TASK-7756 - Implement Catalog Operation Services #2605
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Task linked: TASK-7756 Implement Catalog Operation Services |
…s/study/CatalogStudyConfiguration.java Co-authored-by: Copilot <[email protected]> Signed-off-by: Pedro Furió <[email protected]>
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Pull Request Overview
This PR implements catalog operation services by adding support for new catalog and quality control configurations and updating clinical analysis CVDB index handling. Key changes include:
- Introducing CatalogStudyConfiguration in StudyConfiguration to provide catalog‐related defaults.
- Propagating QualityControlStatus throughout Sample, Individual, and Family models.
- Migrating CVDB index fields and updating related DB query parameters and migration tasks.
Reviewed Changes
Copilot reviewed 25 out of 105 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| opencga-core/src/main/java/org/opencb/opencga/core/models/study/configuration/StudyConfiguration.java | Added CatalogStudyConfiguration field and updated constructors/toString. |
| opencga-core/src/main/java/org/opencb/opencga/core/models/study/CatalogStudyConfiguration.java & CatalogServiceConfiguration.java | Introduced configuration defaults for catalog operations. |
| opencga-core/src/main/java/org/opencb/opencga/core/models/common/QualityControlStatus.java | Added new quality control status with updated valid statuses. |
| opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/CvdbIndexStatus.java & CvdbIndex.java | Revised CVDB index types and status handling. |
| opencga-catalog/... | Updated clinical analysis managers, MongoDB adaptors, and DB API keys to accommodate new fields. |
| opencga-app/src/test/java/...MigrationTask7756Test.java & ClinicalMigrationTask7756.java | Added migration support and tests for new catalog and CVDB index configurations. |
| opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/CatalogCommandExecutor.java | Adjusted method visibility for configuration validation. |
Comments suppressed due to low confidence (2)
opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/CatalogCommandExecutor.java:244
- Review whether changing the method visibility from private to protected is intentional and does not unintentionally expose internal configuration logic.
protected void validateConfiguration(AdminCliOptionsParser.CatalogDatabaseCommandOptions catalogOptions) {
opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ClinicalAnalysisMongoDBAdaptor.java:466
- Ensure that the change from using the key INTERNAL_CVDB_INDEX to INTERNAL_CVDB_INDEX_STATUS is backward compatible and that all downstream consumers are updated accordingly.
QueryParams.CONSENT.key(), QueryParams.STATUS.key(), QueryParams.INTERPRETATION.key(), REPORT.key(),
opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManager.java
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| } | ||
| break; | ||
| case CvdbIndexStatus.ERROR: | ||
| if (!Arrays.asList(CvdbIndexStatus.PENDING_REMOVE, CvdbIndexStatus.PENDING_OVERWRITE, CvdbIndexStatus.PENDING_INDEX) |
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What about adding a method "isPending" to the class "CvdbIndexStatus" ?
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And what's the purpose for that? I find it better this way
| } | ||
| break; | ||
| case CvdbIndexStatus.READY: | ||
| if (!Arrays.asList(CvdbIndexStatus.ERROR, CvdbIndexStatus.PENDING_REMOVE, CvdbIndexStatus.PENDING_OVERWRITE) |
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Why can't change to pending_remove or pending_overwrite, but it's ok to change to pending_index? What's the logic of this?
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The state diagram of CvdbIndexStatus is somehow convoluted..
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It's completely the opposite. From READY it's OK to move to ERROR, PENDING_REMOVE or PENDING_OVERWRITE. Nothing else is allowed
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| public class CatalogServiceConfiguration { | ||
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| private boolean active; |
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Please, remember to add @DataField() annotations to any new catalog object with meaningfull descriptions
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