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Use Species for allele display names, normalize nameKey field #1540

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Merged
oblodgett merged 6 commits into from
Mar 27, 2026
Merged

Use Species for allele display names, normalize nameKey field #1540

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0fd36d0
Added Species to Allele
oblodgett Mar 27, 2026
73b402a
Fix checkstyle
oblodgett Mar 27, 2026
3342cd9
refactor: rename name_key to nameKey across all references
oblodgett Mar 27, 2026
7a3b9cf
Merge branch 'stage' into add_species
oblodgett Mar 27, 2026
66331e5
Merge branch 'stage' into add_species
oblodgett Mar 27, 2026
da23b82
feat: bump curation dependency to v0.47.15
oblodgett Mar 27, 2026
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5 changes: 1 addition & 4 deletions agr_api/src/main/java/org/alliancegenome/api/service/AutoCompleteService.java
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Expand Up @@ -42,7 +42,6 @@ public BoolQueryBuilder buildBasicQuery(String queryTerm, String category) {
MultiMatchQueryBuilder multi = QueryBuilders.multiMatchQuery(queryTerm);
multi.field("symbol", 5.0F);
multi.field("symbol.keyword", 8.0F);
multi.field("name_key.autocomplete", 3.0F);
multi.field("nameKey.autocomplete", 3.0F);
multi.field("name.keyword", 2.0F);
multi.field("name.autocomplete");
Expand Down Expand Up @@ -77,11 +76,9 @@ public ArrayList<Map<String, Object>> formatResults(SearchResponse res) {
for (SearchHit hit: res.getHits()) {
String category = (String) hit.getSourceAsMap().get("category");

//this comes over from the Python code, use symbol for geneMap,
//seems like maybe it could also use name_key for everyone...
//this comes over from the Python code, use symbol for geneMap
if (StringUtils.equals(category, Category.GENE.getName())) {
hit.getSourceAsMap().put("name", hit.getSourceAsMap().get("symbol"));
hit.getSourceAsMap().put("name_key", hit.getSourceAsMap().get("nameKey"));
}
ret.add(hit.getSourceAsMap());
}
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9 changes: 1 addition & 8 deletions agr_api/src/main/java/org/alliancegenome/api/service/SearchService.java
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Expand Up @@ -153,16 +153,13 @@ public FunctionScoreQueryBuilder.FilterFunctionBuilder[] buildBoostFunctions(Str
functionList.add(rnaBoost());
functionList.add(pseudogeneBoost());

functionList.add(new FunctionScoreQueryBuilder.FilterFunctionBuilder(matchQuery("name_key.keyword", q), ScoreFunctionBuilders.weightFactorFunction(1000F)));
functionList.add(new FunctionScoreQueryBuilder.FilterFunctionBuilder(matchQuery("nameKey.keyword", q), ScoreFunctionBuilders.weightFactorFunction(1000F)));

functionList.add(new FunctionScoreQueryBuilder.FilterFunctionBuilder(matchQuery("primaryKey", q), ScoreFunctionBuilders.weightFactorFunction(1000F)));
functionList.add(new FunctionScoreQueryBuilder.FilterFunctionBuilder(matchQuery("curie", q), ScoreFunctionBuilders.weightFactorFunction(1000F)));

functionList.add(new FunctionScoreQueryBuilder.FilterFunctionBuilder(matchQuery("name_key.keywordAutocomplete", q), ScoreFunctionBuilders.weightFactorFunction(500F)));
functionList.add(new FunctionScoreQueryBuilder.FilterFunctionBuilder(matchQuery("nameKey.keywordAutocomplete", q), ScoreFunctionBuilders.weightFactorFunction(500F)));

functionList.add(new FunctionScoreQueryBuilder.FilterFunctionBuilder(matchQuery("name_key.standardBigrams", q), ScoreFunctionBuilders.weightFactorFunction(500F)));
functionList.add(new FunctionScoreQueryBuilder.FilterFunctionBuilder(matchQuery("nameKey.standardBigrams", q), ScoreFunctionBuilders.weightFactorFunction(500F)));

functionList.add(new FunctionScoreQueryBuilder.FilterFunctionBuilder(matchQuery("species", q), ScoreFunctionBuilders.weightFactorFunction(2F)));
Expand Down Expand Up @@ -325,11 +322,7 @@ public void addRelatedDataLinks(Map<String, Object> result) {
if (result.containsKey("relatedData")) {
return;
}
String nameKey = (String) result.get("name_key");
// Gene documents use "name_key" (snake_case), GO search result documents use "nameKey" (camelCase)
if (nameKey == null) {
nameKey = (String) result.get("nameKey");
}
String nameKey = (String) result.get("nameKey");
// String name = (String) result.get("name");
String category = (String) result.get("category");

