903, #TASK-5564
  jtarraga
  committed
  3dd6361
Commits on Sep 16, 2025
- server: improve the API key check before executing the CellBase endpoints, #TASK-7912, #TASK-5564
  jtarraga
  committed
  ba0f293
- lib: update PharmGKB to ClinPGx, #TASK-7911, #TASK-5564
  jtarraga
  committed
  926b3d2
Commits on Sep 17, 2025
- lib: add rating and evidence_level in additional properties, #TASK-7903, #TASK-5564
  jtarraga
  committed
  b951b3c
- config: fix some version dates
  imedina
  committed
  e78048d
Commits on Sep 18, 2025
- core: update the configuration file, #TASK-5564
  jtarraga
  committed
  7536db4
- Merge branch 'TASK-5564' of https://github.com/opencb/cellbase into TASK-5564
  jtarraga
  committed
  a5961bb
- lib: fix clinical variant builder, #TASK-5564
  jtarraga
  committed
  538212c
- lib: fix GWAS download path, #TASK-5564
  jtarraga
  committed
  7a17ed5
- lib: improve clinical variants download/build paths, #TASK-5564
  jtarraga
  committed
  a8b6de7
Commits on Sep 25, 2025
- lib: improve CIViC indexer, #TASK-7903, #TASK-5564
  jtarraga
  committed
  1e88be5
Commits on Nov 4, 2025
- app: fix CADD loading, #TASK-6142, #TASK-5564
  jtarraga
  committed
  0b33170
- app: fix ClinPGx loader, #TASK-7911, #TASK-5564
  jtarraga
  committed
  26e08f0
Commits on Nov 5, 2025
- app: fix CIViC loader (clinical variants), #TASK-7903, #TASK-5564
  jtarraga
  committed
  0a6c2d8
Commits on Nov 7, 2025
- lib: add indexes for PGS collections, #TASK-5410, TASK-5564
  jtarraga
  committed
  2ccfaa0
Commits on Nov 10, 2025
- lib: reduce batch size for PubMed data when loading, #TASK-6142, #TASK-5564
  jtarraga
  committed
  edf4515
- lib: fix sonnar issues, #TASK-6142, #TASK-5564
  jtarraga
  committed
  7d1f297
Commits on Nov 12, 2025
- Merge branch 'release-6.x.x' into TASK-5564
  jtarraga
  committed
  46de716
- core: fix configuration file for JUnit test, #TASK-5564
  jtarraga
  committed
  604e42e
Commits on Nov 18, 2025
- lib: fix loader (PubMed), #TASK-6142, #TASK-5564
  jtarraga
  committed
  28afbdd
Commits on Nov 20, 2025
Commits on Nov 21, 2025
Commits on Nov 24, 2025
- server: add some admin/endpoints to API key management, TASK-7912, #TASK-5564
  jtarraga
  committed
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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
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  committed
  167dcf1
Commits on Dec 12, 2025
- lib: backwards compatibility, #TASK-5564
  jtarraga
  committed
  31286ce
Commits on Dec 16, 2025
- lib: fix typo, #TASK-5564
  jtarraga
  committed
  0a2d312
- lib: catch exceptions in the different consequence type calculators, #TASK-5564
  jtarraga
  committed
  210a4d7
- lib: fix PGS include, and remove some System.out, #TASK-5564
  jtarraga
  committed
  3873120
Commits on Dec 17, 2025
Commits on Jan 9, 2026
- lib: fix NPE for conservation scores in breakends, #TASK-5564
  jtarraga
  committed
  6df8576
Commits on Jan 19, 2026
- Merge branch 'release-6.x.x' into TASK-5564
  jtarraga
  authored
  93e86fd
Commits on Jan 20, 2026
- client: update Meta endpoint to backward compatibility, #TASK-5564
  jtarraga
  committed
  b7c0adc
- Merge branch 'TASK-5564' of https://github.com/opencb/cellbase into TASK-5564
  juanfeSanahuja
  committed
  1e0e24e
Commits on Jan 21, 2026
- cicd:Added deploy in task yml #TASK-5564
  juanfeSanahuja
  committed
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- cicd:Fix pull request approved #TASK-5564
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- cicd:Fix pull request approved #TASK-5564
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- cicd:Fix pull request approved #TASK-5564
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  committed
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- cicd:Fix pull request approved #TASK-5564
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  committed
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- cicd:Fix pull request approved #TASK-5564
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  committed
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- cicd:Fix pull request approved #TASK-5564
  juanfeSanahuja
  committed
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- cicd:Fix pull request approved #TASK-5564
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  committed
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Commits on Jan 22, 2026
- cicd:Fix pull request approved #TASK-5564
  juanfeSanahuja
  committed
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Commits on Jan 23, 2026
- cicd:Fix pull request approved #TASK-5564
  juanfeSanahuja
  committed
  13dc96b

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