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TASK-5318 - Implement custom annotator to allow clients private files #2460
Commits on Mar 20, 2024
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Commits on Mar 21, 2024
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Commits on Apr 4, 2024
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Commits on Jun 4, 2024
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Commits on Jun 5, 2024
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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
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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
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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
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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
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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
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Commits on Jun 6, 2024
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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
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Commits on Jun 11, 2024
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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
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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
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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
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Commits on Jul 22, 2024
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Commits on Sep 20, 2024
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Commits on Sep 26, 2024
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