Clear stray JUnit graphs after using them

sparqlGraphLibrary/src/main/java/com/ge/research/semtk/test/TestConnection.java

@@ -28,10 +28,6 @@
 import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
 
-import com.ge.research.semtk.belmont.NodeGroup;
-import com.ge.research.semtk.load.DataLoader;
-import com.ge.research.semtk.load.dataset.CSVDataset;
-import com.ge.research.semtk.load.dataset.Dataset;
 import com.ge.research.semtk.load.utility.SparqlGraphJson;
 import com.ge.research.semtk.resultSet.GeneralResultSet;
 import com.ge.research.semtk.resultSet.SimpleResultSet;
@@ -41,8 +37,6 @@
 import com.ge.research.semtk.sparqlX.SparqlEndpointInterface;
 import com.ge.research.semtk.sparqlX.SparqlResultTypes;
 import com.ge.research.semtk.sparqlX.SparqlToXUtils;
-import com.ge.research.semtk.sparqlX.VirtuosoSparqlEndpointInterface;
-import com.ge.research.semtk.utility.Utility;
 
 /**
  * A utility class to load data to a semantic graph.  Intended for use in tests.
@@ -61,11 +55,11 @@ public TestConnection(int modelCount, int dataCount, String domain) throws Excep
 
 		SparqlEndpointInterface sei = TestGraph.getSei();
 		for (int i=0; i < modelCount; i++) {
-			sei.setDataset(generateDatasetName(String.format("model%d", i)));
+			sei.setGraph(generateDatasetName(String.format("model%d", i)));
 			conn.addModelInterface( sei );
 		}
 		for (int i=0; i < dataCount; i++) {
-			sei.setDataset(generateDatasetName(String.format("data%d", i)));
+			sei.setGraph(generateDatasetName(String.format("data%d", i)));
 			conn.addModelInterface( sei );
 		}
 
@@ -87,7 +81,7 @@ public void clearGraphs() throws Exception {
 		seiList.addAll(this.conn.getDataInterfaces());
 
 		for (SparqlEndpointInterface sei : seiList) {
-			sei.clearGraph();
+			IntegrationTestUtility.clearGraph(sei);
 		}
 	}
 

sparqlGraphLibrary/src/main/java/com/ge/research/semtk/test/TestGraph.java

@@ -91,11 +91,9 @@ public static SparqlEndpointInterface getSei(String graphName) throws Exception
 		}
 
 		if (sei instanceof NeptuneSparqlEndpointInterface) {
-
 			String region = IntegrationTestUtility.get("neptuneupload.s3ClientRegion");
 			String iamRoleArn = IntegrationTestUtility.get("neptuneupload.awsIamRoleArn");
 			String name =   IntegrationTestUtility.get("neptuneupload.s3BucketName");
-
 			((NeptuneSparqlEndpointInterface) sei).setS3Config(region, name, iamRoleArn);
 		}
 		return sei;
@@ -108,7 +106,6 @@ public static EndpointProperties getEndpointProperties() throws Exception {
 		ret.setEndpointServerUrl(sei.getServerAndPort());
 		ret.setEndpointUsername(sei.getUserName());
 		ret.setEndpointPassword(sei.getPassword());
-
 		return ret;
 	}
 
@@ -218,57 +215,43 @@ public static void execDeletionQuery(String query) throws Exception{
 		}		
 	}
 
+	/**
+	 * Execute a select query
+	 */
 	public static Table execTableSelect(String query) throws Exception {
-		// execute a select query
-		// exception if there's any problem
-		// return the table
 		SparqlEndpointInterface sei = getSei();
 		TableResultSet res = (TableResultSet) sei.executeQueryAndBuildResultSet(query, SparqlResultTypes.TABLE);
 		res.throwExceptionIfUnsuccessful();
-
 		return res.getResults();
 	}
 	public static Table execTableSelect(SparqlGraphJson sgJson) throws Exception {
-		// execute a select query
-		// exception if there's any problem
-		// return the table
-
 		return SparqlGraphJson.executeSelectToTable(sgJson.toJson(), getSparqlConn(), IntegrationTestUtility.getOntologyInfoClient());
 	}
 	public static Table execTableSelect(JSONObject sgJsonJson, OntologyInfoClient oInfoClient) throws Exception {
-		// execute a select query
-		// exception if there's any problem
-		// return the table
 		return SparqlGraphJson.executeSelectToTable(sgJsonJson, getSparqlConn(), oInfoClient);
 	}
+	public static Table execSelectFromResource(Object o, String resourceName) throws Exception {
+		return execSelectFromResource(o.getClass(), resourceName);
+	}
+	@SuppressWarnings("rawtypes")
+	public static Table execSelectFromResource(Class c, String resourceName) throws Exception {
+		SparqlGraphJson sgjson = TestGraph.getSparqlGraphJsonFromResource(c, resourceName);
+		return execTableSelect(sgjson.toJson(), IntegrationTestUtility.getOntologyInfoClient());
+	}
 
