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feat: add diseasesWithParents to allele search results (SCRUM-5829) #1536

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Merged
oblodgett merged 3 commits into from
Mar 26, 2026
Merged

feat: add diseasesWithParents to allele search results (SCRUM-5829) #1536

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8202d00
feat: add diseasesWithParents to allele search results (SCRUM-5829)
oblodgett Mar 26, 2026
6760b9a
fix: correct comment from OpenSearch to ES
oblodgett Mar 26, 2026
00abf83
Update to new curation library
oblodgett Mar 26, 2026
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12 changes: 8 additions & 4 deletions .../main/java/org/alliancegenome/indexer/indexers/curation/AlleleSummaryCurationIndexer.java
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Expand Up @@ -75,12 +75,16 @@ protected void startSingleThread(LinkedBlockingDeque<String> queue) {
continue;
}

indexDocuments(response.getResults());

// Convert to derived documents first (consumes transport-only fields)
List<SequenceSummaryDocument> sequenceDocs = sequenceSummaryConverter.convert(response.getResults());
indexDocuments(sequenceDocs, CurationView.SequenceSummaryDocument.class);

List<AlleleSearchResultDocument> searchDocs = alleleSearchResultConverter.convert(response.getResults());

// Strip fields only needed by derived documents before indexing to ES
response.getResults().forEach(AlleleSummaryDocument::removeTransportFields);

// Index all document types
indexDocuments(response.getResults());
indexDocuments(sequenceDocs, CurationView.SequenceSummaryDocument.class);
indexDocuments(searchDocs);
} catch (Exception e) {
log.error("Error while indexing...", e);
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3 changes: 3 additions & 0 deletions ...src/main/java/org/alliancegenome/core/variant/converters/AlleleSearchResultConverter.java
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Expand Up @@ -102,6 +102,9 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
if (doc.getDiseasesAgrSlim() != null && !doc.getDiseasesAgrSlim().isEmpty()) {
searchDoc.setDiseasesAgrSlim(new ArrayList<>(doc.getDiseasesAgrSlim()));
}
if (doc.getDiseasesWithParents() != null && !doc.getDiseasesWithParents().isEmpty()) {
searchDoc.setDiseasesWithParents(new ArrayList<>(doc.getDiseasesWithParents()));
}

if (doc.getConstructExpressedComponents() != null && !doc.getConstructExpressedComponents().isEmpty()) {
searchDoc.setConstructExpressedComponent(doc.getConstructExpressedComponents());
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1 change: 1 addition & 0 deletions agr_java_core/src/main/java/org/alliancegenome/es/model/AlleleSearchResultDocument.java
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Expand Up @@ -39,6 +39,7 @@ public AlleleSearchResultDocument() {
private List<String> genes;
private List<String> diseases;
private List<String> diseasesAgrSlim;
private List<String> diseasesWithParents;
private List<String> phenotypeStatements;
private String globalId;
private String localId;
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2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -23,7 +23,7 @@
<maven-checkstyle-plugin.version>3.3.1</maven-checkstyle-plugin.version>
<checkstyle.version>10.17.0</checkstyle.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<curation.version>v0.47.9</curation.version>
<curation.version>v0.47.12</curation.version>
</properties>
<dependencyManagement>
<dependencies>
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