SCRUM-5952 enable transgenic constructs to be displayed.

[cmpich]

No description provided.

[claude]

Code Review

Changes reviewed: Type replacement (TransgenicAlleleDocument → TransgenicAlleleSummaryDocument) in the API layer, and new severity-based sorting of variant consequences.

Verdict: Looks correct

Type replacement (API layer): This is a good fix. The indexer (TransgenicAlleleCurationIndexer) already indexes documents as TransgenicAlleleSummaryDocument, so the API/service layer should deserialize from Elasticsearch using the same type. The previous code was deserializing into TransgenicAlleleDocument (the curation API source type), which likely caused fields like transgenicAlleleConstructs, hasDiseaseAnnotations, and hasPhenotypeAnnotations to be missing or mismatched in the response.

Note: This changes the REST endpoint return type for GET /api/allele/{id}/constructs, which will change the JSON response shape. This is intentional and likely needed to make the endpoint actually return the indexed data correctly.

Consequence sorting (VariantSummaryConverter): The new sorting logic correctly handles null/empty vepConsequences and null severityOrder values, pushing unknowns to the end with Integer.MAX_VALUE. The consequences list is a mutable ArrayList, so the in-place sort is safe.

No bugs, security issues, or performance concerns found.