Add go indexer

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

@@ -8,6 +8,7 @@
 import org.alliancegenome.indexer.indexers.ModelIndexer;
 import org.alliancegenome.indexer.indexers.curation.DiseaseAnnotationCurationIndexer;
 import org.alliancegenome.indexer.indexers.curation.DiseaseSummaryCurationIndexer;
+import org.alliancegenome.indexer.indexers.curation.GOSearchResultCurationIndexer;
 import org.alliancegenome.indexer.indexers.curation.GeneGeneticInteractionCurationIndexer;
 import org.alliancegenome.indexer.indexers.curation.GeneMolecularInteractionCurationIndexer;
 import org.alliancegenome.indexer.indexers.curation.GeneToGeneOrthologyIndexer;
@@ -34,6 +35,7 @@ public enum IndexerConfig {
 	ReleaseInfoIndexer("release", ReleaseInfoIndexer.class, 1, 1, 1, 1, 1),
 	DiseaseSummaryIndexer("diseaseSummary", DiseaseSummaryCurationIndexer.class, 4, 1500, 1500, 4, 1),
 	GeneToGeneOrthologyIndexer("geneToGeneOrthology", GeneToGeneOrthologyIndexer.class, 4, 1500, 1500, 8, 1),
+	GOSearchResultCurationIndexer("goCuration", GOSearchResultCurationIndexer.class, 4, 1500, 1500, 8, 1),
 	//GeneExpressionAnnotationIndexer("geneExpressionAnnotation", GeneExpressionAnnotationIndexer.class, 4, 1500, 1500, 2, 1),
 	//GeneSearchResultCurationIndexer("geneSearchResult", GeneSearchResultCurationIndexer.class, 4, 250, 1000, 4, 1),
 

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

@@ -0,0 +1,79 @@
+package org.alliancegenome.indexer.indexers.curation;
+
+import java.util.HashMap;
+import java.util.concurrent.LinkedBlockingDeque;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import org.alliancegenome.core.config.ConfigHelper;
+import org.alliancegenome.curation_api.interfaces.document.GODocumentInterface;
+import org.alliancegenome.curation_api.model.document.es.GOSearchResultDocument;
+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.apache.commons.collections.CollectionUtils;
+
+import lombok.extern.slf4j.Slf4j;
+import si.mazi.rescu.RestProxyFactory;
+
+@Slf4j
+public class GOSearchResultCurationIndexer extends Indexer {
+
+	private final GODocumentInterface goApi = RestProxyFactory.createProxy(GODocumentInterface.class,
+			ConfigHelper.getCurationApiUrl(), RestConfig.config);
+
+	private HashMap<String, Object> params = new HashMap<String, Object>() {
+		{
+			put("internal", false);
+			put("obsolete", false);
+		}
+	};
+
+	public GOSearchResultCurationIndexer(IndexerConfig indexerConfig) {
+		super(indexerConfig);
+	}
+
+	@Override
+	protected void index() {
+		try {
+			SearchResponse<GOSearchResultDocument> response = goApi.findSearchResult(0, 0, params);
+			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 (Exception e) {
+			e.printStackTrace();
+		}
+	}
+
+	@Override
+	protected void startSingleThread(LinkedBlockingDeque<String> queue) {
+		while (true) {
+			try {
+				if (queue.isEmpty()) {
+					return;
+				}
+				String page = queue.takeFirst();
+				SearchResponse<GOSearchResultDocument> response = goApi.findSearchResult(Integer.valueOf(page),
+						indexerConfig.getBufferSize(), params);
+				if (response == null || CollectionUtils.isEmpty(response.getResults())) {
+					return;
+				}
+
+				indexDocuments(response.getResults());
+			} catch (Exception e) {
+				log.error("Error while indexing...", e);
+				System.exit(-1);
+				return;
+			}
+		}
+	}
+
+	@Override
+	protected ObjectMapper customizeObjectMapper(ObjectMapper objectMapper) {
+		return RestConfig.config.getJacksonObjectMapperFactory().createObjectMapper();
+	}
+}