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[BI-3033] - Deprecate Genotypic Data Visualization #552

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Merged
jloux-brapi merged 1 commit into from
Sep 2, 2026
Merged

[BI-3033] - Deprecate Genotypic Data Visualization #552

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14 changes: 12 additions & 2 deletions src/main/java/org/breedinginsight/services/geno/impl/GigwaGenotypeServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -281,15 +281,25 @@ public GermplasmGenotype retrieveGenotypeData(UUID programId, UUID germplasmId)
// get samples from gigwa given sample names
List<BrAPISample> gigwaSamples = fetchGigwaSamples(brAPIClient, program, sampleNames);
List<BrAPICallSet> callSets = fetchCallsets(brAPIClient, gigwaSamples);
List<BrAPICall> calls = fetchCalls(brAPIClient, callSets);
List<BrAPIVariant> variants = fetchVariants(brAPIClient, calls);
//Deprecated to avoid running out of memory destabilizing the system
/*
List<BrAPICall> calls = fetchCalls(brAPIClient, callSets)
List<BrAPIVariant> variants = fetchVariants(brAPIClient, calls);

return GermplasmGenotype.builder()
.germplasm(germplasm)
.calls(calls.stream().collect(Collectors.groupingBy(BrAPICall::getCallSetDbId)))
.callSets(callSets.stream().collect(Collectors.toMap(BrAPICallSet::getCallSetDbId, callset -> callset)))
.variants(variants.stream().collect(Collectors.toMap(BrAPIVariant::getVariantDbId, variant -> variant)))
.build();
*/

return GermplasmGenotype.builder()
.germplasm(germplasm)
.calls(null)
.callSets(callSets.stream().collect(Collectors.toMap(BrAPICallSet::getCallSetDbId, callset -> callset)))
.variants(null)
.build();
} else {
return new GermplasmGenotype();
}
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