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SCRUM-5829#1558

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oblodgett merged 12 commits intostagefrom
SCRUM-5829
Apr 8, 2026
Merged

SCRUM-5829#1558
oblodgett merged 12 commits intostagefrom
SCRUM-5829

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@cmpich
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@cmpich cmpich commented Apr 7, 2026

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@cmpich cmpich requested a review from a team as a code owner April 7, 2026 13:31
@claude
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claude bot commented Apr 7, 2026

Code Review

Changes look correct. The PR cleanly adds the variantSynonym field (HGVS notation from curated variant genomic locations) across all four required layers:

  1. Model (AlleleSearchResultDocument) — new Set<String> field
  2. Converter (AlleleSearchResultConverter) — collects HGVS values with proper null checks and deduplication via HashSet
  3. ES Mappingtext + keyword (no standardText, appropriate for HGVS notation which shouldn't be stemmed/analyzed)
  4. Search fields — both variantSynonym and variantSynonym.keyword added

No bugs, no performance concerns, no security issues found.

Comment thread agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java Outdated
cmpich and others added 4 commits April 7, 2026 18:12
Add VariantSearchResultConverter to VariantSummaryCurationIndexer so
low throughput variant HGVS names are indexed and searchable.
@oblodgett
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@cmpich I need to get some code in to fix the filters and stuff on the allele-detail page.

oblodgett and others added 2 commits April 7, 2026 16:07
…ch results

- Add crossReferences field (allele ID + gene ID) so alleles are
  discoverable by gene cross reference (e.g. MGI:104735, ZFIN:ZDB-GENE-*)
- Populate phenotypeStatements from AlleleSummaryDocument so alleles
  are searchable by phenotype terms (e.g. "embryonic lethality")

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@oblodgett oblodgett self-requested a review April 8, 2026 16:50
cmpich and others added 2 commits April 8, 2026 19:39
(cherry picked from commit 0aa7b3cc2ebbce62f0289fbd9203c57c807050c5)
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I think thats all the locations.

@oblodgett oblodgett merged commit e90f950 into stage Apr 8, 2026
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@oblodgett oblodgett deleted the SCRUM-5829 branch April 8, 2026 21:14
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2 participants