+	/**
+	 * Execute a construct query
+	 */
 	public static JSONArray execJsonConstruct(SparqlGraphJson sgJson) throws Exception {
-		// execute a construct query
-		// exception if there's any problem
-		// return the jsonArray
 		return SparqlGraphJson.executeConstructToJson(sgJson.toJson(), getSparqlConn(), IntegrationTestUtility.getOntologyInfoClient());
 	}
 	public static JSONArray execJsonConstruct(NodeGroup ng) throws Exception {
 		SparqlGraphJson sgJson = new SparqlGraphJson(ng, getSparqlConn());
 		return SparqlGraphJson.executeConstructToJson(sgJson.toJson(), getSparqlConn(), IntegrationTestUtility.getOntologyInfoClient());
 	}
 	public static JSONArray execJsonConstruct(JSONObject sgJsonJson, OntologyInfoClient oInfoClient) throws Exception {
-		// execute a construct query
-		// exception if there's any problem
-		// return the table
 		return SparqlGraphJson.executeConstructToJson(sgJsonJson, getSparqlConn(), oInfoClient);
 	}
-
-	public static Table execSelectFromResource(Object o, String resourceName) throws Exception {
-		return execSelectFromResource(o.getClass(), resourceName);
-	}
-	@SuppressWarnings("rawtypes")
-	public static Table execSelectFromResource(Class c, String resourceName) throws Exception {
-		SparqlGraphJson sgjson = TestGraph.getSparqlGraphJsonFromResource(c, resourceName);
-		return execTableSelect(sgjson.toJson(), IntegrationTestUtility.getOntologyInfoClient());
-	}
-
-
 	public static JSONArray execConstructFromResource(Object o, String resourceName) throws Exception {
 		return execConstructFromResource(o.getClass(), resourceName);
 	}
@@ -278,7 +261,6 @@ public static JSONArray execConstructFromResource(Class c, String resourceName)
 		return execJsonConstruct(sgjson.toJson(), IntegrationTestUtility.getOntologyInfoClient());
 	}
 
-
 	/**
 	 * Get the number of triples in the test graph.
 	 */
@@ -294,7 +276,6 @@ public static int getNumTriples() throws Exception {
 	// Use uploadOwlResource 
 	@Deprecated 
 	public static void uploadOwl(String owlFilename) throws Exception {
-
 		SparqlEndpointInterface sei = getSei();		
 		Path path = Paths.get(owlFilename);
 		byte[] owl = Files.readAllBytes(path);
@@ -332,7 +313,6 @@ public static void syncOwlToItsGraph(String owlFilename) throws Exception {
 		String base = Utility.getXmlBaseFromOwlRdf(new FileInputStream(owlFilename));
 
 		SparqlEndpointInterface sei = getSei();
-
 		sei.setGraph(base);
 		sei.clearGraph();
 
@@ -358,7 +338,6 @@ public static void uploadTurtleResource(Class c, String resourceName) throws Exc
 		uploadTurtleString(Utility.getResourceAsString(c, resourceName));
 	}
 	public static void uploadTurtle(String owlFilename) throws Exception {
-
 		SparqlEndpointInterface sei = getSei();
 		Path path = Paths.get(owlFilename);
 		byte[] owl = Files.readAllBytes(path);
@@ -368,11 +347,8 @@ public static void uploadTurtle(String owlFilename) throws Exception {
 		}
 		IntegrationTestUtility.getOntologyInfoClient().uncacheChangedConn(sei);
 	}
-
 	public static void uploadTurtleString(String turtleData) throws Exception {
-
 		SparqlEndpointInterface sei = getSei();
-
 		SimpleResultSet resultSet = SimpleResultSet.fromJson(sei.executeAuthUploadTurtle(turtleData.getBytes()));
 		if (!resultSet.getSuccess()) {
 			throw new Exception(resultSet.getRationaleAsString(" "));

sparqlGraphLibrary/src/test/java/com/ge/research/semtk/nodegroupexecution/test/NodeGroupExecutionClientTest_IT.java

@@ -598,7 +598,7 @@ public void testCopyGraph() throws Exception{
 
 			// copy to this graph
 			SparqlEndpointInterface toGraphSei = TestGraph.getSei(TestGraph.getDataset() + "/copy");
-			toGraphSei.clearGraph();
+			IntegrationTestUtility.clearGraph(toGraphSei);
 			assertEquals(toGraphSei.getNumTriples(), 0);	// assert empty before copy
 
 			String statusMessage = nodeGroupExecutionClient.copyGraph(
@@ -607,6 +607,7 @@ public void testCopyGraph() throws Exception{
 
 			assertTrue(statusMessage.contains("Successfully copied"));
 			assertEquals(toGraphSei.getNumTriples(), 50);	// assert populated after copy
+			IntegrationTestUtility.clearGraph(toGraphSei);
 		}
 
 		@Test

sparqlGraphLibrary/src/test/java/com/ge/research/semtk/ontologyTools/test/OntologyInfoTests_IT.java

@@ -31,7 +31,6 @@
 import com.ge.research.semtk.test.TestConnection;
 import com.ge.research.semtk.test.TestGraph;
 import com.ge.research.semtk.utility.Utility;
-import com.ge.research.semtk.belmont.NodeGroup;
 import com.ge.research.semtk.belmont.test.QueryGenTest_IT;
 import com.ge.research.semtk.load.DataLoader;
 import com.ge.research.semtk.load.dataset.CSVDataset;
@@ -222,6 +221,7 @@ public void testDoubleModel() throws Exception {
 		OntologyClass flower = oInfo.getClass("http://research.ge.com/kdl/plant#Flower");
 		assertTrue(cat != null);
 		assertTrue(flower != null);
+		testConn.clearGraphs();
 	}
 
 	@Test
@@ -242,10 +242,12 @@ public void testDoubleModelViaQueryService() throws Exception {
 		OntologyClass flower = oInfo.getClass("http://research.ge.com/kdl/plant#Flower");
 		assertTrue(cat != null);
 		assertTrue(flower != null);
+		testConn.clearGraphs();
 	}
 
 	private TestConnection setupDoubleModel() throws Exception {
 		TestConnection conn = new TestConnection(2, 1, "http://research.ge.com/kdl/");
+		conn.clearGraphs();
 		conn.uploadOwl(0, "src/test/resources/Pet.owl");
 		conn.uploadOwl(1, "src/test/resources/Plant.owl");
 		return conn;