SCRUM-4066

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

@@ -12,6 +12,7 @@
 import org.alliancegenome.api.entity.GeneGeneticInteractionDocument;
 import org.alliancegenome.api.entity.GeneMolecularInteractionDocument;
 import org.alliancegenome.api.entity.GeneToGeneParalogyDocument;
+import org.alliancegenome.api.entity.GeneToGeneOrthologyDocument;
 import org.alliancegenome.api.rest.interfaces.GeneRESTInterface;
 import org.alliancegenome.api.service.*;
 import org.alliancegenome.api.service.helper.APIServiceHelper;
@@ -56,6 +57,9 @@ public class GeneController implements GeneRESTInterface {
 	@Inject
 	ExpressionCacheRepository expressionCacheRepository;
 
+	@Inject
+	OrthologyESService orthologyESService;
+
 	@Inject
 	DiseaseService diseaseService;
 
@@ -628,7 +632,7 @@ private JsonResultResponse<DiseaseAnnotation> getEmpiricalDiseaseAnnotation(Stri
 	}
 
 	@Override
-	public JsonResultResponse<HomologView> getGeneOrthology(String id,
+	public JsonResultResponse<GeneToGeneOrthologyDocument> getGeneOrthology(String id,
 															List<String> geneIDs,
 															String geneLister,
 															String stringencyFilter,
@@ -652,7 +656,7 @@ public JsonResultResponse<HomologView> getGeneOrthology(String id,
 		pagination.addFieldFilter(FieldFilter.STRINGENCY, stringencyFilter);
 		pagination.addFieldFilter(FieldFilter.ORTHOLOGY_METHOD, method);
 		pagination.addFieldFilter(FieldFilter.ORTHOLOGY_TAXON, taxonID);
-		final JsonResultResponse<HomologView> response = orthologyCacheService.getOrthologyMultiGeneJson(geneList, pagination);
+		final JsonResultResponse<GeneToGeneOrthologyDocument> response = orthologyESService.getOrthologyList(id, pagination);
 		response.setHttpServletRequest(null);
 		return response;
 	}

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

@@ -79,12 +79,6 @@ public JsonResultResponse<HomologView> getMultiSpeciesOrthology(List<String> tax
 		return response;
 	}
 
-	@Override
-	public JsonResultResponse<HomologView> getMultiGeneOrthology(List<String> geneIDs, String geneList, String stringencyFilter, String method, Integer rows, Integer page) {
-		// controller.setRequest(request);
-		return controller.getGeneOrthology(null, geneIDs, geneList, stringencyFilter, null, method, rows, page);
-	}
-
 	@Override
 	public JsonResultResponse<OrthoAlgorithm> getAllMethodsCalculations() {
 		LocalDateTime startDate = LocalDateTime.now();

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

@@ -10,6 +10,7 @@
 import org.alliancegenome.api.entity.GeneMolecularInteractionDocument;
 import org.alliancegenome.api.entity.GeneToGeneParalogyDocument;
 import org.alliancegenome.api.entity.GenePhenotypeAnnotationDocument;
+import org.alliancegenome.api.entity.GeneToGeneOrthologyDocument;
 import org.alliancegenome.cache.repository.helper.JsonResultResponse;
 import org.alliancegenome.neo4j.entity.DiseaseAnnotation;
 import org.alliancegenome.neo4j.entity.DiseaseSummary;
@@ -406,10 +407,9 @@ JsonResultResponse<PrimaryAnnotatedEntity> getPrimaryAnnotatedEntityForModel(
 
 	@GET
 	@Path("/{id}/orthologs")
-	@JsonView(value = {View.Homology.class})
-	@Operation(summary = "Download homology records.")
+	@Operation(summary = "Get orthology records.")
 	@APIResponses(value = { @APIResponse(responseCode = "200", content = @Content(mediaType = "application/json", schema = @Schema(implementation = Null.class))) })
-	JsonResultResponse<HomologView> getGeneOrthology(
+	JsonResultResponse<GeneToGeneOrthologyDocument> getGeneOrthology(
 		@Parameter(in = ParameterIn.PATH, name = "id", description = "Source Gene ID: the gene for which you are searching homologous gene, e.g. 'MGI:109583'", required = true, schema = @Schema(type = SchemaType.STRING))
 		@PathParam("id") String id,
 		@Parameter(in = ParameterIn.QUERY, name = "geneId", description = "List of additional source gene IDs for which homology is retrieved.", schema = @Schema(type = SchemaType.STRING))

