Change simulation entity checks

Author: zakharc

org.insilico.vissim.sbscl/src/org/insilico/vissim/sbscl/simulation/SEDMLSimulation.java

@@ -11,8 +11,8 @@
 import org.jlibsedml.Output;
 import org.jlibsedml.SEDMLDocument;
 import org.jlibsedml.SedML;
+import org.jlibsedml.execution.IProcessedSedMLSimulationResults;
 import org.jlibsedml.execution.IRawSedmlSimulationResults;
-import org.simulator.math.odes.MultiTable;
 import org.simulator.sedml.SedMLSBMLSimulatorExecutor;
 
 public class SEDMLSimulation extends AbstractSimulation {
@@ -33,13 +33,10 @@ public SimulationResult simulate(String path) throws Exception {
 		SedMLSBMLSimulatorExecutor exe = new SedMLSBMLSimulatorExecutor(sedml, wanted, sedmlDir);
 		Map<AbstractTask, List<IRawSedmlSimulationResults>> res = exe.run();
 		if (res == null || res.isEmpty() || !exe.isExecuted()) {
-			// XXX: throw Ex. and log
+			//
 		} else {
-			@SuppressWarnings("rawtypes")
-			Map results = exe.runSimulations();
-			@SuppressWarnings("unchecked")
-			MultiTable solution = (MultiTable) exe.processSimulationResults(wanted, results);
-			return new ResultAdapter(solution).getResult();
+			IProcessedSedMLSimulationResults results = exe.processSimulationResults(wanted, res);
+			return new ResultAdapter(results, sedml.getElementName()).getResult();
 		}
 		return null;
 	}

org.insilico.vissim.sbscl/src/org/insilico/vissim/sbscl/utils/Utils.java

@@ -4,48 +4,51 @@
 import static org.junit.Assert.assertTrue;
 
 import java.io.File;
+import java.io.IOException;
 
 import javax.xml.stream.XMLStreamException;
 
+import org.insilico.vissim.sbscl.factory.SimulationResult;
 import org.insilico.vissim.sbscl.simulation.SimulationType;
 import org.jlibsedml.Libsedml;
+import org.sbml.jsbml.Model;
 import org.sbml.jsbml.SBMLReader;
 import org.simulator.omex.OMEXArchive;
 
 /**
- * Some basic utilities which need to be in helping project (for shifting operations or
- * other reasons), which are not toolkit dependent.
+ * Some basic utilities which need to be in helping project (for shifting
+ * operations or other reasons), which are not toolkit dependent.
  */
 public class Utils {
 
 	/**
 	 * Provides the type of corresponding simulation
 	 * 
 	 * <p>
-	 * Every simulation is eponymous to the type of the file specified.
-	 * e.g SimulationType.SEDML is a simulation described with SED-ML file. 
+	 * Every simulation is eponymous to the type of the file specified. e.g
+	 * SimulationType.SEDML is a simulation described with SED-ML file.
 	 * 
 	 * @param path absolute path to the file
 	 * @return {@link SimulationType}
-	 * */
+	 */
 	public SimulationType getSimulationType(String path) {
-			if (Libsedml.isSEDML(new File(path)))
-				return SimulationType.SEDML;
-			if (isOMEXArchiv(path)) {
-				return SimulationType.OMEX;
-			}
-			if (isSBML(path)) {
-				return SimulationType.SBML;
-			}
+		if (isSBML(path)) {
+			return SimulationType.SBML;
+		}
+		if (Libsedml.isSEDML(new File(path)))
+			return SimulationType.SEDML;
+		if (isOMEXArchiv(path)) {
+			return SimulationType.OMEX;
+		}
 		return SimulationType.UNKNOWN_ENTITY;
 	}
 
 	/**
-	 * Checks if provided file is a OMEXArchiv (combination of SED-ML
-	 * and SBML file with additional data)
+	 * Checks if provided file is a OMEXArchiv (combination of SED-ML and SBML file
+	 * with additional data)
 	 * 
 	 * @param path absolute path to the file
-	 * */
+	 */
 	private boolean isOMEXArchiv(String path) {
 		OMEXArchive archive;
 		try {
@@ -59,20 +62,21 @@ private boolean isOMEXArchiv(String path) {
 			return Boolean.FALSE;
 		}
 	}
-	
+
 	/**
-	 * Checks if provided file is a SBML file
-	 * XXX: more efficient check should be considered
+	 * Checks if provided file is a SBML file XXX: more efficient check should be
+	 * considered
 	 * 
 	 * @param path absolute path to the file
-	 * */
+	 */
 	private boolean isSBML(String path) {
 		try {
 			// this check should be changed
 			// reading file to define file type is inefficient
-			SBMLReader.read(path);
+			SBMLReader reader = new SBMLReader();
+			assertNotNull(reader.readSBML(path).getModel());
 			return Boolean.TRUE;
-		} catch (XMLStreamException e) {
+		} catch (XMLStreamException | IOException e) {
 			return Boolean.FALSE;
 		}
 	}