SCRUM-5829

agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

@@ -105,12 +105,12 @@ public JsonResultResponse<ESDocument> getAllelesPerGene(String id, Integer limit
 		Pagination pagination = new Pagination(page, limit, sortBy, asc);
 		pagination.addFilterOption("symbol", symbol);
 		pagination.addFilterOption("allele.alleleSynonyms.displayText", synonym);
-		pagination.addFilterOption("variants.curatedVariantGenomicLocations.hgvs", variant);
+		pagination.addFilterOption("variantList.curatedVariantGenomicLocations.hgvs", variant);
 		pagination.addFilterOption("alterationType.keyword", category);
-		pagination.addFilterOption("variants.variantType.name.keyword", variantType);
+		pagination.addFilterOption("variantList.variantType.name.keyword", variantType);
 		pagination.addFilterOption("hasDisease", hasDisease);
 		pagination.addFilterOption("hasPhenotype", hasPhenotype);
-		pagination.addFilterOption("variants.curatedVariantGenomicLocations.predictedVariantConsequences.vepConsequences.name.keyword", molecularConsequence);
+		pagination.addFilterOption("variantList.curatedVariantGenomicLocations.predictedVariantConsequences.vepConsequences.name.keyword", molecularConsequence);
 
 		if (pagination.hasErrors()) {
 			RestErrorMessage message = new RestErrorMessage();

agr_api/src/main/java/org/alliancegenome/api/service/AlleleESService.java

@@ -41,13 +41,13 @@ public class AlleleESService extends ESService {
 	}};
 
 	LinkedHashMap<String, SortOrder> variantTypeSortMap = new LinkedHashMap<>() {{
-		put("variants.variantType.name.sort", SortOrder.ASC);
+		put("variantList.variantType.name.sort", SortOrder.ASC);
 		put("symbol.sort", SortOrder.ASC);
 	}};
 
 	LinkedHashMap<String, SortOrder> molecualarConsequenceSortMap = new LinkedHashMap<>() {{
-		put("variants.curatedVariantGenomicLocations.predictedVariantConsequences.vepConsequences.name.sort", SortOrder.ASC);
-		put("variants.variantType.name.sort", SortOrder.ASC);
+		put("variantList.curatedVariantGenomicLocations.predictedVariantConsequences.vepConsequences.name.sort", SortOrder.ASC);
+		put("variantList.variantType.name.sort", SortOrder.ASC);
 		put("symbol.sort", SortOrder.ASC);
 	}};
 
@@ -171,8 +171,8 @@ private Map<String, Object> getAlleleSupplementalData(BoolQueryBuilder unfiltere
 
 		Map<String, String> aggregationFields = new HashMap<>();
 		aggregationFields.put("alterationType.keyword", "alleleCategory");
-		aggregationFields.put("variants.variantType.name.keyword", "variantType");
-		aggregationFields.put("variants.curatedVariantGenomicLocations.predictedVariantConsequences.vepConsequences.name.keyword", "molecularConsequence");
+		aggregationFields.put("variantList.variantType.name.keyword", "variantType");
+		aggregationFields.put("variantList.curatedVariantGenomicLocations.predictedVariantConsequences.vepConsequences.name.keyword", "molecularConsequence");
 
 		Map<String, List<String>> distinctFieldValueMap = getAggregations(unfilteredQuery, aggregationFields, null, false, false);
 		Map<String, Object> supplementalData = new LinkedHashMap<>();

agr_indexer/src/main/java/org/alliancegenome/indexer/TestSynonyms.java

@@ -37,9 +37,9 @@ public static void main(String[] args) throws Exception {
 		System.out.println("=== Step 1: AlleleSummaryDocument from API ===");
 		for (AlleleSummaryDocument doc : response.getResults()) {
 			System.out.println("Allele symbol: " + (doc.getAllele() != null && doc.getAllele().getAlleleSymbol() != null ? doc.getAllele().getAlleleSymbol().getDisplayText() : "null"));
-			System.out.println("Variants: " + (doc.getVariants() != null ? doc.getVariants().size() : "null"));
-			if (doc.getVariants() != null) {
-				for (Variant v : doc.getVariants()) {
+			System.out.println("Variants: " + (doc.getVariantList() != null ? doc.getVariantList().size() : "null"));
+			if (doc.getVariantList() != null) {
+				for (Variant v : doc.getVariantList()) {
 					System.out.println("  Variant type: " + (v.getVariantType() != null ? v.getVariantType().getName() : "null"));
 					if (v.getCuratedVariantGenomicLocations() != null) {
 						for (CuratedVariantGenomicLocationAssociation loc : v.getCuratedVariantGenomicLocations()) {

