merging stage code and optimize classes

Author: cmpich

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

@@ -71,6 +71,7 @@ public class GeneController implements GeneRESTInterface {
 
 	@Inject
 	GeneToGeneParalogyESService geneToGeneParalogyESService;
+	@Inject
 	PhenotypeESService phenotypeESService;
 
 	private static final PhenotypeAnnotationToTdfTranslator translator = new PhenotypeAnnotationToTdfTranslator();

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

@@ -1,19 +1,14 @@
 package org.alliancegenome.api.service;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
-import io.quarkus.logging.Log;
 import jakarta.enterprise.context.RequestScoped;
 import jakarta.inject.Inject;
 import org.alliancegenome.api.entity.AllelePhenotypeAnnotationDocument;
 import org.alliancegenome.api.entity.GenePhenotypeAnnotationDocument;
 import org.alliancegenome.api.service.helper.GeneDiseaseSearchHelper;
 import org.alliancegenome.cache.repository.helper.JsonResultResponse;
-import org.alliancegenome.core.api.service.DiseaseRibbonService;
 import org.alliancegenome.es.index.site.dao.SearchDAO;
 import org.alliancegenome.es.model.query.Pagination;
-import org.alliancegenome.neo4j.entity.SpeciesType;
-import org.alliancegenome.neo4j.repository.DiseaseRepository;
-import org.alliancegenome.neo4j.repository.GeneRepository;
 import org.elasticsearch.action.search.SearchResponse;
 import org.elasticsearch.index.query.BoolQueryBuilder;
 import org.elasticsearch.search.aggregations.AggregationBuilder;
@@ -29,9 +24,6 @@ public class PhenotypeESService extends ESService {
 	@Inject
 	ObjectMapper mapper;
 
-	private static final GeneRepository geneRepository = new GeneRepository();
-	private static final DiseaseRepository diseaseRepository = new DiseaseRepository();
-	private static final DiseaseRibbonService diseaseRibbonService = new DiseaseRibbonService(diseaseRepository);
 	private static final SearchDAO searchDAO = new SearchDAO();
 	private static final GeneDiseaseSearchHelper geneDiseaseSearchHelper = new GeneDiseaseSearchHelper();
 
@@ -116,22 +108,6 @@ public JsonResultResponse<AllelePhenotypeAnnotationDocument> getAllelePhenotypeA
 		return ret;
 	}
 
-/*
-	private Map<String, Object> getSupplementalData(String focusTaxonId, boolean useSpeciesAggregation, boolean debug, BoolQueryBuilder unfilteredQuery) {
-		// create histogram of select columns of unfiltered query
-		Map<String, String> aggregationFields = new HashMap<>();
-		if (useSpeciesAggregation) {
-			aggregationFields.put("subject.taxon.name.keyword", "species");
-		}
-		aggregationFields.put("generatedRelationString.keyword", "associationType");
-		aggregationFields.put("diseaseQualifiers.keyword", "diseaseQualifiers");
-		Map<String, List<String>> distinctFieldValueMap = getAggregations(unfilteredQuery, aggregationFields, focusTaxonId, useSpeciesAggregation, debug);
-		Map<String, Object> supplementalData = new LinkedHashMap<>();
-		supplementalData.put(DISTINCT_FIELD_VALUES, distinctFieldValueMap);
-		return supplementalData;
-	}
-*/
-
 	private SearchResponse getSearchResponse(BoolQueryBuilder bool, Pagination pagination, LinkedHashMap<String, SortOrder> focusTaxonId, boolean debug) {
 		List<AggregationBuilder> aggBuilders = new ArrayList<>();
 		HighlightBuilder hlb = new HighlightBuilder();
@@ -141,21 +117,4 @@ private SearchResponse getSearchResponse(BoolQueryBuilder bool, Pagination pagin
 			pagination.getLimit(), pagination.getOffset(), hlb, focusTaxonId, debug);
 	}
 
-	private LinkedHashMap<String, SortOrder> getAnnotationSorts(String focusTaxonId, boolean debug) {
-		SpeciesType type = SpeciesType.getTypeByID(focusTaxonId);
-		LinkedHashMap<String, SortOrder> sorts = new LinkedHashMap<>();
-		if (type != null) {
-			sorts.put("speciesOrder." + type.getTaxonIDPart(), SortOrder.ASC);
-		} else {
-			if (debug) {
-				Log.info("Species could not be found for: " + focusTaxonId);
-			} else {
-				Log.debug("Species could not be found for: " + focusTaxonId);
-			}
-		}
-		sorts.put("object.name.sort", SortOrder.ASC);
-		if (debug) Log.info(sorts);
-		return sorts;
-	}
-
 }