TASK-7645 - Integrated Clinical Preprocessing, Variant Assessment, and Reporting

[pfurio]

No description provided.

[imedina]

Task linked: TASK-7645 Implement Variant Review and Summaries

[Copilot]

Pull request overview

This PR enhances the clinical variant interpretation models and creators by introducing new filtering capabilities, expanding the clinical variant data model with additional fields, and refactoring the status workflow. The changes support integrated clinical preprocessing, variant assessment, and reporting capabilities.

Key Changes:

• Introduced ClinicalVariantFilter class to capture query parameters and version information for clinical variant filtering
• Enhanced ClinicalVariant model with new fields including modesOfInheritance, images, version, and replaced deprecated filters Map with structured filter object
• Updated MiniPubmed model to rename name field to title and add authors field with backward compatibility through deprecated methods
• Expanded ClinicalVariant.Status enum with new workflow states (UNDER_CONSIDERATION, CANDIDATE, VALIDATION_REQUESTED, VALIDATED) replacing REVIEW_REQUESTED

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
ClinicalVariantFilter.java	New class added to encapsulate variant filter queries and version tracking for OpenCGA and CellBase
ClinicalVariant.java	Updated constructor signatures, added new fields (modesOfInheritance, images, version), deprecated old filter field, and modified Status enum values
MiniPubmed.java	Renamed name field to title with backward compatibility, added authors field, and updated constructors
ClinicalEvidenceReview.java	Added tags and score fields to support enhanced evidence review capabilities
TieringClinicalVariantCreator.java	Updated ClinicalVariant constructor calls to use new signature with ClinicalVariantFilter and additional parameters
TeamClinicalVariantCreator.java	Updated ClinicalVariant constructor calls to match new API signature
DefaultClinicalVariantCreator.java	Updated ClinicalVariant constructor calls to match new API signature
ClinicalVariantCreator.java	Updated ClinicalVariant constructor calls in createSecondaryFindings method

Comments suppressed due to low confidence (1)

biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java:64

• The enum value 'REVIEW_REQUESTED' has been removed and replaced with new values including 'UNDER_CONSIDERATION', 'CANDIDATE', 'VALIDATION_REQUESTED', and 'VALIDATED'. This is a breaking change that will affect any code checking for the REVIEW_REQUESTED status. Ensure that all code using this enum value has been updated to handle the new workflow states appropriately.

    public enum Status {
        NOT_REVIEWED,
        UNDER_CONSIDERATION,
        CANDIDATE,
        REVIEWED,
        VALIDATION_REQUESTED,
        VALIDATED,
        DISCARDED,
        REPORTED,
        ARTIFACT
    }

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[Copilot]

Pull request overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated 9 comments.

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