Expand Down
8 changes: 1 addition & 7 deletions agr_api/src/main/java/org/alliancegenome/api/service/helper/SearchHelper.java
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Expand Up @@ -185,12 +185,6 @@ public List<String> getSearchFields() {
add("curie");
add("id");
add("localId");
add("name_key");
add("name_key.autocomplete");
add("name_key.htmlSmoosh");
add("name_key.keyword");
add("name_key.standardBigrams");
add("name_key.keywordAutocomplete");
add("nameKey");
add("nameKey.autocomplete");
add("nameKey.htmlSmoosh");
Expand Down Expand Up @@ -273,7 +267,7 @@ public List<String> getSearchFields() {
add("molecularConsequence");
add("molecularFunction");
add("name");
add("name_key");
add("nameKey");
add("nameKey");
add("primaryKey");
add("soTermName");
Expand Down
4 changes: 2 additions & 2 deletions .../src/test/groovy/org/alliancegenome/api/tests/integration/QueryRankIntegrationSpec.groovy
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Expand Up @@ -105,13 +105,13 @@ class QueryRankIntegrationSpec extends Specification {

@Unroll
@Ignore
def "When querying for #query first result name_key should be #nameKey"() {
def "When querying for #query first result nameKey should be #nameKey"() {
when:
def encodedQuery = URLEncoder.encode(query, "UTF-8")
//todo: need to set the base search url in a nicer way
def results = ApiTester.getApiResults("/api/search?limit=50&offset=0&q=$encodedQuery")

def firstResultNameKey = results.first().get("name_key")
def firstResultNameKey = results.first().get("nameKey")

then:
results //should be some results
Expand Down
15 changes: 12 additions & 3 deletions ...src/main/java/org/alliancegenome/core/variant/converters/AlleleSearchResultConverter.java
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Expand Up @@ -2,6 +2,7 @@

import org.alliancegenome.curation_api.model.document.es.AlleleSummaryDocument;
import org.alliancegenome.curation_api.model.entities.Allele;
import org.alliancegenome.curation_api.model.entities.Species;
import org.alliancegenome.curation_api.model.entities.ontology.NCBITaxonTerm;
import org.alliancegenome.curation_api.model.entities.slotAnnotations.NameSlotAnnotation;
import org.alliancegenome.es.model.AlleleSearchResultDocument;
Expand Down Expand Up @@ -39,9 +40,17 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle

NCBITaxonTerm taxon = allele.getTaxon();
if (taxon != null) {
searchDoc.setSpecies(taxon.getName());
if (allele.getAlleleSymbol() != null) {
searchDoc.setNameKey(allele.getAlleleSymbol().getFormatText() + " (" + taxon.getName() + ")");
Species species = taxon.getSpecies();
if (species != null) {
searchDoc.setSpecies(species.getFullName());
if (allele.getAlleleSymbol() != null) {
searchDoc.setNameKey(allele.getAlleleSymbol().getFormatText() + " (" + species.getAbbreviation() + ")");
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}
} else {
searchDoc.setSpecies(taxon.getName());
if (allele.getAlleleSymbol() != null) {
searchDoc.setNameKey(allele.getAlleleSymbol().getFormatText() + " (" + taxon.getName() + ")");
}
}
} else if (allele.getAlleleSymbol() != null) {
searchDoc.setNameKey(allele.getAlleleSymbol().getFormatText());
Expand Down
2 changes: 1 addition & 1 deletion agr_java_core/src/main/java/org/alliancegenome/es/index/site/dao/AutoCompleteDAO.java
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Expand Up @@ -16,7 +16,7 @@
public class AutoCompleteDAO extends ESDAO {

private List<String> responseFields = Arrays.asList(
"name", "symbol", "curie", "primaryKey", "category", "go_type", "name_key", "nameKey"
"name", "symbol", "curie", "primaryKey", "category", "go_type", "nameKey"
);

