Merge branch 'development'

.gitignore

@@ -64,3 +64,5 @@ src/main/scripts/Lib/IDCTClassifier$py.class
 nbactions.xml
 *.n3
 *.ttl
+
+*.rdf

src/main/java/edu/isi/karma/controller/command/alignment/GenerateR2RMLModelCommand.java

@@ -154,15 +154,15 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 		try {
 			semanticModel.writeJson(ModelingConfiguration.getModelsJsonDir() + 
 					semanticModel.getName() + 
-					".json");
+					".model.json");
 		} catch (Exception e) {
 			logger.error("error in exporting the model to JSON!");
 //			e.printStackTrace();
 		}
 		try {
 			semanticModel.writeGraphviz(ModelingConfiguration.getModelsGraphvizDir() + 
 					semanticModel.getName() + 
-					".dot", false, false);
+					".model.dot", false, false);
 		} catch (Exception e) {
 			logger.error("error in exporting the model to GRAPHVIZ!");
 //			e.printStackTrace();
@@ -194,12 +194,11 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 
 			// Generate the KR2RML data structures for the RDF generation
 			final ErrorReport errorReport = new ErrorReport();
-			OntologyManager ontMgr = workspace.getOntologyManager();
-			KR2RMLMappingGenerator mappingGen = new KR2RMLMappingGenerator(ontMgr, alignment, 
+			KR2RMLMappingGenerator mappingGen = new KR2RMLMappingGenerator(workspace, alignment, 
 					worksheet.getSemanticTypes(), prefix, namespace, true, errorReport);
 
 			// Write the model
-			writeModel(workspace, ontMgr, mappingGen, worksheet, modelFileLocalPath);
+			writeModel(workspace, workspace.getOntologyManager(), mappingGen, worksheet, modelFileLocalPath);
 
 			// Write the model to the triple store
 			TripleStoreUtil utilObj = new TripleStoreUtil();

src/main/java/edu/isi/karma/controller/command/alignment/InvokeDataMiningServiceCommand.java

@@ -56,7 +56,6 @@
 import edu.isi.karma.modeling.Prefixes;
 import edu.isi.karma.modeling.alignment.Alignment;
 import edu.isi.karma.modeling.alignment.AlignmentManager;
-import edu.isi.karma.modeling.ontology.OntologyManager;
 import edu.isi.karma.rep.Worksheet;
 import edu.isi.karma.rep.Workspace;
 import edu.isi.karma.util.HTTPUtil;
@@ -200,12 +199,11 @@ public UpdateContainer doIt(Workspace workspace) throws CommandException {
 			Worksheet worksheet = workspace.getWorksheet(worksheetId);
 			// Generate the KR2RML data structures for the RDF generation
 			final ErrorReport errorReport = new ErrorReport();
-			OntologyManager ontMgr = workspace.getOntologyManager();
-			KR2RMLMappingGenerator mappingGen = new KR2RMLMappingGenerator(ontMgr, alignment, 
+			KR2RMLMappingGenerator mappingGen = new KR2RMLMappingGenerator(workspace, alignment, 
 					worksheet.getSemanticTypes(), prefix, namespace, true, errorReport);
 
 			SPARQLGeneratorUtil genObj = new SPARQLGeneratorUtil();
-			String query = genObj.get_query(mappingGen.getR2RMLMapping(), this.modelContext);
+			String query = genObj.get_query(mappingGen.getKR2RMLMapping(), this.modelContext);
 
 			// execute the query on the triple store
 			TripleStoreUtil utilObj = new TripleStoreUtil();