SCRUM-4932: index gene expression experiments

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

@@ -6,13 +6,7 @@
 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.*;
 
 public enum IndexerConfig {
 
@@ -27,6 +21,7 @@ public enum IndexerConfig {
 	// Curation Indexers
 	DiseaseAnnotationIndexer("diseaseAnnotation", DiseaseAnnotationCurationIndexer.class, 1, 1500, 1500, 2, 1),
 	GeneExpressionAnnotationIndexer("geneExpressionAnnotation", GeneExpressionAnnotationIndexer.class, 4, 1500, 1500, 2, 1),
+	GeneExpressionExperimentIndexer("geneExpressionExperiment", GeneExpressionExperimentIndexer.class, 4, 1500, 1500, 2, 1),
 	GeneGeneticInteractionIndexers("geneGeneticInteraction", GeneGeneticInteractionCurationIndexer.class, 4, 1500, 1500, 2, 1),
 	GeneMolecularInteractionIndexers("geneMolecularInteraction", GeneMolecularInteractionCurationIndexer.class, 4, 1500, 1500, 2, 1),
 	ParalogyIndexer("paralogy", GeneToGeneParalogyIndexer.class, 4, 5000, 5000, 8, 1),

agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/GeneExpressionExperimentIndexer.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.GeneExpressionExperimentDocument;
+import org.alliancegenome.curation_api.model.entities.GeneExpressionExperiment;
+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.GeneExpressionExperimentService;
+import org.apache.commons.collections.CollectionUtils;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.LinkedBlockingDeque;
+
+@Slf4j
+public class GeneExpressionExperimentIndexer extends Indexer {
+	GeneExpressionExperimentService geneExpressionExperimentService;
+
+	public GeneExpressionExperimentIndexer(IndexerConfig indexerConfig) {
+		super(indexerConfig);
+	}
+
+	@Override
+	protected void index() {
+		geneExpressionExperimentService = new GeneExpressionExperimentService();
+		try {
+			SearchResponse<GeneExpressionExperiment> response = geneExpressionExperimentService.getGeneExpressionExperiments(0, 0);
+			log.info("GeneExpressionExperiment count: " + response.getTotalResults());
+			int totalPages = (int) (response.getTotalResults() / indexerConfig.getBufferSize());
+			LinkedBlockingDeque<String> queue = new LinkedBlockingDeque<>();
+			for (int i = 0; i <= totalPages; i++) {
+				queue.add(String.valueOf(i));
+			}
+			initiateThreading(queue);
+		} catch (InterruptedException e) {
+			e.printStackTrace();
+		}
+	}
+
+	@Override
+	protected void startSingleThread(LinkedBlockingDeque<String> queue) {
+		while (true) {
+			try {
+				if (queue.isEmpty()) {
+					return;
+				}
+
+				String page = queue.takeFirst();
+				log.debug(queue.size() + " pages to process " + Thread.currentThread().getName() + " starting page: " + page);
+				SearchResponse<GeneExpressionExperiment> response = geneExpressionExperimentService.getGeneExpressionExperiments(Integer.valueOf(page), indexerConfig.getBufferSize());
+				if (response == null || CollectionUtils.isEmpty(response.getResults())) {
+					return;
+				}
+				List<GeneExpressionExperimentDocument> documentsToIndex = new ArrayList<>();
+				for (GeneExpressionExperiment gee : response.getResults()) {
+					GeneExpressionExperimentDocument geneExpressionExperimentDocument = new GeneExpressionExperimentDocument();
+					geneExpressionExperimentDocument.setGeneExpressionExperiment(gee);
+					documentsToIndex.add(geneExpressionExperimentDocument);
+				}
+				indexDocuments(documentsToIndex);
+			} catch (Exception e) {
+				log.error("Error while indexing...", e);
+				System.exit(-1);
+				return;
+			}
+		}
+	}
+
+	@Override
+	protected ObjectMapper customizeObjectMapper(ObjectMapper objectMapper) {
+		return RestConfig.config.getJacksonObjectMapperFactory().createObjectMapper();
+	}
+}

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

@@ -0,0 +1,24 @@
+package org.alliancegenome.indexer.indexers.curation.interfaces;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import jakarta.ws.rs.*;
+import org.alliancegenome.curation_api.model.entities.GeneExpressionExperiment;
+import org.alliancegenome.curation_api.response.SearchResponse;
+import org.alliancegenome.curation_api.view.View;
+
+import java.util.HashMap;
+
+@Path("/gene-expression-experiment")
+@Produces({"application/json"})
+@Consumes({"application/json"})
+
+public interface GeneExpressionExperimentInterface {
+	@POST
+	@Path("/findForPublic")
+	@JsonView({View.ForPublic.class})
+	SearchResponse<GeneExpressionExperiment> findForPublic(
+			@DefaultValue("0") @QueryParam("page") Integer page,
+			@DefaultValue("10") @QueryParam("limit") Integer limit,
+			HashMap<String, Object> params
+	);
+}

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

@@ -0,0 +1,21 @@
+package org.alliancegenome.indexer.indexers.curation.service;
+
+import org.alliancegenome.core.config.ConfigHelper;
+import org.alliancegenome.curation_api.model.entities.GeneExpressionExperiment;
+import org.alliancegenome.curation_api.response.SearchResponse;
+import org.alliancegenome.indexer.RestConfig;
+import org.alliancegenome.indexer.indexers.curation.interfaces.GeneExpressionExperimentInterface;
+import si.mazi.rescu.RestProxyFactory;
+
+import java.util.HashMap;
+
+public class GeneExpressionExperimentService {
+	private GeneExpressionExperimentInterface geneExpressionExperimentClient = RestProxyFactory.createProxy(GeneExpressionExperimentInterface.class, ConfigHelper.getCurationApiUrl(), RestConfig.config);
+
+	public SearchResponse<GeneExpressionExperiment> getGeneExpressionExperiments(Integer page, Integer limit) {
+		HashMap<String, Object> params = new HashMap<>();
+		params.put("internal", false);
+		params.put("obsolete", false);
+		return geneExpressionExperimentClient.findForPublic(page, limit, params);
+	}
+}

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

@@ -0,0 +1,19 @@
+package org.alliancegenome.api.entity;
+
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import org.alliancegenome.curation_api.model.entities.GeneExpressionExperiment;
+import org.alliancegenome.es.index.ESDocument;
+
+@Data
+@EqualsAndHashCode(callSuper = true)
+public class GeneExpressionExperimentDocument extends ESDocument {
+
+	String category = "gene_expression_experiment";
+	GeneExpressionExperiment geneExpressionExperiment;
+
+	@Override
+	public String getType() {
+		return category;
+	}
+}