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TASK-5318 - Implement custom annotator to allow clients private files #2460

Merged
merged 17 commits into from
Sep 26, 2024
Merged

TASK-5318 - Implement custom annotator to allow clients private files #2460

merged 17 commits into from
Sep 26, 2024

Commits on Mar 20, 2024

  1. storage: Add VariantAnnotatorExtension scaffolding. #TASK-5318

    @j-coll
    j-coll committed Mar 20, 2024
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Commits on Mar 21, 2024

  1. core: implement the CosmicVariantAnnotatorExtensionTask, #TASK-5902, … 

    …#TASK-5318
    @jtarraga
    jtarraga committed Mar 21, 2024
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Commits on Apr 4, 2024

  1. Merge branch 'develop' into TASK-5318

    @imedina
    imedina committed Apr 4, 2024
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Commits on Jun 4, 2024

  1. Merge branch 'develop' into TASK-5318

    @jtarraga
    jtarraga committed Jun 4, 2024
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Commits on Jun 5, 2024

  1. storage-core: configure normalization and use logger instead of print… 

    …StackTrace, #TASK-5902, #TASK-5318

Changes to be committed:
       modified:   opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/extensions/cosmic/CosmicExtensionTaskCallback.java
    @jtarraga
    jtarraga committed Jun 5, 2024
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  2. storage-core: add options to VariantStorageOptions and update the COS… 

    …MIC annotator extension, #TASK-5902, #TASK-5318

On branch TASK-5318
Changes to be committed:
	modified:   opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageOptions.java
	modified:   opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/extensions/VariantAnnotatorExtensionsFactory.java
	modified:   opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/extensions/cosmic/CosmicVariantAnnotatorExtensionTask.java
    @jtarraga
    jtarraga committed Jun 5, 2024
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  3. test: update COSMIC annotator extension JUnit tests, #TASK-5902, #TAS… 

    …K-5318

On branch TASK-5318
Changes to be committed:
	modified:   opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/extensions/CosmicVariantAnnotatorExtensionTaskTest.java
    @jtarraga
    jtarraga committed Jun 5, 2024
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  4. storage-core: check valid variants in COSMIC annotator extension, #TA… 

    …SK-5902, #TASK-5318

On branch TASK-5318
Changes to be committed:
	modified:   opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/extensions/cosmic/CosmicVariantAnnotatorExtensionTask.java
    @jtarraga
    jtarraga committed Jun 5, 2024
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  5. test: add VariantAnnotationManager JUnit tests to check the COSMIC an… 

    …notator extension, #TASK-5902, #TASK-5318

On branch TASK-5318
Changes to be committed:
	modified:   opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/VariantStorageBaseTest.java
	modified:   opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/VariantAnnotationManagerTest.java
	modified:   opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/extensions/CosmicVariantAnnotatorExtensionTaskTest.java
	new file:   opencga-storage/opencga-storage-core/src/test/resources/variant-test-file-annotator-extension.vcf.gz
    @jtarraga
    jtarraga committed Jun 5, 2024
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Commits on Jun 6, 2024

  1. test: add JUnit tests to check COSMIC file format, missing COSMIC fil… 

    …e, version and assembly; and assembly match, #TASK-5902, #TASK-5318

On branch TASK-5318
Changes to be committed:
	modified:   opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/extensions/cosmic/CosmicVariantAnnotatorExtensionTask.java
	modified:   opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/VariantAnnotationManagerTest.java
	modified:   opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/extensions/CosmicVariantAnnotatorExtensionTaskTest.java
    @jtarraga
    jtarraga committed Jun 6, 2024
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Commits on Jun 11, 2024

  1. test: rename JUnit test, #TASK-5902, #TASK-5318 

    On branch TASK-5318
Changes to be committed:
	modified:   opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/VariantAnnotationManagerTest.java
    @jtarraga
    jtarraga committed Jun 11, 2024
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  2. test: set JUnit test as @category(ShortTests.class), #TASK-5902, #TAS… 

    …K-5318

On branch TASK-5318
Changes to be committed:
	modified:   opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/extensions/CosmicVariantAnnotatorExtensionTaskTest.java
    @jtarraga
    jtarraga committed Jun 11, 2024
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  3. storage-core: fix sonnar issues, #TASK-5902, #TASK-5318 

    On branch TASK-5318
Changes to be committed:
	modified:   opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/extensions/cosmic/CosmicVariantAnnotatorExtensionTask.java
    @jtarraga
    jtarraga committed Jun 11, 2024
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  4. Merge branch 'develop' into TASK-5318

    @jtarraga
    jtarraga committed Jun 11, 2024
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Commits on Jul 22, 2024

  1. Merge branch 'release-3.2.x' into TASK-5318

    @jtarraga
    jtarraga committed Jul 22, 2024
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Commits on Sep 20, 2024

  1. Merge branch 'release-3.x.x' into TASK-5318

    @jtarraga
    jtarraga authored Sep 20, 2024
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Commits on Sep 26, 2024

  1. Merge branch 'release-3.x.x' into TASK-5318

    @jtarraga
    jtarraga authored Sep 26, 2024
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