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

@@ -69,19 +69,6 @@ JsonResultResponse<HomologView> getSingleSpeciesOrthology(
 	JsonResultResponse<HomologView> getMultiSpeciesOrthology(@QueryParam("taxonID") List<String> taxonID, @QueryParam("taxonIdList") String taxonIdList, @QueryParam("stringencyFilter") String stringencyFilter, @QueryParam("methods") String methods,
 		@DefaultValue("20") @QueryParam("rows") Integer rows, @DefaultValue("1") @QueryParam("start") Integer start) throws IOException;
 
-	@GET
-	@Path("/geneMap")
-	@JsonView(value = { View.Homology.class })
-	@Operation(summary = "Retrieve homologous gene records for given list of geneMap")
-	@APIResponses(value = { @APIResponse(responseCode = "200", content = @Content(mediaType = "application/json", schema = @Schema(implementation = Null.class))) })
-	JsonResultResponse<HomologView> getMultiGeneOrthology(
-		@Parameter(in = ParameterIn.QUERY, name = "geneID", description = "List of geneMap (specified by their ID) for which homology is retrieved, e.g. 'MGI:109583'", schema = @Schema(type = SchemaType.STRING)) @QueryParam("geneID") List<String> geneID,
-		@Parameter(in = ParameterIn.QUERY, name = "geneIdList", description = "List of additional source gene IDs for which homology is retrieved in a comma-delimited list, e.g. 'MGI:109583,RGD:2129,MGI:97570", schema = @Schema(type = SchemaType.STRING)) @QueryParam("geneIdList") String geneList,
-		@Parameter(in = ParameterIn.QUERY, name = "filter.stringency", description = "apply stringency containsFilterValue", schema = @Schema(type = SchemaType.STRING)) @DefaultValue("stringent") @QueryParam("filter.stringency") String stringency,
-		@Parameter(in = ParameterIn.QUERY, name = "filter.method", description = "calculation methods", schema = @Schema(type = SchemaType.STRING)) @QueryParam("filter.method") String method,
-		@Parameter(in = ParameterIn.QUERY, name = "limit", description = "Number of rows returned", schema = @Schema(type = SchemaType.INTEGER)) @DefaultValue("20") @QueryParam("limit") Integer limit,
-		@Parameter(in = ParameterIn.QUERY, name = "page", description = "Page number", schema = @Schema(type = SchemaType.INTEGER)) @DefaultValue("1") @QueryParam("page") Integer page) throws IOException;
-
 	@GET
 	@Path("/methods")
 	@JsonView(value = { View.OrthologyMethod.class })

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

@@ -0,0 +1,52 @@
+package org.alliancegenome.api.service;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.elasticsearch.index.query.QueryBuilders.boolQuery;
+
+import org.alliancegenome.api.entity.GeneToGeneOrthologyDocument;
+import org.alliancegenome.cache.repository.helper.JsonResultResponse;
+import org.alliancegenome.cache.repository.helper.OrthologyFiltering;
+import org.alliancegenome.core.api.service.FilterService;
+import org.alliancegenome.es.model.query.Pagination;
+import org.elasticsearch.action.search.SearchResponse;
+import org.elasticsearch.index.query.BoolQueryBuilder;
+import org.elasticsearch.index.query.TermQueryBuilder;
+import org.elasticsearch.search.SearchHit;
+
+import jakarta.enterprise.context.RequestScoped;
+
+@RequestScoped
+public class OrthologyESService extends ESService {
+
+	public JsonResultResponse<GeneToGeneOrthologyDocument> getOrthologyList(String geneID, Pagination pagination) {
+		BoolQueryBuilder bool = boolQuery();
+		bool.filter(new TermQueryBuilder("geneToGeneOrthologyGenerated.subjectGene.primaryExternalId.keyword", geneID));
+
+		SearchResponse searchResponse = getSearchResponse(bool, pagination, null, false);
+
+		JsonResultResponse<GeneToGeneOrthologyDocument> response = new JsonResultResponse<>();
+		response.setTotal((int) searchResponse.getHits().getTotalHits().value);
+
+		List<GeneToGeneOrthologyDocument> list = new ArrayList<>();
+
+		for (SearchHit searchHit : searchResponse.getHits().getHits()) {
+			try {
+				String source = searchHit.getSourceAsString();
+				GeneToGeneOrthologyDocument object = mapper.readValue(source, GeneToGeneOrthologyDocument.class);
+				list.add(object);
+			} catch (Exception e) {
+				e.printStackTrace();
+			}
+		}
+
+		FilterService<GeneToGeneOrthologyDocument> filterService = new FilterService<>(new OrthologyFiltering());
+		List<GeneToGeneOrthologyDocument> gene2GeneOrthoFiltered = filterService.filterAnnotations(list, pagination.getFieldFilterValueMap());
+
+		response.setResults(gene2GeneOrthoFiltered);
+		return response;
+	}
+
+
+}

