TASK-5318 - Implement custom annotator to allow clients private files #2460
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…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
…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
…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
…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
…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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…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
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
…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
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
j-coll
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Jun 25, 2024
j-coll
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Aug 9, 2024
j-coll
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Sep 26, 2024
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Implement a custom extension framework to annotate variants. This requirement implements the COSMIC annotator extension.
TASK-5318