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SCRUM-5829 generate variant summary docs for alleles #1560

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Merged
cmpich merged 2 commits into from
Apr 9, 2026
Merged

SCRUM-5829 generate variant summary docs for alleles #1560

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34604ee
SCRUM-5829 generate variant summary docs for alleles
cmpich Apr 9, 2026
32d7136
SCRUM-5829 add AlleleToVariantSummaryConverter for LTP variants
cmpich Apr 9, 2026
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5 changes: 5 additions & 0 deletions .../main/java/org/alliancegenome/indexer/indexers/curation/AlleleSummaryCurationIndexer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,11 @@
import org.alliancegenome.core.config.ConfigHelper;
import org.alliancegenome.core.variant.converters.AlleleSearchResultConverter;
import org.alliancegenome.core.variant.converters.AlleleSequenceSummaryConverter;
import org.alliancegenome.core.variant.converters.AlleleToVariantSummaryConverter;
import org.alliancegenome.curation_api.interfaces.document.AlleleDocumentInterface;
import org.alliancegenome.curation_api.model.document.es.AlleleSummaryDocument;
import org.alliancegenome.curation_api.model.document.es.SequenceSummaryDocument;
import org.alliancegenome.curation_api.model.document.es.VariantSummaryDocument;
import org.alliancegenome.es.model.AlleleSearchResultDocument;
import org.alliancegenome.curation_api.response.SearchResponse;
import org.alliancegenome.curation_api.view.CurationView;
Expand All @@ -30,6 +32,7 @@ public class AlleleSummaryCurationIndexer extends Indexer {
private final AlleleDocumentInterface alleleApi = RestProxyFactory.createProxy(AlleleDocumentInterface.class, ConfigHelper.getCurationApiUrl(), RestConfig.config);
private final AlleleSequenceSummaryConverter sequenceSummaryConverter = new AlleleSequenceSummaryConverter();
private final AlleleSearchResultConverter alleleSearchResultConverter = new AlleleSearchResultConverter();
private final AlleleToVariantSummaryConverter variantSummaryConverter = new AlleleToVariantSummaryConverter();

private List<List<Long>> idBatches;

Expand Down Expand Up @@ -79,6 +82,7 @@ protected void startSingleThread(LinkedBlockingDeque<String> queue) {
// Convert to derived documents first (consumes transport-only fields)
List<SequenceSummaryDocument> sequenceDocs = sequenceSummaryConverter.convert(response.getResults());
List<AlleleSearchResultDocument> searchDocs = alleleSearchResultConverter.convert(response.getResults());
List<VariantSummaryDocument> variantDocs = variantSummaryConverter.convert(response.getResults());
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cmpich marked this conversation as resolved.

// Strip fields only needed by derived documents before indexing to ES
response.getResults().forEach(AlleleSummaryDocument::removeTransportFields);
Expand All @@ -87,6 +91,7 @@ protected void startSingleThread(LinkedBlockingDeque<String> queue) {
indexDocuments(response.getResults());
indexDocuments(sequenceDocs, CurationView.SequenceSummaryDocument.class);
indexDocuments(searchDocs);
indexDocuments(variantDocs);
} catch (Exception e) {
log.error("Error while indexing...", e);
ExceptionCatcher.report(e);
Expand Down
49 changes: 49 additions & 0 deletions ...main/java/org/alliancegenome/core/variant/converters/AlleleToVariantSummaryConverter.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,49 @@
package org.alliancegenome.core.variant.converters;

import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;

import org.alliancegenome.curation_api.model.document.es.AlleleSummaryDocument;
import org.alliancegenome.curation_api.model.document.es.VariantSummaryDocument;
import org.alliancegenome.curation_api.model.entities.Variant;
import org.apache.commons.collections4.CollectionUtils;

/**
* Converts AlleleSummaryDocument objects into VariantSummaryDocument objects
* for LTP (Low Throughput) variants that come through the curation API allele endpoint.
* Produces one variant_summary document per allele x variant combination.
*/
public class AlleleToVariantSummaryConverter {

public List<VariantSummaryDocument> convert(List<AlleleSummaryDocument> alleleDocs) {
List<VariantSummaryDocument> result = new ArrayList<>();

for (AlleleSummaryDocument doc : alleleDocs) {
if (CollectionUtils.isEmpty(doc.getVariantList())) {
continue;
}

for (Variant variant : doc.getVariantList()) {
if (CollectionUtils.isEmpty(variant.getCuratedVariantGenomicLocations())) {
continue;
}

VariantSummaryDocument vsd = new VariantSummaryDocument();
vsd.setAllele(doc.getAllele());
vsd.setSymbol(doc.getSymbol());
vsd.setVariantList(List.of(variant));
vsd.setHasPhenotype(doc.getHasPhenotype() != null && doc.getHasPhenotype());
vsd.setHasDisease(doc.getHasDisease() != null && doc.getHasDisease());

if (doc.getGeneIds() != null) {
vsd.setGeneIds(new HashSet<>(doc.getGeneIds()));
}

result.add(vsd);
}
}

return result;
}
}
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