agr_api/src/test/java/org/alliancegenome/api/tests/integration/GeneIT.java

@@ -23,6 +23,7 @@
 import org.alliancegenome.api.dto.ExpressionSummary;
 import org.alliancegenome.api.dto.ExpressionSummaryGroup;
 import org.alliancegenome.api.dto.ExpressionSummaryGroupTerm;
+import org.alliancegenome.api.entity.GeneToGeneOrthologyDocument;
 import org.alliancegenome.api.service.GeneService;
 import org.alliancegenome.cache.repository.helper.JsonResultResponse;
 import org.alliancegenome.core.ExpressionDetail;
@@ -98,15 +99,15 @@ public void checkOrthologyAPIWithFilter() {
 
 		GeneController controller = new GeneController();
 		String[] geneIDs = {"RGD:2129"};
-		JsonResultResponse<HomologView> response = controller.getGeneOrthology("MGI:109583", asList(geneIDs), null, "stringENT", null, null, 20, 1);
+		JsonResultResponse<GeneToGeneOrthologyDocument> response = controller.getGeneOrthology("MGI:109583", asList(geneIDs), null, "stringENT", null, null, 20, 1);
 		assertThat("Matches found for containsFilterValue 'stringent", response.getTotal(), greaterThan(0));
 	}
 
 	@Test
 	public void checkOrthologyForListOfGenes() {
 
 		GeneController controller = new GeneController();
-		JsonResultResponse<HomologView> response = controller.getGeneOrthology("MGI:109583", null, null, "stringENT", null, null, 20, 1);
+		JsonResultResponse<GeneToGeneOrthologyDocument> response = controller.getGeneOrthology("MGI:109583", null, null, "stringENT", null, null, 20, 1);
 		assertThat("Matches found for containsFilterValue 'stringent", response.getTotal(), greaterThan(0));
 	}
 
@@ -122,7 +123,7 @@ public void checkOrthologyForSingleSpecies() throws IOException {
 	public void checkOrthologyAPIWithSpecies() {
 
 		GeneController controller = new GeneController();
-		JsonResultResponse<HomologView> response = controller.getGeneOrthology("MGI:109583", null, null, "stringent", null, null, 20, 1);
+		JsonResultResponse<GeneToGeneOrthologyDocument> response = controller.getGeneOrthology("MGI:109583", null, null, "stringent", null, null, 20, 1);
 		assertThat("No matches found for species 'NCBITaxon:10115", response.getTotal(), greaterThan(5));
 
 		String taxonArray = "NCBITaxon:10116";
@@ -147,7 +148,7 @@ public void checkOrthologyAPIWithMethods() {
 
 		GeneController controller = new GeneController();
 		String methods = "ZFIN";
-		JsonResultResponse<HomologView> response = controller.getGeneOrthology("MGI:109583", null, null, null, null, methods, 20, 1);
+		JsonResultResponse<GeneToGeneOrthologyDocument> response = controller.getGeneOrthology("MGI:109583", null, null, null, null, methods, 20, 1);
 		assertThat("No match against method 'ZFIN'", response.getTotal(), greaterThan(0));
 
 		methods = "OrthoFinder";
@@ -167,7 +168,7 @@ public void checkOrthologyAPIWithMethods() {
 	public void checkOrthologyAPINoFilters() {
 
 		GeneController controller = new GeneController();
-		JsonResultResponse<HomologView> response = controller.getGeneOrthology("MGI:109583", null, null, null, null, null, 20, 1);
+		JsonResultResponse<GeneToGeneOrthologyDocument> response = controller.getGeneOrthology("MGI:109583", null, null, null, null, null, 20, 1);
 		assertThat("matches found for gene MGI:109583'", response.getTotal(), greaterThan(0));
 	}
 

