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SCRUM-5881 add variants as attributes on allele document #1557

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SCRUM-5881 add variants as attributes on allele document #1557

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2 changes: 2 additions & 0 deletions agr_api/src/main/java/org/alliancegenome/api/service/helper/SearchHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -216,6 +216,8 @@ public List<String> getSearchFields() {
add("variants");
add("variants.keyword");
add("variants.standardText");
add("variantHgvs");
add("variantHgvs.keyword");
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@oblodgett oblodgett Apr 7, 2026

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These should be added to the variantSynonyms field and not add an extra field.

add("variantSynonyms");
add("variantSynonyms.keyword");
add("variantSynonyms.standardText");
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7 changes: 7 additions & 0 deletions ...src/main/java/org/alliancegenome/core/variant/converters/AlleleSearchResultConverter.java
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Expand Up @@ -126,11 +126,15 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
}

Set<String> consequences = new HashSet<>();
Set<String> variantHgvs = new HashSet<>();
for (var variant : doc.getVariants()) {
if (variant.getCuratedVariantGenomicLocations() == null) {
continue;
}
for (var location : variant.getCuratedVariantGenomicLocations()) {
if (location.getHgvs() != null) {
variantHgvs.add(location.getHgvs());
}
if (location.getPredictedVariantConsequences() == null) {
continue;
}
Expand All @@ -149,6 +153,9 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
if (!consequences.isEmpty()) {
searchDoc.setMolecularConsequence(consequences);
}
if (!variantHgvs.isEmpty()) {
searchDoc.setVariantHgvs(variantHgvs);
}
}

result.add(searchDoc);
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1 change: 1 addition & 0 deletions agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java
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Expand Up @@ -99,6 +99,7 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {
new FieldBuilder(builder, "symbolText", "text").keyword().standardText().build(); // allele

//new FieldBuilder(builder, "variants", "text").keyword().standardText().build(); // allele
new FieldBuilder(builder, "variantHgvs", "text").keyword().build(); // allele - HGVS notation for searchability
new FieldBuilder(builder, "variantType", "text").keyword().build(); // variant search result
//new FieldBuilder(builder, "variantSynonyms", "text").keyword().standardText().build(); // allele

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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 @@ -27,6 +27,7 @@ public AlleleSearchResultDocument() {
private String alterationType;
private List<String> variantType;
private Set<String> molecularConsequence;
private Set<String> variantHgvs;
private Set<String> constructExpressedComponent;
private Set<String> constructRegulatoryRegion;
private Set<String> constructKnockdownComponent;
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