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TASK-6515 - Port Patch 1.10.6(.1) -> 2.2.1 #702

Merged
merged 15 commits into from
Aug 20, 2024
Merged

TASK-6515 - Port Patch 1.10.6(.1) -> 2.2.1 #702

merged 15 commits into from
Aug 20, 2024

Commits on Apr 30, 2024

  1. Prepare next release 5.8.4-SNAPSHOT

    @juanfeSanahuja
    juanfeSanahuja committed Apr 30, 2024
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Commits on May 30, 2024

  1. cicd: Update action version to test for compatibility with test and r… 

    …elease process #TASK-6264
    @juanfeSanahuja
    juanfeSanahuja committed May 30, 2024
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Commits on Jun 4, 2024

  1. lib: use the same OpenCGA normalization parameters in the "build" for… 

    … clinical variants, #TASK-6347

On branch TASK-6347
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinicalIndexer.java
    @jtarraga
    jtarraga committed Jun 4, 2024
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  2. lib: update configuration file to download last versions of ClinVar a… 

    …nd Gwas, files to download; and update Cosmic version, #TASK-6347

On branch TASK-6347
Changes to be committed:
	modified:   cellbase-core/src/main/resources/configuration.yml
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/CosmicIndexer.java
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/ClinicalDownloadManager.java
    @jtarraga
    jtarraga committed Jun 4, 2024
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  3. core: update the configuration file to download the most recent versi… 

    …on of the GWAS Catalog, #TASK-6347

On branch TASK-6347
Changes to be committed:
	modified:   cellbase-core/src/main/resources/configuration.yml
    @jtarraga
    jtarraga committed Jun 4, 2024
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  4. lib: update ClinVar filename, version and date to the most recent ver… 

    …sion, #TASK-6347

On branch TASK-6347
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java
    @jtarraga
    jtarraga committed Jun 4, 2024
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Commits on Jun 12, 2024

  1. lib: catch exceptions when parsing ClinVar file, #TASK-6347 

    On branch TASK-6347
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinVarIndexer.java
    @jtarraga
    jtarraga committed Jun 12, 2024
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Commits on Jun 18, 2024

  1. lib: add NCBI ID support for dbSNP file (and .tbi) when parsing GWAS … 

    …file; and fix some sonnar issues, #TASK-6347

On branch TASK-6347
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/GwasIndexer.java
    @jtarraga
    jtarraga committed Jun 18, 2024
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Commits on Jun 25, 2024

  1. lib: improve log messages for ClinVar indexer, #TASK-6347 

    On branch TASK-6347
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinVarIndexer.java
    @jtarraga
    jtarraga committed Jun 25, 2024
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Commits on Jun 26, 2024

  1. Merge pull request #693 from opencb/TASK-6347 

    TASK-6347 Fix normalization issue in ClinVar
    @jtarraga
    jtarraga authored Jun 26, 2024
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Commits on Jul 5, 2024

  1. Prepare release 5.8.4

    @juanfeSanahuja
    juanfeSanahuja committed Jul 5, 2024
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Commits on Jul 30, 2024

  1. Prepare Port patch #TASK-6515

    @juanfeSanahuja
    juanfeSanahuja committed Jul 30, 2024
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  2. Merge branch 'release-6.2.x' into TASK-6515

    @juanfeSanahuja
    juanfeSanahuja committed Jul 30, 2024
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Commits on Aug 8, 2024

  1. Merge branch 'release-6.2.x' into TASK-6515

    @juanfeSanahuja
    juanfeSanahuja committed Aug 8, 2024
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Commits on Aug 19, 2024

  1. Merge branch 'release-6.2.x' into TASK-6515

    @pfurio
    pfurio authored Aug 19, 2024
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