Improve getJenaGraph() error handling for connections with nonexisten…

…t/empty graphs

connectionUtils/src/main/java/com/ge/research/semtk/sparqlX/SparqlConnection.java

@@ -28,6 +28,8 @@
 import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
 
+import com.ge.research.semtk.utility.LocalLogger;
+
 public class SparqlConnection {
 /**
  * SparqlConnection is a "SparqlGraph" connection consisting of multiple Sparql Endpoints
@@ -605,31 +607,45 @@ public String getUniqueKey() {
 
 	/**
 	 * Create a Jena Graph from this SparqlConnection
+	 * @throws Exception if nothing loaded from connection
 	 */
-	public Graph getJenaGraph() {
-		ArrayList<String> fetched = new ArrayList<String>();
-
+	public Graph getJenaGraph() throws Exception {
+
 		Model model = null;
+		String serverAndPort = null;
+		String graphName = null;
 		RDFConnection rdfConn = null;
-		try {
-			for(SparqlEndpointInterface sei : this.getAllInterfaces()) {
-				rdfConn = RDFConnection.connect(sei.getServerAndPort());
-				String graphName = sei.getGraph();
-				if(fetched.contains(sei.getServerAndPort() + graphName)) {
-					continue;  // skip if already fetched it (e.g. if model graph is the same as data graph)
+		ArrayList<String> fetched = new ArrayList<String>();  // remember which graphs are already fetched, to avoid repeat	work (e.g. if data and model are using the same graph)
+
+		for (SparqlEndpointInterface sei : this.getAllInterfaces()) {
+
+			try {
+				serverAndPort = sei.getServerAndPort();
+				graphName = sei.getGraph();
+				if (fetched.contains(serverAndPort + graphName)) {
+					continue; // skip if already fetched it 
 				}
+				fetched.add(serverAndPort + graphName);
+
+				rdfConn = RDFConnection.connect(serverAndPort);
 				Model m = rdfConn.fetch(graphName);
-				fetched.add(sei.getServerAndPort() + graphName);
-				if(model == null) {
+				if (model == null) {
 					model = m;
-				}else {
+				} else {
 					model.add(m);
 				}
+			} catch (Exception e) {
+				// log but do not error (allow a subset of graphs in the connection to be nonexistent/empty)
+				LocalLogger.logToStdErr("Cannot get Jena graph from graph '" + graphName + "' in " + serverAndPort + " (graph may be empty)");
+			} finally {
 				rdfConn.close();
 			}
-			return model.getGraph();
-		}finally {
-			rdfConn.close();
+
+		}
+		// if nothing was loaded from the connection, error
+		if (model == null) {
+			throw new Exception("Cannot get Jena graph for this connection (all graphs may be empty)");
 		}
+		return model.getGraph();
 	}
 }

sparqlGraphLibrary/src/main/java/com/ge/research/semtk/services/client/UtilityClient.java

@@ -92,6 +92,8 @@ public BufferedReader execLoadIngestionPackage(File ingestionPackageFile, String
 	 */
 	@SuppressWarnings("unchecked")
 	public String execGetShaclResults(File shaclTtlFile, SparqlConnection conn, Severity severity) throws Exception {
+
+		Thread.sleep(5000); // TODO remove
 
 		if(!shaclTtlFile.exists()) {
 			throw new Exception("File does not exist: " + shaclTtlFile.getAbsolutePath());

sparqlGraphLibrary/src/test/java/com/ge/research/semtk/sparqlX/test/SparqlConnectionTest_IT.java

@@ -17,20 +17,42 @@
 package com.ge.research.semtk.sparqlX.test;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
 
 import org.apache.jena.graph.Graph;
 import org.junit.Test;
 
+import com.ge.research.semtk.sparqlX.SparqlConnection;
+import com.ge.research.semtk.sparqlX.SparqlEndpointInterface;
 import com.ge.research.semtk.test.TestGraph;
 
 public class SparqlConnectionTest_IT {
 
 	@Test
 	public void testGetJenaGraph() throws Exception {
+
+		// test connection with all (1) graphs containing data
 		TestGraph.clearGraph();
 		TestGraph.uploadTurtleResource(this, "musicTestDataset_2017.q2.ttl");
-		Graph g = TestGraph.getSparqlConn().getJenaGraph();
+		SparqlConnection conn = TestGraph.getSparqlConn();
+		Graph g = conn.getJenaGraph();
 		assertEquals(g.size(), 215);
+
+		// test connection with one graph containing data, one graph empty
+		SparqlEndpointInterface sei = TestGraph.getSei("nonexistentGraph");
+		conn.addDataInterface(sei);
+		g = conn.getJenaGraph();
+		assertEquals(g.size(), 215);
+
+		// test connection with no graphs containing data
+		try {
+			TestGraph.clearGraph();
+			conn = TestGraph.getSparqlConn();
+			g = conn.getJenaGraph();
+			fail(); // shouldn't get here
+		}catch(Exception e) {
+			assertTrue(e.getMessage().equals("Cannot get Jena graph for this connection (all graphs may be empty)"));
+		}
 	}
-
 }