agr_indexer/src/main/java/org/alliancegenome/indexer/config/IndexerConfig.java

@@ -21,7 +21,6 @@
 import org.alliancegenome.indexer.indexers.curation.ReleaseInfoIndexer;
 import org.alliancegenome.indexer.indexers.curation.SiteMapAccessionCurationIndexer;
 import org.alliancegenome.indexer.indexers.curation.TransgenicAlleleCurationIndexer;
-import org.alliancegenome.indexer.indexers.curation.VariantSummaryCurationIndexer;
 
 public enum IndexerConfig {
 
@@ -39,7 +38,7 @@ public enum IndexerConfig {
 	AffectedGenomicModelAnnotationIndexer("agmAnnotation", AGMAnnotationCurationIndexer.class, 4, 1500, 1500, 8, 1, true),
 	GeneSearchResultCurationIndexer("geneSearchResult", GeneSearchResultCurationIndexer.class, 4, 1000, 1500, 4, 1, true),
 	GeneSummaryIndexer("geneSummary", GeneSummaryCurationIndexer.class, 4, 1500, 1500, 4, 1, true),
-	VariantSummaryIndexer("variantSummary", VariantSummaryCurationIndexer.class, 1, 3000, 1500, 8, 1, true),
+	//VariantSummaryIndexer("variantSummary", VariantSummaryCurationIndexer.class, 1, 3000, 1500, 8, 1, true),
 	GeneGeneticInteractionIndexers("geneGeneticInteraction", GeneGeneticInteractionCurationIndexer.class, 4, 1500, 1500, 2, 1, true),
 	HTPDatasetSearchResultCurationIndexer("htpDatasetSearchResult", HTPDatasetSearchResultCurationIndexer.class, 4, 1500, 1500, 4, 1, true),
 	LiteratureIndexer("literature", LiteratureIndexer.class, 4, 5000, 5000, 1, 1, true),

agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/AlleleToTdfTranslator.java

@@ -64,8 +64,8 @@ public List<AlleleDownloadRow> getAlleleDownloadRowsForGenes(List<ESDocument> an
 
 	private List<Variant> getVariants(AVSParentDocument doc) {
 		return switch (doc) {
-			case AlleleSummaryDocument asd -> asd.getVariants();
-			case VariantSummaryDocument vsd -> vsd.getVariants();
+			case AlleleSummaryDocument asd -> asd.getVariantList();
+			case VariantSummaryDocument vsd -> vsd.getVariantList();
 			default -> null;
 		};
 	}
@@ -252,7 +252,7 @@ public List<VariantDownloadRow> getVariantDownloadRowsForAlleles(List<VariantSum
 
 	private VariantDownloadRow getBaseDownloadVariantRow(VariantSummaryDocument annotation) {
 		VariantDownloadRow row = new VariantDownloadRow();
-		Variant rootVariant = annotation.getVariants().getFirst();
+		Variant rootVariant = annotation.getVariantList().getFirst();
 		CuratedVariantGenomicLocationAssociation variant = rootVariant.getCuratedVariantGenomicLocations().getFirst();
 		if (variant == null) {
 			return row;

agr_java_core/src/main/java/org/alliancegenome/core/variant/converters/AlleleSearchResultConverter.java

@@ -87,6 +87,13 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
 				searchDoc.setModCrossRefCompleteUrl(doc.getCrossReference().getReferencedCurie());
 			}
 
+			Set<String> crossRefs = new HashSet<>();
+			crossRefs.add(allele.getPrimaryExternalId());
+			if (doc.getAlleleOfGene() != null && doc.getAlleleOfGene().getPrimaryExternalId() != null) {
+				crossRefs.add(doc.getAlleleOfGene().getPrimaryExternalId());
+			}
+			searchDoc.setCrossReferences(crossRefs);
+
 			if (allele.getPopularity() != null) {
 				searchDoc.setPopularity(allele.getPopularity());
 			} else {
@@ -103,6 +110,10 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
 				searchDoc.setDiseasesWithParents(new ArrayList<>(doc.getDiseasesWithParents()));
 			}
 
+			if (doc.getPhenotypeStatements() != null && !doc.getPhenotypeStatements().isEmpty()) {
+				searchDoc.setPhenotypeStatements(new ArrayList<>(doc.getPhenotypeStatements()));
+			}
+
 			if (doc.getConstructExpressedComponents() != null && !doc.getConstructExpressedComponents().isEmpty()) {
 				searchDoc.setConstructExpressedComponent(doc.getConstructExpressedComponents());
 			}
@@ -115,8 +126,8 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
 				searchDoc.setConstructKnockdownComponent(doc.getConstructKnockdownComponents());
 			}
 
