Merge pull request #1540 from alliance-genome/add_species

oblodgett · web-flow · commit e0b417d12a20 · 2026-03-27T13:13:43.000-04:00
Use Species for allele display names, normalize nameKey field
diff --git a/agr_api/src/main/java/org/alliancegenome/api/service/AutoCompleteService.java b/agr_api/src/main/java/org/alliancegenome/api/service/AutoCompleteService.java
@@ -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");
@@ -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());
 		}
diff --git a/agr_api/src/main/java/org/alliancegenome/api/service/SearchService.java b/agr_api/src/main/java/org/alliancegenome/api/service/SearchService.java
@@ -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)));
@@ -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");
 
diff --git a/agr_api/src/main/java/org/alliancegenome/api/service/helper/SearchHelper.java b/agr_api/src/main/java/org/alliancegenome/api/service/helper/SearchHelper.java
@@ -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");
@@ -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");
diff --git a/agr_api/src/test/groovy/org/alliancegenome/api/tests/integration/QueryRankIntegrationSpec.groovy b/agr_api/src/test/groovy/org/alliancegenome/api/tests/integration/QueryRankIntegrationSpec.groovy
@@ -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
diff --git a/agr_java_core/src/main/java/org/alliancegenome/core/variant/converters/AlleleSearchResultConverter.java b/agr_java_core/src/main/java/org/alliancegenome/core/variant/converters/AlleleSearchResultConverter.java
@@ -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;
@@ -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() + ")");
+					}
+				} 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());
diff --git a/agr_java_core/src/main/java/org/alliancegenome/es/index/site/dao/AutoCompleteDAO.java b/agr_java_core/src/main/java/org/alliancegenome/es/index/site/dao/AutoCompleteDAO.java
@@ -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) {
diff --git a/agr_java_core/src/main/java/org/alliancegenome/es/index/site/document/SearchableItemDocument.java b/agr_java_core/src/main/java/org/alliancegenome/es/index/site/document/SearchableItemDocument.java
@@ -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;
@@ -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;
diff --git a/agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java b/agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java
@@ -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
diff --git a/agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/VariantMapping.java b/agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/VariantMapping.java
@@ -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();
diff --git a/agr_java_core/src/main/java/org/alliancegenome/es/model/AlleleSearchResultDocument.java b/agr_java_core/src/main/java/org/alliancegenome/es/model/AlleleSearchResultDocument.java
@@ -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;
 
@@ -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;
diff --git a/agr_java_core/src/main/java/org/alliancegenome/es/model/VariantSearchResultDocument.java b/agr_java_core/src/main/java/org/alliancegenome/es/model/VariantSearchResultDocument.java
@@ -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;
@@ -22,7 +21,6 @@ public VariantSearchResultDocument() {
 
 	private boolean searchable;
 	private String name;
-	@JsonProperty("name_key")
 	private String nameKey;
 	private String primaryKey;
 	private String species;
diff --git a/agr_java_core/src/main/java/org/alliancegenome/es/model/search/RelatedDataLink.java b/agr_java_core/src/main/java/org/alliancegenome/es/model/search/RelatedDataLink.java
@@ -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;
diff --git a/pom.xml b/pom.xml
@@ -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>
