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SCRUM-5881 add gene synonyms to allele search doc #1554

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Merged
oblodgett merged 4 commits into from
Apr 6, 2026
Merged

SCRUM-5881 add gene synonyms to allele search doc #1554

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9c6e0cd
SCRUM-5881 add gene synonyms to allele search doc
cmpich Apr 6, 2026
98a6960
Merge branch 'stage' into SCRUM-5881
oblodgett Apr 6, 2026
0ea95d0
Removed combining alleles and variants
oblodgett Apr 6, 2026
ef5623d
Bump curation
oblodgett Apr 6, 2026
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10 changes: 2 additions & 8 deletions agr_api/src/main/java/org/alliancegenome/api/service/SearchService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,6 @@
import static org.elasticsearch.index.query.QueryBuilders.multiMatchQuery;
import static org.elasticsearch.index.query.QueryBuilders.queryStringQuery;
import static org.elasticsearch.index.query.QueryBuilders.termQuery;
import static org.elasticsearch.index.query.QueryBuilders.termsQuery;

import java.util.ArrayList;
import java.util.Arrays;
Expand Down Expand Up @@ -242,12 +241,7 @@ public BoolQueryBuilder buildQuery(String queryTerm, String category, Multivalue

// apply filters if a category has been set
if (StringUtils.isNotEmpty(category)) {
if (Category.ALLELE.getName().equals(category)) {
bool.filter(termsQuery("category", Category.ALLELE.getName(), Category.VARIANT.getName()));
} else {
bool.filter(new TermQueryBuilder("category", category));
}

bool.filter(new TermQueryBuilder("category", category));
// expand the map of lists and add each key,value pair as filters
filters.entrySet().stream().forEach(entry -> entry.getValue().stream().forEach(value -> {
if (value.charAt(0) == '-') {
Expand Down Expand Up @@ -338,7 +332,7 @@ public void addRelatedDataLinks(Map<String, Object> result) {
links.add(getRelatedDataLink(Category.GENE.getName(), "diseasesWithParents", nameKey));
links.add(getRelatedDataLink(Category.ALLELE.getName(), "diseasesWithParents", nameKey));
links.add(getRelatedDataLink(Category.MODEL.getName(), "diseasesWithParents", nameKey));
} else if (StringUtils.equals(category, Category.ALLELE.getName()) && StringUtils.equals((String) result.get("alterationType"), "allele")) {
} else if (StringUtils.equals(category, Category.ALLELE.getName())) {
links.add(getRelatedDataLink(Category.DISEASE.getName(), "alleles", nameKey));
links.add(getRelatedDataLink(Category.GENE.getName(), "alleles", nameKey));
links.add(getRelatedDataLink(Category.MODEL.getName(), "alleles", nameKey));
Expand Down
21 changes: 1 addition & 20 deletions agr_api/src/main/java/org/alliancegenome/api/service/helper/SearchHelper.java
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Expand Up @@ -8,7 +8,6 @@
import java.util.Map;
import java.util.Set;

import org.alliancegenome.es.model.search.AggDocCount;
import org.alliancegenome.es.model.search.AggResult;
import org.alliancegenome.es.model.search.Category;
import org.elasticsearch.action.search.SearchResponse;
Expand Down Expand Up @@ -96,6 +95,7 @@ public class SearchHelper {
add("alterationType");
add("variantType");
add("molecularConsequence");
add("diseasesAgrSlim");
add("genes");
}
});
Expand Down Expand Up @@ -338,7 +338,6 @@ public ArrayList<AggResult> formatAggResults(String category, SearchResponse res
Terms aggs = res.getAggregations().get("categories");
Set<String> acceptableKeys = new HashSet<>(categoryFilters.keySet());
AggResult ares = new AggResult("category", aggs, acceptableKeys);
mergeAlleleVariantBuckets(ares);
orderCategoryBuckets(ares);
ret.add(ares);
} else {
Expand All @@ -354,24 +353,6 @@ public ArrayList<AggResult> formatAggResults(String category, SearchResponse res
return ret;
}

/**
* Merge the "allele_search_results" and "variant_search_results" aggregation buckets into a single "allele_search_results" bucket.
*/
private void mergeAlleleVariantBuckets(AggResult aggResult) {
long combinedCount = 0;
List<AggDocCount> toRemove = new ArrayList<>();
for (AggDocCount bucket : aggResult.getValues()) {
if (bucket.getKey().equals(Category.ALLELE.getName()) || bucket.getKey().equals(Category.VARIANT.getName())) {
combinedCount += bucket.getTotal();
toRemove.add(bucket);
}
}
aggResult.getValues().removeAll(toRemove);
if (combinedCount > 0) {
aggResult.getValues().add(new AggDocCount(Category.ALLELE.getName(), combinedCount));
}
}

private void orderCategoryBuckets(AggResult aggResult) {
aggResult.getValues().sort((a, b) -> Long.compare(b.getTotal(), a.getTotal()));
}
Expand Down
4 changes: 4 additions & 0 deletions ...src/main/java/org/alliancegenome/core/variant/converters/AlleleSearchResultConverter.java
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Expand Up @@ -79,6 +79,10 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
searchDoc.setGenes(List.of(geneSymbol));
}

if (doc.getGeneSynonyms() != null && !doc.getGeneSynonyms().isEmpty()) {
searchDoc.setGeneSynonyms(doc.getGeneSynonyms());
}

if (doc.getCrossReference() != null && doc.getCrossReference().getReferencedCurie() != null) {
searchDoc.setModCrossRefCompleteUrl(doc.getCrossReference().getReferencedCurie());
}
Expand Down
1 change: 1 addition & 0 deletions agr_java_core/src/main/java/org/alliancegenome/es/model/AlleleSearchResultDocument.java
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Expand Up @@ -31,6 +31,7 @@ public AlleleSearchResultDocument() {
private Set<String> constructRegulatoryRegion;
private Set<String> constructKnockdownComponent;
private List<String> synonyms;
private Set<String> geneSynonyms;
private List<String> secondaryIds;
private List<String> genes;
private List<String> diseases;
Expand Down
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>v0.47.31</curation.version>
<curation.version>v0.47.32</curation.version>
</properties>
<dependencyManagement>
<dependencies>
Expand Down
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