-			if (CollectionUtils.isNotEmpty(doc.getVariants())) {
-				List<String> variantTypes = doc.getVariants().stream()
+			if (CollectionUtils.isNotEmpty(doc.getVariantList())) {
+				List<String> variantTypes = doc.getVariantList().stream()
 					.filter(v -> v.getVariantType() != null && v.getVariantType().getName() != null)
 					.map(v -> v.getVariantType().getName())
 					.distinct()
@@ -126,11 +137,15 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
 				}
 
 				Set<String> consequences = new HashSet<>();
-				for (var variant : doc.getVariants()) {
+				Set<String> variantHgvs = new HashSet<>();
+				for (var variant : doc.getVariantList()) {
 					if (variant.getCuratedVariantGenomicLocations() == null) {
 						continue;
 					}
 					for (var location : variant.getCuratedVariantGenomicLocations()) {
+						if (location.getHgvs() != null) {
+							variantHgvs.add(location.getHgvs());
+						}
 						if (location.getPredictedVariantConsequences() == null) {
 							continue;
 						}
@@ -149,6 +164,9 @@ public List<AlleleSearchResultDocument> convert(List<AlleleSummaryDocument> alle
 				if (!consequences.isEmpty()) {
 					searchDoc.setMolecularConsequence(consequences);
 				}
+				if (!variantHgvs.isEmpty()) {
+					searchDoc.setVariants(variantHgvs);
+				}
 			}
 
 			result.add(searchDoc);

agr_java_core/src/main/java/org/alliancegenome/core/variant/converters/AlleleSequenceSummaryConverter.java

@@ -17,7 +17,7 @@ public List<SequenceSummaryDocument> convert(List<AlleleSummaryDocument> alleleD
 		List<SequenceSummaryDocument> result = new ArrayList<>();
 
 		for (AlleleSummaryDocument doc : alleleDocs) {
-			if (CollectionUtils.isEmpty(doc.getVariants())) {
+			if (CollectionUtils.isEmpty(doc.getVariantList())) {
 				continue;
 			}
 
@@ -26,7 +26,7 @@ public List<SequenceSummaryDocument> convert(List<AlleleSummaryDocument> alleleD
 				geneIds.add(doc.getAlleleOfGene().getPrimaryExternalId());
 			}
 
-			for (Variant variant : doc.getVariants()) {
+			for (Variant variant : doc.getVariantList()) {
 				if (CollectionUtils.isEmpty(variant.getCuratedVariantGenomicLocations())) {
 					continue;
 				}

agr_java_core/src/main/java/org/alliancegenome/core/variant/converters/SequenceSummaryConverter.java

@@ -21,7 +21,7 @@ public List<SequenceSummaryDocument> convertToSequenceSummary(List<VariantSummar
 		List<SequenceSummaryDocument> result = new ArrayList<>();
 
 		for (VariantSummaryDocument doc : docs) {
-			CuratedVariantGenomicLocationAssociation variantLocation = doc.getVariants().get(0).getCuratedVariantGenomicLocations().get(0);
+			CuratedVariantGenomicLocationAssociation variantLocation = doc.getVariantList().getFirst().getCuratedVariantGenomicLocations().get(0);
 			if (variantLocation == null || variantLocation.getPredictedVariantConsequences() == null) {
 				continue;
 			}
@@ -31,7 +31,7 @@ public List<SequenceSummaryDocument> convertToSequenceSummary(List<VariantSummar
 					SequenceSummaryDocument ssd = new SequenceSummaryDocument();
 					ssd.setAllele(doc.getAllele());
 					ssd.setSymbol(doc.getSymbol());
-					ssd.setVariant(doc.getVariants().get(0));
+					ssd.setVariant(doc.getVariantList().getFirst());
 					ssd.setConsequence(consequence);
 					ssd.setAlterationType("variant");
 					ssd.setAlterationTypeSortOrder(4);

agr_java_core/src/main/java/org/alliancegenome/core/variant/converters/VariantSearchResultConverter.java

@@ -18,7 +18,7 @@ public List<VariantSearchResultDocument> convertToVariantSearchDocument(List<Var
 		List<VariantSearchResultDocument> result = new ArrayList<>();
 
 		for (VariantSummaryDocument doc : variantSummaryDocuments) {
-			CuratedVariantGenomicLocationAssociation variantLocation = doc.getVariants().get(0).getCuratedVariantGenomicLocations().get(0);
+			CuratedVariantGenomicLocationAssociation variantLocation = doc.getVariantList().get(0).getCuratedVariantGenomicLocations().get(0);
 			if (variantLocation == null) {
 				continue;
 			}

agr_java_core/src/main/java/org/alliancegenome/core/variant/converters/VariantSummaryConverter.java

