SCRUM-5952 enable transgenic constructs to be displayed. (#1564)

Author: cmpich

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

@@ -19,7 +19,7 @@
 import org.alliancegenome.core.exceptions.RestErrorMessage;
 import org.alliancegenome.core.translators.tdf.AlleleToTdfTranslator;
 import org.alliancegenome.curation_api.model.document.es.AlleleSummaryDocument;
-import org.alliancegenome.curation_api.model.document.es.TransgenicAlleleDocument;
+import org.alliancegenome.api.entity.TransgenicAlleleSummaryDocument;
 import org.alliancegenome.curation_api.model.document.es.VariantSummaryDocument;
 import org.alliancegenome.es.model.query.FieldFilter;
 import org.alliancegenome.es.model.query.Pagination;
@@ -67,8 +67,8 @@ public AlleleSummaryDocument getAllele(String id) {
 	}
 
 	@Override
-	public TransgenicAlleleDocument getAlleleConstructs(String alleleId) {
-		JsonResultResponse<TransgenicAlleleDocument> transgenicAlleles = alleleEsService.getTransgenicAlleles(alleleId);
+	public TransgenicAlleleSummaryDocument getAlleleConstructs(String alleleId) {
+		JsonResultResponse<TransgenicAlleleSummaryDocument> transgenicAlleles = alleleEsService.getTransgenicAlleles(alleleId);
 		if (transgenicAlleles == null) {
 			return null;
 		}

agr_api/src/main/java/org/alliancegenome/api/rest/interfaces/AlleleRESTInterface.java

@@ -4,7 +4,7 @@
 import org.alliancegenome.api.entity.AllelePhenotypeAnnotationDocument;
 import org.alliancegenome.cache.repository.helper.JsonResultResponse;
 import org.alliancegenome.curation_api.model.document.es.AlleleSummaryDocument;
-import org.alliancegenome.curation_api.model.document.es.TransgenicAlleleDocument;
+import org.alliancegenome.api.entity.TransgenicAlleleSummaryDocument;
 import org.alliancegenome.curation_api.model.document.es.VariantSummaryDocument;
 import org.alliancegenome.neo4j.view.PublicView;
 import org.apache.commons.lang3.ObjectUtils.Null;
@@ -48,7 +48,7 @@ public interface AlleleRESTInterface {
 	@Operation(description = "Searches for transgenic alleles", summary = "Transgenic Alleles")
 	@APIResponses(value = {@APIResponse(responseCode = "404", description = "Missing transgenic alleles", content = @Content(mediaType = "text/plain")),
 		@APIResponse(responseCode = "200", description = "Search for alleles.", content = @Content(mediaType = "application/json", schema = @Schema(implementation = Null.class)))})
-	TransgenicAlleleDocument getAlleleConstructs(@Parameter(in = ParameterIn.PATH, name = "id", description = "Search for constructs for a given Allele by ID", required = true, schema = @Schema(type = SchemaType.STRING)) @PathParam("id") String id);
+	TransgenicAlleleSummaryDocument getAlleleConstructs(@Parameter(in = ParameterIn.PATH, name = "id", description = "Search for constructs for a given Allele by ID", required = true, schema = @Schema(type = SchemaType.STRING)) @PathParam("id") String id);
 
 	@GET
 	@Path("/{id}/variants")

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

@@ -13,7 +13,7 @@
 import org.alliancegenome.cache.repository.helper.JsonResultResponse;
 import org.alliancegenome.curation_api.model.document.es.AlleleSummaryDocument;
 import org.alliancegenome.curation_api.model.document.es.ESDocument;
-import org.alliancegenome.curation_api.model.document.es.TransgenicAlleleDocument;
+import org.alliancegenome.api.entity.TransgenicAlleleSummaryDocument;
 import org.alliancegenome.curation_api.model.document.es.VariantSummaryDocument;
 import org.alliancegenome.es.model.query.Pagination;
 import org.elasticsearch.action.search.SearchResponse;
@@ -64,23 +64,23 @@ public class AlleleESService extends ESService {
 		put(null, defaultSortMap);
 	}};
 
-	public JsonResultResponse<TransgenicAlleleDocument> getTransgenicAlleles(String alleleId) {
+	public JsonResultResponse<TransgenicAlleleSummaryDocument> getTransgenicAlleles(String alleleId) {
 		BoolQueryBuilder bool = boolQuery();
 		BoolQueryBuilder bool2 = boolQuery();
 		bool.must(bool2);
 		// ToDo: Change this class such that the category is public
-		// TransgenicAlleleDocument.category
+		// TransgenicAlleleSummaryDocument.category
 		bool.filter(new TermQueryBuilder("category", "transgenic_allele_summary"));
 		bool2.should(new MatchQueryBuilder("allele.primaryExternalId.keyword", alleleId));
 
-		JsonResultResponse<TransgenicAlleleDocument> ret = new JsonResultResponse<>();
+		JsonResultResponse<TransgenicAlleleSummaryDocument> ret = new JsonResultResponse<>();
 
 		SearchResponse searchResponse = getSearchResponse(bool, new Pagination(), null, false);
 		ret.setTotal((int) searchResponse.getHits().getTotalHits().value);
-		List<TransgenicAlleleDocument> list = new ArrayList<>();
+		List<TransgenicAlleleSummaryDocument> list = new ArrayList<>();
 		Arrays.stream(searchResponse.getHits().getHits()).forEach(searchHit -> {
 			try {
-				TransgenicAlleleDocument object = mapper.readValue(searchHit.getSourceAsString(), TransgenicAlleleDocument.class);
+				TransgenicAlleleSummaryDocument object = mapper.readValue(searchHit.getSourceAsString(), TransgenicAlleleSummaryDocument.class);
 				list.add(object);
 			} catch (Exception e) {
 				e.printStackTrace();

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

@@ -262,6 +262,15 @@ public List<VariantSummaryDocument> convertContextToDocument(VariantContext ctx,
 			allele.setTaxon(taxon);
 			// If we want to show
 
+			// Sort PVCs by most severe consequence
+			consequences.sort(Comparator.comparingInt(pvc -> {
+				if (pvc.getVepConsequences() == null || pvc.getVepConsequences().isEmpty()) {
+					return Integer.MAX_VALUE;
+				}
+				return pvc.getVepConsequences().stream()
+					.mapToInt(c -> c.getSeverityOrder() != null ? c.getSeverityOrder() : Integer.MAX_VALUE)
+					.min().orElse(Integer.MAX_VALUE);
+			}));
 			cvgla.setPredictedVariantConsequences(consequences);
 			// Create the document for each consequence (full flattening)
 			VariantSummaryDocument doc = new VariantSummaryDocument();