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SCRUM-5953 Split allele_variant into separate allele and variant categories #1546

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Merged
oblodgett merged 1 commit into from
Apr 1, 2026
Merged

SCRUM-5953 Split allele_variant into separate allele and variant categories #1546

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13 changes: 7 additions & 6 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 @@ -242,8 +242,8 @@ public BoolQueryBuilder buildQuery(String queryTerm, String category, Multivalue

// apply filters if a category has been set
if (StringUtils.isNotEmpty(category)) {
if (Category.ALLELE_VARIANT.getName().equals(category)) {
bool.filter(termsQuery("category", Category.ALLELE_VARIANT.getName(), Category.VARIANT.getName()));
if (Category.ALLELE.getName().equals(category)) {
bool.filter(termsQuery("category", Category.ALLELE.getName(), Category.VARIANT.getName()));
} else {
bool.filter(new TermQueryBuilder("category", category));
}
Expand Down Expand Up @@ -330,20 +330,21 @@ public void addRelatedDataLinks(Map<String, Object> result) {

if (StringUtils.equals(category, Category.GENE.getName())) {
links.add(getRelatedDataLink(Category.DISEASE.getName(), "genes", nameKey));
links.add(getRelatedDataLink(Category.ALLELE_VARIANT.getName(), "genes", nameKey));
links.add(getRelatedDataLink(Category.ALLELE.getName(), "genes", nameKey));
links.add(getRelatedDataLink(Category.VARIANT.getName(), "genes", nameKey));
links.add(getRelatedDataLink(Category.GO.getName(), "genes", nameKey));
links.add(getRelatedDataLink(Category.MODEL.getName(), "genes", nameKey));
} else if (StringUtils.equals(category, Category.DISEASE.getName())) {
links.add(getRelatedDataLink(Category.GENE.getName(), "diseasesWithParents", nameKey));
links.add(getRelatedDataLink(Category.ALLELE_VARIANT.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_VARIANT.getName()) && StringUtils.equals((String) result.get("alterationType"), "allele")) {
} else if (StringUtils.equals(category, Category.ALLELE.getName()) && StringUtils.equals((String) result.get("alterationType"), "allele")) {
links.add(getRelatedDataLink(Category.DISEASE.getName(), "alleles", nameKey));
links.add(getRelatedDataLink(Category.GENE.getName(), "alleles", nameKey));
links.add(getRelatedDataLink(Category.MODEL.getName(), "alleles", nameKey));
} else if (StringUtils.equals(category, Category.MODEL.getName())) {
links.add(getRelatedDataLink(Category.GENE.getName(), "models", nameKey));
links.add(getRelatedDataLink(Category.ALLELE_VARIANT.getName(), "models", nameKey));
links.add(getRelatedDataLink(Category.ALLELE.getName(), "models", nameKey));
links.add(getRelatedDataLink(Category.DISEASE.getName(), "models", nameKey));
} else if (StringUtils.equals(category, Category.GO.getName())) {
String goType = (String) result.get("branch");
Expand Down
28 changes: 18 additions & 10 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
@@ -1,8 +1,13 @@
package org.alliancegenome.api.service.helper;

import jakarta.ws.rs.core.UriInfo;
import lombok.Getter;
import lombok.extern.slf4j.Slf4j;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
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;
Expand All @@ -17,7 +22,9 @@
import org.elasticsearch.search.aggregations.bucket.terms.TermsAggregationBuilder;
import org.elasticsearch.search.fetch.subphase.highlight.HighlightBuilder;

import java.util.*;
import jakarta.ws.rs.core.UriInfo;
import lombok.Getter;
import lombok.extern.slf4j.Slf4j;

@Slf4j
public class SearchHelper {
Expand Down Expand Up @@ -62,7 +69,7 @@ public class SearchHelper {
add("associatedSpecies");
}
});
put(Category.ALLELE_VARIANT.getName(), new ArrayList<>() {
put(Category.ALLELE.getName(), new ArrayList<>() {
{
add("species");
add("alterationType");
Expand Down Expand Up @@ -348,30 +355,31 @@ public ArrayList<AggResult> formatAggResults(String category, SearchResponse res
}

/**
* Merge the "allele_variant_search_results" and "variant_search_results" aggregation buckets into a single "allele_variant_search_results" bucket.
* 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_VARIANT.getName()) || bucket.getKey().equals(Category.VARIANT.getName())) {
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_VARIANT.getName(), combinedCount));
aggResult.getValues().add(new AggDocCount(Category.ALLELE.getName(), combinedCount));
}
}

private static final List<String> CATEGORY_ORDER = List.of(
Category.ALLELE_VARIANT.getName(),
Category.ALLELE.getName(),
Category.GENE.getName(),
Category.GO.getName(),
Category.DISEASE.getName(),
Category.MODEL.getName(),
Category.DATASET.getName()
Category.DATASET.getName(),
Category.VARIANT.getName()
);

