update how gene DA and EA booleans are indexed

Author: adamgibs

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

@@ -1,7 +1,9 @@
 package org.alliancegenome.api.service;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import static org.elasticsearch.index.query.QueryBuilders.boolQuery;
 
@@ -34,8 +36,16 @@ public JsonResultResponse<GeneToGeneOrthologyDocument> getOrthologyList(String g
 		for (SearchHit searchHit : searchResponse.getHits().getHits()) {
 			try {
 				String source = searchHit.getSourceAsString();
-				GeneToGeneOrthologyDocument object = mapper.readValue(source, GeneToGeneOrthologyDocument.class);
-				list.add(object);
+				GeneToGeneOrthologyDocument doc = mapper.readValue(source, GeneToGeneOrthologyDocument.class);
+				
+				Map<String, Map<String, Object>> geneAnnotationsMap = new HashMap<>();
+				doc.setGeneAnnotationsMap(geneAnnotationsMap);
+				for (Map<String, Object> geneAnnotation : doc.getGeneAnnotations()) {
+					String geneIdentifier = (String) geneAnnotation.get("geneIdentifier");
+					geneAnnotationsMap.put(geneIdentifier, geneAnnotation);
+				}
+
+				list.add(doc);
 			} catch (Exception e) {
 				e.printStackTrace();
 			}

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

@@ -33,7 +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)
+	GeneToGeneOrthologyIndexer("geneToGeneOrthology", GeneToGeneOrthologyIndexer.class, 4, 1426, 1426, 8, 1)
 	;
 
 

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

@@ -36,7 +36,7 @@ public void index() {
 
 			SearchResponse<GeneToGeneOrthologyGenerated> orthologyResponse = service.getGeneToGeneOrthology(0, 0);
 
-			log.info("GeneToGeneParalogy count: " + orthologyResponse.getTotalResults());
+			log.info("GeneToGeneOrthology count: " + orthologyResponse.getTotalResults());
 
 			int totalPages = (int) (orthologyResponse.getTotalResults() / indexerConfig.getBufferSize());
 
@@ -78,8 +78,7 @@ protected void startSingleThread(LinkedBlockingDeque<String> queue) {
 		}
 	}
 
-	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();
@@ -103,17 +102,18 @@ private void createStringencyFilter(GeneToGeneOrthologyGenerated g2gOrtho, GeneT
 	}
 
 	private void createGeneAnnotations(GeneToGeneOrthologyGenerated g2gOrtho, GeneToGeneOrthologyDocument document) {
-		Map<String, Object> map = new HashMap<>();
-		putGeneInfo(map, g2gOrtho.getSubjectGene());
-		putGeneInfo(map, g2gOrtho.getObjectGene());
-		document.setGeneAnnotations(map);
+		List<Map<String, Object>> geneAnnotationsList = new ArrayList<>();
+		putGeneInfo(geneAnnotationsList, g2gOrtho.getSubjectGene());
+		putGeneInfo(geneAnnotationsList, g2gOrtho.getObjectGene());
+		document.setGeneAnnotations(geneAnnotationsList);
 	}
 
-	private void putGeneInfo(Map<String, Object> map, Gene gene) {
+	private void putGeneInfo(List<Map<String, Object>> list, Gene gene) {
 		Map<String, Object> data = new HashMap<>();
+		data.put("geneIdentifier", gene.getIdentifier());
 		data.put("hasExpressionAnnotations", hasExpressionAnnotations(gene));
 		data.put("hasDiseaseAnnotations", hasDiseaseAnnotations(gene));
-		map.put(gene.getIdentifier(), data);
+		list.add(data);
 	}
 
 	private boolean hasDiseaseAnnotations(Gene gene) {

agr_java_core/src/main/java/org/alliancegenome/api/entity/GeneToGeneOrthologyDocument.java

@@ -1,5 +1,6 @@
 package org.alliancegenome.api.entity;
 
+import java.util.List;
 import java.util.Map;
 
 import org.alliancegenome.curation_api.model.entities.orthology.GeneToGeneOrthologyGenerated;
@@ -8,18 +9,19 @@
 import lombok.Data;
 import lombok.EqualsAndHashCode;
 
-@Data @EqualsAndHashCode(callSuper = true)
+@Data 
+@EqualsAndHashCode(callSuper = true)
 public class GeneToGeneOrthologyDocument extends ESDocument {
 
 	protected String category = "gene_to_gene_orthology";
 	private String stringencyFilter = "all";
-	private Map<String, Object> geneAnnotations;
-
+	private List<Map<String, Object>> geneAnnotations;
+	private Map<String, Map<String, Object>> geneAnnotationsMap;
 	private GeneToGeneOrthologyGenerated geneToGeneOrthologyGenerated;
 
+	
 	@Override
 	public String getType() {
 		return category;
 	}
-	
 }