SCRUM-4936 create GeneSummary documents in ES

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

@@ -1,30 +1,18 @@
 package org.alliancegenome.indexer.config;
 
-import org.alliancegenome.indexer.indexers.AlleleIndexer;
-import org.alliancegenome.indexer.indexers.DatasetIndexer;
-import org.alliancegenome.indexer.indexers.DiseaseIndexer;
-import org.alliancegenome.indexer.indexers.GeneIndexer;
-import org.alliancegenome.indexer.indexers.GoIndexer;
-import org.alliancegenome.indexer.indexers.ModelIndexer;
-import org.alliancegenome.indexer.indexers.curation.DiseaseAnnotationCurationIndexer;
-import org.alliancegenome.indexer.indexers.curation.GeneExpressionAnnotationIndexer;
-import org.alliancegenome.indexer.indexers.curation.GeneGeneticInteractionCurationIndexer;
-import org.alliancegenome.indexer.indexers.curation.GeneMolecularInteractionCurationIndexer;
-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;
+import org.alliancegenome.indexer.indexers.*;
+import org.alliancegenome.indexer.indexers.curation.*;
 
 public enum IndexerConfig {
-	
+
 	// Neo Indexers
 	GeneIndexer("gene", GeneIndexer.class, 4, 359, 359, 8, 1),
 	DatasetIndexer("dataset", DatasetIndexer.class, 4, 566, 566, 8, 1),
 	DiseaseIndexer("disease", DiseaseIndexer.class, 4, 680, 680, 8, 1),
 	AlleleIndexer("allele", AlleleIndexer.class, 4, 1517, 1517, 8, 1),
 	GoIndexer("go", GoIndexer.class, 4, 914, 914, 8, 1),
 	ModelIndexer("model", ModelIndexer.class, 4, 1426, 1426, 8, 1),
-	
+
 	// Curation Indexers
 	DiseaseAnnotationIndexer("diseaseAnnotation", DiseaseAnnotationCurationIndexer.class, 1, 1500, 1500, 2, 1),
 	GeneExpressionAnnotationIndexer("geneExpressionAnnotation", GeneExpressionAnnotationIndexer.class, 4, 1500, 1500, 2, 1),
@@ -33,8 +21,8 @@ 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, 1500, 1500, 8, 1)
-	;
+	GeneToGeneOrthologyIndexer("geneToGeneOrthology", GeneToGeneOrthologyIndexer.class, 4, 1500, 1500, 8, 1),
+	GeneSummaryIndexer("geneSummary", GeneSummaryIndexer.class, 4, 2000, 2000, 8, 1);
 
 
 	private String typeName;

agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/Indexer.java

@@ -186,14 +186,9 @@ public <D extends ESDocument> void indexDocuments(Iterable<D> docs, Class<?> vie
 	public void initiateThreading(LinkedBlockingDeque<String> queue) throws InterruptedException {
 		Integer numberOfThreads = indexerConfig.getThreadCount();
 
-		List<Thread> threads = new ArrayList<Thread>();
+		List<Thread> threads = new ArrayList<>();
 		for (int i = 0; i < numberOfThreads; i++) {
-			Thread t = new Thread(new Runnable() {
-				@Override
-				public void run() {
-					startSingleThread(queue);
-				}
-			});
+			Thread t = new Thread(() -> startSingleThread(queue));
 			threads.add(t);
 			t.start();
 		}

