SCRUM-4066 remove unused imports

Author: adamgibs

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

@@ -54,11 +54,11 @@ public class GeneController implements GeneRESTInterface {
 	@Inject
 	AlleleService alleleService;
 
-	@Inject OrthologyCacheRepository orthologyService;
-
-	@Inject OrthologyESService orthologyESService;
+	@Inject
+	ExpressionCacheRepository expressionCacheRepository;
 
-	@Inject ExpressionCacheRepository expressionCacheRepository;
+	@Inject
+	OrthologyESService orthologyESService;
 
 	@Inject
 	DiseaseService diseaseService;

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

@@ -1,10 +1,8 @@
 package org.alliancegenome.api.service;
 
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
-import java.util.Map;
 
 import static org.elasticsearch.index.query.QueryBuilders.boolQuery;
 
@@ -14,7 +12,6 @@
 import org.alliancegenome.cache.repository.helper.JsonResultResponse;
 import org.alliancegenome.cache.repository.helper.OrthologyCurationFiltering;
 import org.alliancegenome.core.api.service.FilterService;
-import org.alliancegenome.curation_api.model.entities.Gene;
 import org.alliancegenome.es.index.site.dao.SearchDAO;
 import org.alliancegenome.es.model.query.Pagination;
 import org.elasticsearch.action.search.SearchResponse;

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

@@ -1,7 +1,6 @@
 package org.alliancegenome.indexer;
 
 import org.alliancegenome.core.config.ConfigHelper;
-import org.alliancegenome.curation_api.model.entities.orthology.GeneToGeneOrthologyGenerated;
 
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.databind.DeserializationFeature;
@@ -34,7 +33,6 @@ public ObjectMapper createObjectMapper() {
 				mapper.disable(MapperFeature.DEFAULT_VIEW_INCLUSION);
 				mapper.setSerializationInclusion(Include.NON_NULL);
 				mapper.setSerializationInclusion(Include.NON_EMPTY);
-
 				return mapper;
 			}
 

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

@@ -33,9 +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),
-	//PhenotypeAnnotationMlIndexer("phenotypeAnnotation", PhenotypeCurationIndexer.class, 1, 1426, 1426, 2, 1),
 	GeneToGeneOrthologyIndexer("geneToGeneOrthology", GeneToGeneOrthologyIndexer.class, 4, 1426, 1426, 8, 1)
-	// still not implemented  VariantIndexer("variant", VariantIndexer.class, 2, 3000, 400, 4, 4)
 	;
 
 

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

@@ -33,20 +33,20 @@ public GeneToGeneOrthologyIndexer(IndexerConfig config) {
 	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());
-	
+
+			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();
 		}
@@ -58,27 +58,28 @@ 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());
+		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;
-            }
-        }
+
+				indexDocuments(docs);
+			} catch (Exception e) {
+				log.error("Error while indexing...", e);
+				System.exit(-1);
+				return;
+			}
+		}
 	}
 
-	private List<GeneToGeneOrthologyDocument> createGeneToGeneOrthologyDocuments(List<GeneToGeneOrthologyGenerated> g2gOrthoList) {
+	private List<GeneToGeneOrthologyDocument> createGeneToGeneOrthologyDocuments(
+			List<GeneToGeneOrthologyGenerated> g2gOrthoList) {
 		List<GeneToGeneOrthologyDocument> documents = new ArrayList<>();
 		for (GeneToGeneOrthologyGenerated g2gOrtho : g2gOrthoList) {
 			GeneToGeneOrthologyDocument document = new GeneToGeneOrthologyDocument();
@@ -93,7 +94,6 @@ private List<GeneToGeneOrthologyDocument> createGeneToGeneOrthologyDocuments(Lis
 		return documents;
 	}
 
-	
 	private void createStringencyFilter(GeneToGeneOrthologyGenerated g2gOrtho, GeneToGeneOrthologyDocument document) {
 		if (Boolean.TRUE.equals(g2gOrtho.getStrictFilter())) {
 			document.setStringencyFilter("stringent");
@@ -108,7 +108,7 @@ private void createGeneAnnotations(GeneToGeneOrthologyGenerated g2gOrtho, GeneTo
 		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));
@@ -131,6 +131,4 @@ private void removeAnnotationLists(GeneToGeneOrthologyDocument document) {
 		document.getGeneToGeneOrthologyGenerated().getObjectGene().setGeneExpressionAnnotations(null);
 	}
 
-
-
 }

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

@@ -15,9 +15,9 @@
 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<>();
+		public SearchResponse<GeneToGeneOrthologyGenerated> getGeneToGeneOrthology(Integer page, Integer limit) {
+
+		HashMap<String, Object> params = new HashMap<>();
 		params.put("internal", false);
 		params.put("obsolete", false);
 

agr_java_core/src/main/java/org/alliancegenome/cache/repository/OrthologyCacheRepository.java

@@ -190,6 +190,7 @@ public static JsonResultResponse<HomologView> getOrthologyJson(Gene gene, Orthol
 	public JsonResultResponse<HomologView> getOrthologyMultiGeneJson(List<String> geneIDs, Pagination pagination) {
 		long start = System.currentTimeMillis();
 		List<HomologView> homologViewList = repo.getAllOrthologyGenes(geneIDs);
+		//filtering
 		FilterService<HomologView> filterService = new FilterService<>(new OrthologyFiltering());
 		List<HomologView> homologViewFiltered = filterService.filterAnnotations(homologViewList, pagination.getFieldFilterValueMap());