@@ -275,7 +275,7 @@ public List<VariantSummaryDocument> convertContextToDocument(VariantContext ctx,
 			variantWrapper.setTaxon(taxon);
 			variantWrapper.setCuratedVariantGenomicLocations(List.of(cvgla));
 			variantWrapper.setCrossReferences(variant.getCrossReferences());
-			doc.setVariants(List.of(variantWrapper));
+			doc.setVariantList(List.of(variantWrapper));
 			doc.setGeneIds(resultPair.getRight());
 			returnDocuments.add(doc);
 		}

agr_java_core/src/main/java/org/alliancegenome/es/index/site/dao/VariantESDAO.java

@@ -143,7 +143,7 @@ public VariantSummaryDocument getVariant(String id) {
 
 		BoolQueryBuilder bool = boolQuery();
 		bool.filter(new TermQueryBuilder("category", "variant_summary"));
-		bool.must(new TermQueryBuilder("variants.curatedVariantGenomicLocations.hgvs.keyword", id));
+		bool.must(new TermQueryBuilder("variantList.curatedVariantGenomicLocations.hgvs.keyword", id));
 
 		SearchSourceBuilder searchSourceBuilder = new SearchSourceBuilder();
 		searchSourceBuilder.query(bool);
@@ -167,7 +167,7 @@ public VariantSummaryDocument getVariant(String id) {
 		for (SearchHit hit : searchHits) {
 			try {
 				VariantSummaryDocument summaryDoc = mapper.readValue(hit.getSourceAsString(), VariantSummaryDocument.class);
-				if (summaryDoc != null && summaryDoc.getVariants() != null && !summaryDoc.getVariants().isEmpty()) {
+				if (summaryDoc != null && summaryDoc.getVariantList() != null && !summaryDoc.getVariantList().isEmpty()) {
 					return summaryDoc;
 				}
 			} catch (IOException e) {

agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java

@@ -98,9 +98,8 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {
 		new FieldBuilder(builder, "molecularConsequence", "text").keyword().build(); // allele
 		new FieldBuilder(builder, "symbolText", "text").keyword().standardText().build(); // allele
 
-		//new FieldBuilder(builder, "variants", "text").keyword().standardText().build(); // allele
+		new FieldBuilder(builder, "variants", "text").keyword().standardText().build(); // allele - HGVS notation
 		new FieldBuilder(builder, "variantType", "text").keyword().build(); // variant search result
-		//new FieldBuilder(builder, "variantSynonyms", "text").keyword().standardText().build(); // allele
 
 		// Gene Only Fields
 		new FieldBuilder(builder, "biologicalProcessAgrSlim", "text").keyword().build(); // gene
@@ -286,13 +285,13 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {
 		builder.endObject();
 
 		new FieldBuilder(builder, "geneIds", "keyword").build();
-		builder.startObject("variants");
+		builder.startObject("variantList");
 		builder.field("type", "object");
 		builder.field("dynamic", false);
 		builder.endObject();
-		new FieldBuilder(builder, "variants.variantType.name", "text").keyword().sortSmartAlpha().build();
-		new FieldBuilder(builder, "variants.curatedVariantGenomicLocations.predictedVariantConsequences.vepConsequences.name", "text").keyword().sortSmartAlpha().build();
-		new FieldBuilder(builder, "variants.curatedVariantGenomicLocations.hgvs", "text").keyword().sortSmartAlpha().build();
+		new FieldBuilder(builder, "variantList.variantType.name", "text").keyword().sortSmartAlpha().build();
+		new FieldBuilder(builder, "variantList.curatedVariantGenomicLocations.predictedVariantConsequences.vepConsequences.name", "text").keyword().sortSmartAlpha().build();
+		new FieldBuilder(builder, "variantList.curatedVariantGenomicLocations.hgvs", "text").keyword().sortSmartAlpha().build();
 		builder.startObject("crossReference");
 		builder.field("type", "object");
 		builder.field("dynamic", false);

agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/VariantMapping.java

@@ -38,7 +38,7 @@ public void buildMapping() {
 			builder.endObject();
 			builder.endObject();
 
-			builder.startObject("variants");
+			builder.startObject("variantList");
 			builder.field("dynamic", false);
 			builder.startObject("properties");
 			new FieldBuilder(builder, "variantType.name", "text").keyword().sortLowercase().build();

agr_java_core/src/main/java/org/alliancegenome/es/model/AlleleSearchResultDocument.java

@@ -27,9 +27,11 @@ public AlleleSearchResultDocument() {
 	private String alterationType;
 	private List<String> variantType;
 	private Set<String> molecularConsequence;
+	private Set<String> variants;
 	private Set<String> constructExpressedComponent;
 	private Set<String> constructRegulatoryRegion;
 	private Set<String> constructKnockdownComponent;
+	private Set<String> crossReferences;
 	private List<String> synonyms;
 	private Set<String> geneSynonyms;
 	private List<String> secondaryIds;

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>v0.47.33</curation.version>
+		<curation.version>v0.47.36</curation.version>
 	</properties>
 	<dependencyManagement>
 		<dependencies>