public SearchResponse performQuery(QueryBuilder query) {
Expand Down
2 changes: 0 additions & 2 deletions ..._core/src/main/java/org/alliancegenome/es/index/site/document/SearchableItemDocument.java
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Expand Up @@ -8,7 +8,6 @@
import org.alliancegenome.es.index.site.doclet.CrossReferenceDoclet;

import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;

import lombok.Getter;
import lombok.Setter;
Expand All @@ -34,7 +33,6 @@ public class SearchableItemDocument extends ESDocument {
String href; //GO terms use this rather than modCrossRefCompleteUrl
String localId;
String name;
@JsonProperty("name_key")
String nameKey;
String nameText;
String modCrossRefCompleteUrl;
Expand Down
3 changes: 1 addition & 2 deletions agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java
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Expand Up @@ -170,8 +170,7 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {

new FieldBuilder(builder, "name", "text").symbol().autocomplete().keyword().keywordAutocomplete().htmlSmoosh().standardBigrams().build(); // allele, gene, model, go, dataset, disease
new FieldBuilder(builder, "nameText", "text").keyword().standardText().build(); // model
new FieldBuilder(builder, "name_key", "text").analyzer("symbols").autocomplete().keyword().keywordAutocomplete().htmlSmoosh().standardBigrams().build(); // allele, gene, model, dataset, disease
new FieldBuilder(builder, "nameKey", "text").analyzer("symbols").autocomplete().keyword().keywordAutocomplete().htmlSmoosh().standardBigrams().build(); // go_search_result
new FieldBuilder(builder, "nameKey", "text").analyzer("symbols").autocomplete().keyword().keywordAutocomplete().htmlSmoosh().standardBigrams().build(); // allele, gene, model, dataset, disease, go_search_result


new FieldBuilder(builder, "subject.alleleSymbol.displayText", "text").keyword().sort().build(); // allele_disease_annotation
Expand Down
2 changes: 1 addition & 1 deletion agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/VariantMapping.java
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Expand Up @@ -15,7 +15,7 @@ public void buildMapping() {
builder.startObject("properties");
new FieldBuilder(builder, "category", "keyword").symbol().autocomplete().keyword().build();
new FieldBuilder(builder, "name", "keyword").build();
new FieldBuilder(builder, "name_key", "keyword").build();
new FieldBuilder(builder, "nameKey", "keyword").build();
new FieldBuilder(builder, "alterationType", "text").keyword().build();
new FieldBuilder(builder, "genes", "text").keyword().build();
new FieldBuilder(builder, "geneIds", "keyword").build();
Expand Down
3 changes: 0 additions & 3 deletions agr_java_core/src/main/java/org/alliancegenome/es/model/AlleleSearchResultDocument.java
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Expand Up @@ -6,8 +6,6 @@
import org.alliancegenome.curation_api.model.document.es.ESDocument;
import org.alliancegenome.es.model.search.RelatedDataLink;

import com.fasterxml.jackson.annotation.JsonProperty;

import lombok.Getter;
import lombok.Setter;

Expand All @@ -23,7 +21,6 @@ public AlleleSearchResultDocument() {
private String symbol;
private String symbolText;
private String name;
@JsonProperty("name_key")
private String nameKey;
private String primaryKey;
private String species;
Expand Down
2 changes: 0 additions & 2 deletions agr_java_core/src/main/java/org/alliancegenome/es/model/VariantSearchResultDocument.java
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Expand Up @@ -2,7 +2,6 @@

import java.util.List;

import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.annotation.JsonView;

import org.alliancegenome.curation_api.model.document.es.ESDocument;
Expand All @@ -22,7 +21,6 @@ public VariantSearchResultDocument() {

private boolean searchable;
private String name;
@JsonProperty("name_key")
private String nameKey;
private String primaryKey;
private String species;
Expand Down
5 changes: 2 additions & 3 deletions agr_java_core/src/main/java/org/alliancegenome/es/model/search/RelatedDataLink.java
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@@ -1,9 +1,8 @@
package org.alliancegenome.es.model.search;

import lombok.Getter;
import lombok.Setter;
import lombok.Data;

@Getter @Setter
@Data
public class RelatedDataLink {

private String category;
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>v0.47.14</curation.version>
<curation.version>v0.47.15</curation.version>
</properties>
<dependencyManagement>
<dependencies>
Expand Down
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