Mergeback release v0.48.2 to alpha

[devopsagr]

Autogenerated through GH-actions.

[claude]

Review: Mergeback release v0.48.2 to alpha

Changes reviewed: AlleleDAO.java, Variant.java

Summary

Three targeted enhancements to allele summary data:

1. Genome assembly added to variant genomic locations — Two new LEFT JOINs (genomeassembly → biologicalentity) to populate GenomeAssembly.primaryExternalId on AssemblyComponent. Both joins are PK lookups with indexed FK (assemblycomponent_genomeassembly_index). Minimal performance impact.

2. HGVS nomenclature added to predicted variant consequences — hgvsCodingNomenclature and hgvsProteinNomenclature selected from the already-joined predictedvariantconsequence table. No new joins needed.

3. Construct ID fallback to modinternalid — COALESCE(r.primaryexternalid, r.modinternalid) ensures constructs lacking a primaryexternalid are still included. Both columns are indexed on reagent.

4. Variant references exposed in AlleleSummaryDocument view — CurationView.AlleleSummaryDocument.class added to @JsonView on Variant.references.

Verification

• Confirmed all referenced columns and tables exist in production schema (genomeassembly, biologicalentity.primaryexternalid, predictedvariantconsequence.hgvscodingnomenclature, predictedvariantconsequence.hgvsproteinnomenclature, reagent.modinternalid)
• Confirmed index coverage on join paths (genomeassembly_pkey, assemblycomponent_genomeassembly_index, biologicalentity PK)
• Verified SELECT column indices: row[26]=genome_assembly, row[27]=hgvs_coding, row[28]=hgvs_protein — all correctly mapped in the result processing code

LGTM — no correctness, performance, or security concerns.