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

@@ -13,6 +13,7 @@
 import org.alliancegenome.indexer.indexers.curation.GeneToGeneParalogyIndexer;
 import org.alliancegenome.indexer.indexers.curation.PhenotypeAnnotationCurationIndexer;
 import org.alliancegenome.indexer.indexers.curation.ReleaseInfoIndexer;
+import org.alliancegenome.indexer.indexers.curation.GeneToGeneOrthologyIndexer;
 
 public enum IndexerConfig {
 
@@ -32,6 +33,7 @@ public enum IndexerConfig {
 	ParalogyIndexer("paralogy", GeneToGeneParalogyIndexer.class, 4, 5000, 5000, 8, 1),
 	PhenotypeAnnotationIndexer("phenotypeAnnotation", PhenotypeAnnotationCurationIndexer.class, 4, 1500, 1500, 2, 1),
 	ReleaseInfoIndexer("release", ReleaseInfoIndexer.class, 1, 1, 1, 1, 1),
+	GeneToGeneOrthologyIndexer("geneToGeneOrthology", GeneToGeneOrthologyIndexer.class, 4, 1426, 1426, 8, 1)
 	;
 
 

agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GeneToGeneOrthologyIndexer.java

@@ -0,0 +1,134 @@
+package org.alliancegenome.indexer.indexers.curation;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.LinkedBlockingDeque;
+
+import org.alliancegenome.api.entity.GeneToGeneOrthologyDocument;
+import org.alliancegenome.curation_api.model.entities.Gene;
+import org.alliancegenome.curation_api.model.entities.orthology.GeneToGeneOrthologyGenerated;
+import org.alliancegenome.curation_api.response.SearchResponse;
+import org.alliancegenome.indexer.RestConfig;
+import org.alliancegenome.indexer.config.IndexerConfig;
+import org.alliancegenome.indexer.indexers.Indexer;
+import org.alliancegenome.indexer.indexers.curation.service.GeneToGeneOrthologyService;
+import org.apache.commons.collections4.CollectionUtils;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import lombok.extern.slf4j.Slf4j;
+
+@Slf4j
+public class GeneToGeneOrthologyIndexer extends Indexer {
+
+	private GeneToGeneOrthologyService service = new GeneToGeneOrthologyService();
+
+	public GeneToGeneOrthologyIndexer(IndexerConfig config) {
+		super(config);
+	}
+
+	@Override
+	public void index() {
+		try {
+			log.info("Getting orthologs");
+
+			SearchResponse<GeneToGeneOrthologyGenerated> orthologyResponse = service.getGeneToGeneOrthology(0, 0);
+
+			log.info("GeneToGeneParalogy count: " + orthologyResponse.getTotalResults());
+
+			int totalPages = (int) (orthologyResponse.getTotalResults() / indexerConfig.getBufferSize());
+
+			LinkedBlockingDeque<String> queue = new LinkedBlockingDeque<>();
+			for (int i = 0; i <= totalPages; i++) {
+				queue.add(String.valueOf(i));
+			}
+
+			initiateThreading(queue);
+
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
+
+	}
+
+	@Override
+	protected ObjectMapper customizeObjectMapper(ObjectMapper objectMapper) {
+		return RestConfig.config.getJacksonObjectMapperFactory().createObjectMapper();
+	}
+
+	protected void startSingleThread(LinkedBlockingDeque<String> queue) {
+		while (true) {
+			try {
+				if (queue.isEmpty()) {
+					return;
+				}
+				String page = queue.takeFirst();
+				SearchResponse<GeneToGeneOrthologyGenerated> resp = service
+						.getGeneToGeneOrthology(Integer.valueOf(page), indexerConfig.getBufferSize());
+				List<GeneToGeneOrthologyDocument> docs = createGeneToGeneOrthologyDocuments(resp.getResults());
+
+				indexDocuments(docs);
+			} catch (Exception e) {
+				log.error("Error while indexing...", e);
+				System.exit(-1);
+				return;
+			}
+		}
+	}
+
+	private List<GeneToGeneOrthologyDocument> createGeneToGeneOrthologyDocuments(
+			List<GeneToGeneOrthologyGenerated> g2gOrthoList) {
+		List<GeneToGeneOrthologyDocument> documents = new ArrayList<>();
+		for (GeneToGeneOrthologyGenerated g2gOrtho : g2gOrthoList) {
+			GeneToGeneOrthologyDocument document = new GeneToGeneOrthologyDocument();
+
+			document.setGeneToGeneOrthologyGenerated(g2gOrtho);
+			createStringencyFilter(g2gOrtho, document);
+			createGeneAnnotations(g2gOrtho, document);
+			removeAnnotationLists(document);
+
+			documents.add(document);
+		}
+		return documents;
+	}
+
+	private void createStringencyFilter(GeneToGeneOrthologyGenerated g2gOrtho, GeneToGeneOrthologyDocument document) {
+		if (Boolean.TRUE.equals(g2gOrtho.getStrictFilter())) {
+			document.setStringencyFilter("stringent");
+		} else if (Boolean.TRUE.equals(g2gOrtho.getModerateFilter())) {
+			document.setStringencyFilter("moderate");
+		}
+	}
+
+	private void createGeneAnnotations(GeneToGeneOrthologyGenerated g2gOrtho, GeneToGeneOrthologyDocument document) {
+		Map<String, Object> map = new HashMap<>();
+		putGeneInfo(map, g2gOrtho.getSubjectGene());
+		putGeneInfo(map, g2gOrtho.getObjectGene());
+		document.setGeneAnnotations(map);
+	}
+
+	private void putGeneInfo(Map<String, Object> map, Gene gene) {
+		Map<String, Object> data = new HashMap<>();
+		data.put("hasExpressionAnnotations", hasExpressionAnnotations(gene));
+		data.put("hasDiseaseAnnotations", hasDiseaseAnnotations(gene));
+		map.put(gene.getIdentifier(), data);
+	}
+
+	private boolean hasDiseaseAnnotations(Gene gene) {
+		return CollectionUtils.isNotEmpty(gene.getGeneDiseaseAnnotations());
+	}
+
+	private boolean hasExpressionAnnotations(Gene gene) {
+		return CollectionUtils.isNotEmpty(gene.getGeneExpressionAnnotations());
+	}
+
+	private void removeAnnotationLists(GeneToGeneOrthologyDocument document) {
+		document.getGeneToGeneOrthologyGenerated().getSubjectGene().setGeneDiseaseAnnotations(null);
+		document.getGeneToGeneOrthologyGenerated().getSubjectGene().setGeneExpressionAnnotations(null);
+		document.getGeneToGeneOrthologyGenerated().getObjectGene().setGeneDiseaseAnnotations(null);
+		document.getGeneToGeneOrthologyGenerated().getObjectGene().setGeneExpressionAnnotations(null);
+	}
+
+}

agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/interfaces/GeneToGeneOrthologyGeneratedInterface.java

@@ -27,4 +27,12 @@ SearchResponse<GeneToGeneOrthologyGenerated> findForPublic(
 		@DefaultValue("0") @QueryParam("page") Integer page,
 		@DefaultValue("10") @QueryParam("limit") Integer limit,
 		HashMap<String, Object> params);
+
+	@POST
+	@Path("/findForPublic")
+	SearchResponse<GeneToGeneOrthologyGenerated> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		@DefaultValue("ForPublic") @QueryParam("view") String view,
+		HashMap<String, Object> params);
 }

agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/service/GeneToGeneOrthologyService.java

@@ -0,0 +1,26 @@
+package org.alliancegenome.indexer.indexers.curation.service;
+
+import java.util.HashMap;
+
+import org.alliancegenome.core.config.ConfigHelper;
+import org.alliancegenome.curation_api.model.entities.orthology.GeneToGeneOrthologyGenerated;
+import org.alliancegenome.curation_api.response.SearchResponse;
+import org.alliancegenome.indexer.RestConfig;
+import org.alliancegenome.indexer.indexers.curation.interfaces.GeneToGeneOrthologyGeneratedInterface;
+
+import si.mazi.rescu.RestProxyFactory;
+import lombok.extern.slf4j.Slf4j;
+
+@Slf4j
+public class GeneToGeneOrthologyService {
+	private final GeneToGeneOrthologyGeneratedInterface orthologyApi = RestProxyFactory.createProxy(GeneToGeneOrthologyGeneratedInterface.class, ConfigHelper.getCurationApiUrl(), RestConfig.config);
+
+		public SearchResponse<GeneToGeneOrthologyGenerated> getGeneToGeneOrthology(Integer page, Integer limit) {
+
+		HashMap<String, Object> params = new HashMap<>();
+		params.put("internal", false);
+		params.put("obsolete", false);
+
+		return orthologyApi.findForPublic(page, limit, "GeneToGeneOrthologyForIndexer", params);
+	}
+}