/**
Expand Down
28 changes: 3 additions & 25 deletions ...main/java/org/alliancegenome/indexer/indexers/curation/VariantSummaryCurationIndexer.java
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Original file line number Diff line number Diff line change
@@ -1,8 +1,6 @@
package org.alliancegenome.indexer.indexers.curation;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.concurrent.LinkedBlockingDeque;

import org.alliancegenome.core.config.ConfigHelper;
Expand All @@ -14,7 +12,6 @@
import org.alliancegenome.exceptional.client.ExceptionCatcher;
import org.alliancegenome.indexer.config.IndexerConfig;
import org.alliancegenome.indexer.indexers.Indexer;
import org.apache.commons.collections4.CollectionUtils;

import com.fasterxml.jackson.databind.ObjectMapper;

Expand Down Expand Up @@ -67,29 +64,10 @@ protected void startSingleThread(LinkedBlockingDeque<String> queue) {
}

String page = queue.takeFirst();
// log.info(queue.size() + " pages to process " +
// Thread.currentThread().getName() + " starting page: " + page);

SearchResponse<VariantSummaryDocument> response = variantApi.findDocuments(Integer.valueOf(page), indexerConfig.getBufferSize(), params);

// log.info("Search Response: " + response);
List<VariantSummaryDocument> results = response.getResults();
if (response == null || CollectionUtils.isEmpty(results)) {
return;
}

List<VariantSummaryDocument> list = new ArrayList<>();
for (VariantSummaryDocument document : results) {
if (document == null) {
continue;
}
document.setAlterationType("variant");
document.setAlterationTypeSortOrder(4);
document.setHasPhenotype(false);
document.setHasDisease(false);
list.add(document);
}

indexDocuments(list);

indexDocuments(response.getResults());
} catch (Exception e) {
log.error("Error while indexing...", e);
ExceptionCatcher.report(e);
Expand Down
13 changes: 9 additions & 4 deletions ...rc/main/java/org/alliancegenome/core/variant/converters/VariantSearchResultConverter.java
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Expand Up @@ -48,13 +48,18 @@ public List<VariantSearchResultDocument> convertToVariantSearchDocument(List<Var
.map(TranscriptGeneAssociation::getTranscriptGeneAssociationObject)
.filter(Objects::nonNull)
.map(gene -> {
String name = null;
if (gene.getGeneSymbol() != null && gene.getGeneSymbol().getDisplayText() != null) {
return gene.getGeneSymbol().getDisplayText();
name = gene.getGeneSymbol().getDisplayText();
} else if (gene.getPrimaryExternalId() != null) {
name = gene.getPrimaryExternalId();
} else {
name = gene.getCurie();
}
if (gene.getPrimaryExternalId() != null) {
return gene.getPrimaryExternalId();
if (name != null && gene.getTaxon() != null && gene.getTaxon().getSpecies() != null) {
name = name + " (" + gene.getTaxon().getSpecies().getAbbreviation() + ")";
}
return gene.getCurie();
return name;
})
.filter(Objects::nonNull)
.distinct()
Expand Down
5 changes: 5 additions & 0 deletions ...ore/src/main/java/org/alliancegenome/core/variant/converters/VariantSummaryConverter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
import org.alliancegenome.curation_api.model.entities.Gene;
import org.alliancegenome.curation_api.model.entities.GenomeAssembly;
import org.alliancegenome.curation_api.model.entities.PredictedVariantConsequence;
import org.alliancegenome.curation_api.model.entities.Species;
import org.alliancegenome.curation_api.model.entities.Transcript;
import org.alliancegenome.curation_api.model.entities.Variant;
import org.alliancegenome.curation_api.model.entities.VocabularyTerm;
Expand Down Expand Up @@ -106,11 +107,15 @@ public List<VariantSummaryDocument> convertContextToDocument(VariantContext ctx,

List<VariantSummaryDocument> returnDocuments = new ArrayList<>();

// TODO remove speciesType altogether and use the correct Species class coming from curation
// Initialize taxon if not already done
if (taxon == null) {
taxon = new NCBITaxonTerm();
taxon.setName(speciesType.getName());
taxon.setCurie(speciesType.getTaxonID());
Species species = new Species();
species.setAbbreviation(speciesType.getAbbreviation());
taxon.setSpecies(species);
}

// Create variant type
Expand Down
3 changes: 1 addition & 2 deletions agr_java_core/src/main/java/org/alliancegenome/es/model/AlleleSearchResultDocument.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@
import java.util.Set;

import org.alliancegenome.curation_api.model.document.es.ESDocument;
import org.alliancegenome.es.model.search.RelatedDataLink;

import lombok.Getter;
import lombok.Setter;
Expand All @@ -14,7 +13,7 @@
public class AlleleSearchResultDocument extends ESDocument {

public AlleleSearchResultDocument() {
category = "allele_variant_search_result";
category = "allele_search_result";
}

private boolean searchable;
Expand Down
2 changes: 1 addition & 1 deletion agr_java_core/src/main/java/org/alliancegenome/es/model/search/Category.java
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Expand Up @@ -3,7 +3,7 @@
public enum Category {

ALLELE_SUMMARY("allele_summary", false),
ALLELE_VARIANT("allele_variant_search_result", true),
ALLELE("allele_search_result", true),
VARIANT("variant_search_result", true),
SEQUENCE_SUMMARY("sequence_summary", false),
DISEASE("disease_search_result", true),
Expand Down
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