Running batch simulations.

Getting the batch simulations results.
For a math model.

Author: danv61

vcell-client/src/main/java/cbit/vcell/client/ClientSimManager.java

@@ -304,22 +304,20 @@ private static void saveFailure(Hashtable<String, Object>hashTable,Simulation si
 
 public void getBatchSimulationsResults(OutputContext outputContext, Simulation simulation) throws java.beans.PropertyVetoException {
 
-	
-
 	// simulation should be a template simulation
 	if(simulation.getName().contains(SimulationContext.ReservedBatchExtensionString)) {
 		throw new RuntimeException("Not a valid name for a batch template Simulation: '" + simulation.getName() + "'.");
 	}
 
 	SimulationOwner simOwner = getSimWorkspace().getSimulationOwner();
-	if(!(simOwner instanceof SimulationContext)) {
-		throw new RuntimeException("Template Simulation Owner must be a SimulationContext");
-	}
-	SimulationContext simContext = (SimulationContext)simOwner;
-	BioModel bioModel = simContext.getBioModel();
-	if(bioModel==null) {
-		throw new RuntimeException("Cannot add simulation, bioModel not set");
-	}
+//	if(!(simOwner instanceof SimulationContext)) {
+//		throw new RuntimeException("Template Simulation Owner must be a SimulationContext");
+//	}
+//	SimulationContext simContext = (SimulationContext)simOwner;
+//	BioModel bioModel = simContext.getBioModel();
+//	if(bioModel==null) {
+//		throw new RuntimeException("Cannot add simulation, bioModel not set");
+//	}
 
 	File batchResultsDir = ResourceUtil.getLocalBatchDir();
 //	File localSimDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
@@ -329,7 +327,7 @@ public void getBatchSimulationsResults(OutputContext outputContext, Simulation s
 		public void run(Hashtable<String, Object> hashTable) throws Exception {
 
 			// recover the list of batch simulations that belong to this template
-			Simulation allSims[] = bioModel.getSimulations();
+			Simulation allSims[] = simOwner.getSimulations();
 			LinkedHashMap<String, String> importsMap = new LinkedHashMap<>();
 			LinkedHashMap <String, Boolean> successMap = new LinkedHashMap<>();
 			String namePrefix = simulation.getName() + SimulationContext.ReservedBatchExtensionString;

vcell-core/src/main/java/cbit/vcell/resource/ResourceUtil.java

@@ -282,22 +282,28 @@ private static void deleteRecursively(File f) throws IOException {
 				deleteRecursively(c);
 			}
 		}
+		String fName = f.getName();
+		if(batchResultsDirName.contentEquals(fName)) {
+			return;			// don't delete the batch results directory
+		}
 		if (!f.delete()) {
 			throw new FileNotFoundException("Failed to delete file: " + f);
 		}
 	}
+	public static final String batchResultsDirName = "batchResults";
 	public static File getLocalBatchDir()
 	{
-		File adir = new File(getVcellHome(), "batchResults");
+		File adir = new File(getVcellHome(), batchResultsDirName);
 		if(adir.exists()) {
 			try {
 				deleteRecursively(adir);	// delete the output directory and all its content recursively
 			} catch (IOException e) {
 				System.err.println("Failed to empty " + adir.getName());
 			}
 		}
+		boolean ret = false;
 		if(!adir.exists()) {
-			adir.mkdirs();
+			ret = adir.mkdirs();
 		}
 		localBatchDir = adir;
 		return localBatchDir;