Fix for ancestors

Author: oblodgett

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

@@ -0,0 +1,57 @@
+package org.alliancegenome.indexer;
+
+import java.util.List;
+
+import org.alliancegenome.core.config.ConfigHelper;
+import org.alliancegenome.curation_api.interfaces.document.GeneDocumentInterface;
+import org.alliancegenome.curation_api.model.document.es.GeneSummaryDocument;
+import org.alliancegenome.curation_api.model.entities.Gene;
+import org.alliancegenome.curation_api.model.entities.ontology.OntologyTermClosure;
+import org.alliancegenome.curation_api.model.entities.ontology.SOTerm;
+import org.alliancegenome.curation_api.response.SearchResponse;
+import org.alliancegenome.es.rest.RestConfig;
+
+import si.mazi.rescu.RestProxyFactory;
+
+public class TestAncestors {
+
+	public static void main(String[] args) throws Exception {
+		long geneId = args.length > 0 ? Long.parseLong(args[0]) : 28821279L;
+
+		GeneDocumentInterface geneApi = RestProxyFactory.createProxy(GeneDocumentInterface.class, ConfigHelper.getCurationApiUrl(), RestConfig.config);
+
+		System.out.println("=== API URL: " + ConfigHelper.getCurationApiUrl() + " ===");
+		System.out.println("=== Gene ID: " + geneId + " ===\n");
+
+		SearchResponse<GeneSummaryDocument> response = geneApi.findByIds(List.of(geneId));
+
+		System.out.println("=== GeneSummaryDocument from API ===");
+		for (GeneSummaryDocument doc : response.getResults()) {
+			Gene gene = doc.getGene();
+			if (gene == null) {
+				System.out.println("Gene is null");
+				continue;
+			}
+			System.out.println("Gene symbol: " + (gene.getGeneSymbol() != null ? gene.getGeneSymbol().getDisplayText() : "null"));
+
+			SOTerm geneType = gene.getGeneType();
+			if (geneType == null) {
+				System.out.println("geneType is null");
+				continue;
+			}
+			System.out.println("geneType curie: " + geneType.getCurie());
+			System.out.println("geneType name: " + geneType.getName());
+
+			if (geneType.getAncestors() == null) {
+				System.out.println("ancestors: null");
+			} else {
+				System.out.println("ancestors count: " + geneType.getAncestors().size());
+				for (OntologyTermClosure closure : geneType.getAncestors()) {
+					System.out.println("  " + closure.getClosureObject().getCurie() + " " + closure.getClosureTypes());
+				}
+			}
+		}
+		System.out.println("\n=== Done ===");
+	}
+
+}

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

@@ -50,7 +50,6 @@ protected void index(ProcessDisplayHelper display) {
 
 	@Override
 	protected void startSingleThread(LinkedBlockingDeque<String> queue) {
-		ObjectMapper mapper = new ObjectMapper();
 		while (!queue.isEmpty()) {
 			String page = null;
 			try {

pom.xml

@@ -23,7 +23,7 @@
 		<maven-checkstyle-plugin.version>3.3.1</maven-checkstyle-plugin.version>
 		<checkstyle.version>10.17.0</checkstyle.version>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-		<curation.version>v0.47.29</curation.version>
+		<curation.version>v0.47.30</curation.version>
 	</properties>
 	<dependencyManagement>
 		<dependencies>