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SCRUM-4937: Run all indexers in parallel and fix allele gene species display#1544

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oblodgett merged 4 commits intostagefrom
SCRUM-4937
Mar 31, 2026
Merged

SCRUM-4937: Run all indexers in parallel and fix allele gene species display#1544
oblodgett merged 4 commits intostagefrom
SCRUM-4937

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@oblodgett
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Summary

  • Run all indexers in parallel: Moved previously sequential indexers (disease annotation, phenotype annotation, orthology, GO search result, allele summary, disease search result, molecular interaction) to the parallel execution pool. Only ReleaseInfoIndexer remains sequential and now runs first before all parallel indexers start.
  • Fix allele gene species display: Use species abbreviation instead of full taxon name in the allele search result genes field (e.g. "Hsa" instead of "Homo sapiens"), with a fallback to taxon name if species is unavailable.
  • Minor cleanup of test output formatting in TestSpeciesOrder.

Test plan

  • Verify indexer runs complete successfully with all indexers in parallel
  • Confirm allele search results show species abbreviation in genes field
  • Check ReleaseInfoIndexer runs and completes before parallel indexers start

@oblodgett oblodgett requested a review from a team as a code owner March 31, 2026 15:49
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claude bot commented Mar 31, 2026

Code Review: SCRUM-4937

The changes look correct. A few observations:

Indexer ordering change (Main.java + IndexerConfig.java): The reordering to run sequential indexers first (ReleaseInfoIndexer) before launching parallel indexers is clean. The executor lifecycle (submit → shutdown → wait) is correctly handled for both phases. Moving the 7 previously-sequential indexers to parallel should work fine since they no longer need to run in isolation per the PR description.

AlleleSearchResultConverter.java: The species abbreviation change has proper null-safety — falls back to taxon.getName() if taxon.getSpecies() is null. No issues here.

One thing to verify: VariantSummaryIndexer is still marked as runInParallel=false (sequential) but the comment above the parallel block says "Run Parallelly". Was this intentionally left sequential, or was it overlooked? It was sequential before this PR too, so not a regression — just worth confirming the intent.

No bugs or issues found. LGTM.

@oblodgett oblodgett merged commit 37553dd into stage Mar 31, 2026
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@oblodgett oblodgett deleted the SCRUM-4937 branch March 31, 2026 17:05
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