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

@@ -0,0 +1,76 @@
+package org.alliancegenome.indexer.indexers.curation;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import lombok.extern.slf4j.Slf4j;
+import org.alliancegenome.api.entity.GeneSummaryDocument;
+import org.alliancegenome.curation_api.model.entities.Gene;
+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.GeneSummaryService;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.LinkedBlockingDeque;
+
+@Slf4j
+public class GeneSummaryIndexer extends Indexer {
+
+	final private GeneSummaryService service = new GeneSummaryService();
+
+	public GeneSummaryIndexer(IndexerConfig config) {
+		super(config);
+	}
+
+	@Override
+	public void index() {
+		try {
+			log.info("Getting Gene Summary Info");
+			SearchResponse<Gene> geneSummaryResponse = service.getGeneSummary(0, 0);
+			log.info("GeneSummary count: " + geneSummaryResponse.getTotalResults());
+			int totalPages = (int) (geneSummaryResponse.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<Gene> resp = service.getGeneSummary(Integer.valueOf(page), indexerConfig.getBufferSize());
+				List<GeneSummaryDocument> docs = createGeneSummaryDocuments(resp.getResults());
+
+				indexDocuments(docs);
+			} catch (Exception e) {
+				log.error("Error while indexing...", e);
+				System.exit(-1);
+				return;
+			}
+		}
+	}
+
+	private List<GeneSummaryDocument> createGeneSummaryDocuments(List<Gene> geneInfoList) {
+		List<GeneSummaryDocument> documents = new ArrayList<>();
+		for (Gene gene : geneInfoList) {
+			GeneSummaryDocument document = new GeneSummaryDocument();
+			document.setGene(gene);
+			documents.add(document);
+		}
+		return documents;
+	}
+}

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

@@ -0,0 +1,28 @@
+package org.alliancegenome.indexer.indexers.curation.interfaces;
+
+import jakarta.ws.rs.*;
+import jakarta.ws.rs.core.MediaType;
+import org.alliancegenome.curation_api.model.entities.Gene;
+import org.alliancegenome.curation_api.response.SearchResponse;
+
+import java.util.HashMap;
+
+@Path("/gene")
+@Produces(MediaType.APPLICATION_JSON)
+@Consumes(MediaType.APPLICATION_JSON)
+public interface GeneSummaryInterface {
+	@POST
+	@Path("/findForPublic")
+	SearchResponse<Gene> findForPublic(
+		@DefaultValue("0") @QueryParam("page") Integer page,
+		@DefaultValue("10") @QueryParam("limit") Integer limit,
+		HashMap<String, Object> params);
+
+	@POST
+	@Path("/findForPublic")
+	SearchResponse<Gene> 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/GeneSummaryService.java

@@ -0,0 +1,26 @@
+package org.alliancegenome.indexer.indexers.curation.service;
+
+import lombok.extern.slf4j.Slf4j;
+import org.alliancegenome.core.config.ConfigHelper;
+import org.alliancegenome.curation_api.model.entities.Gene;
+import org.alliancegenome.curation_api.response.SearchResponse;
+import org.alliancegenome.indexer.RestConfig;
+import org.alliancegenome.indexer.indexers.curation.interfaces.GeneSummaryInterface;
+import si.mazi.rescu.RestProxyFactory;
+
+import java.util.HashMap;
+
+@Slf4j
+public class GeneSummaryService {
+	private final GeneSummaryInterface geneSummaryApi = RestProxyFactory.createProxy(GeneSummaryInterface.class, ConfigHelper.getCurationApiUrl(), RestConfig.config);
+
+	public SearchResponse<Gene> getGeneSummary(Integer page, Integer limit) {
+
+		HashMap<String, Object> params = new HashMap<>();
+		params.put("internal", false);
+		params.put("obsolete", false);
+//		params.put("primaryExternalId", "MGI:109583");
+
+		return geneSummaryApi.findForPublic(page, limit, "GeneView", params);
+	}
+}

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

@@ -0,0 +1,20 @@
+package org.alliancegenome.api.entity;
+
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import org.alliancegenome.curation_api.model.entities.Gene;
+import org.alliancegenome.es.index.ESDocument;
+
+@Data
+@EqualsAndHashCode(callSuper = true)
+public class GeneSummaryDocument extends ESDocument {
+
+	protected String category = "gene_summary";
+	private Gene gene;
+
+	@Override
+	public String getType() {
+		return category;
+	}
+
+}