Proper management of jobCount and scanCount when adding numTrials

vcell-admin/src/main/java/org/vcell/admin/VCComprehensiveStatistics.java

@@ -281,8 +281,8 @@ private void collectMathModelStats(long startDateInMs, long endDateInMs) throws
 						boolean bHasCompletedSim = false;
 						for (Simulation sim : mathModel.getSimulations()) {
 							SimulationStatusPersistent ss = dbServerImpl.getSimulationStatus(sim.getKey());
-							for (int scan = 0; ss != null && scan < sim.getScanCount(); scan ++) {
-								SimulationJobStatusPersistent jobStatus = ss.getJobStatus(scan);
+							for (int jobIndex = 0; ss != null && jobIndex < sim.getJobCount(); jobIndex ++) {
+								SimulationJobStatusPersistent jobStatus = ss.getJobStatus(jobIndex);
 								if (jobStatus != null) {
 									if (jobStatus.getSchedulerStatus() == SchedulerStatus.COMPLETED) {								
 										bHasCompletedSim = true;
@@ -422,8 +422,8 @@ private void collectBioModelStats(long startDateInMs, long endDateInMs) throws D
 						for (Simulation sim : bioModel.getSimulations()) {
 							SimulationStatusPersistent ss = dbServerImpl.getSimulationStatus(sim.getKey());
 							if (ss != null) {
-								for (int scan = 0; scan < sim.getScanCount(); scan ++) {
-									SimulationJobStatusPersistent jobStatus = ss.getJobStatus(scan);
+								for (int jobIndex = 0; jobIndex < sim.getJobCount(); jobIndex ++) {
+									SimulationJobStatusPersistent jobStatus = ss.getJobStatus(jobIndex);
 									if (jobStatus != null) {
 										if (jobStatus.getSchedulerStatus() == SchedulerStatus.COMPLETED) {								
 											bHasCompletedSim = true;

vcell-admin/src/test/java/cbit/vcell/util/TestMissingSimData.java

@@ -188,7 +188,7 @@ public int compare(RerunMissing o1, RerunMissing o2) {
 				System.out.println(
 					BeanUtils.forceStringLength(rerunArr[i].getVCSimulationIdentifier().getSimulationKey().toString(), 12, " ", true)+" "+
 					BeanUtils.forceStringLength((rerunArr[i].getSimulation()!=null?"'"+rerunArr[i].getSimulation().getVersion().getOwner().getName()+"'":"null"), 15, " ", false)+" "+
-					BeanUtils.forceStringLength((rerunArr[i].getSimulation()!=null?"scan="+rerunArr[i].getSimulation().getScanCount():"null"), 10, " ", false)+" "+
+					BeanUtils.forceStringLength((rerunArr[i].getSimulation()!=null?"jobs="+rerunArr[i].getSimulation().getJobCount():"null"), 10, " ", false)+" "+
 					rerunArr[i].getLastSimStatus());
 			}
 			System.out.println("-----\n-----");
@@ -202,7 +202,7 @@ private static boolean acquireThread(VCSimulationIdentifier vcSimulationIdentifi
 			while(rerunIter.hasNext()){
 				RerunMissing rerunMissing = rerunIter.next();
 				if(rerunMissing.getSimulation() != null){
-					if(rerunMissing.getSimulation().getScanCount() > 1){
+					if(rerunMissing.getSimulation().getJobCount() > 1){
 						//don't proceed until scancounts are done
 						return false;
 					}
@@ -321,15 +321,15 @@ public void run() {
 //					continue;
 //				}
 
-				int scanCount = simulation.getScanCount();
+				int jobCount = simulation.getJobCount();
 //				if(true){return;}
 				SimulationStatusPersistent simulationStatus = null;
 				SimulationInfo simulationInfo = simulation.getSimulationInfo();
 				if(!simulationInfo.getAuthoritativeVCSimulationIdentifier().getSimulationKey().equals(vcSimulationIdentifier.getSimulationKey())){
 					throw new Exception("Unexpected authoritative and sim id are not the same");
 				}
 
-			vcellConnection.getSimulationController().startSimulation(vcSimulationIdentifier, scanCount);
+			vcellConnection.getSimulationController().startSimulation(vcSimulationIdentifier, jobCount);
 			startTime = System.currentTimeMillis();
 //			SimulationStatusPersistent lastSimStatus = simulationStatus;
 			while(simulationStatus == null || simulationStatus.isStopped() || simulationStatus.isCompleted() || simulationStatus.isFailed()){
@@ -1036,8 +1036,8 @@ private static void runSim(SimIDAndJobID simIDAndJobID) throws Exception{
 //				notCompletedSimIDs.add(simIDAndJobID.simID.toString());
 				return;
 			}
-			int scanCount = sim.getScanCount();
-			vcellConnection.getSimulationController().startSimulation(vcSimulationIdentifier, scanCount);
+			int jobCount = sim.getJobCount();
+			vcellConnection.getSimulationController().startSimulation(vcSimulationIdentifier, jobCount);
 			long startTime = System.currentTimeMillis();
 			while(simulationStatus.isStopped() || simulationStatus.isCompleted() || simulationStatus.isFailed()){
 				Thread.sleep(250);

vcell-api/src/main/java/org/vcell/rest/health/HealthService.java

@@ -210,7 +210,7 @@ private void runsimLoop() {
 				long eventTimestamp = System.currentTimeMillis();
 
 				// submit simulation via an RPC call
-				RestDatabaseService.callStartSimulation(vcMessagingService, user, vcSimId.getSimulationKey(), sim.getSimulationVersion().getOwner(), sim.getScanCount());
+				RestDatabaseService.callStartSimulation(vcMessagingService, user, vcSimId.getSimulationKey(), sim.getSimulationVersion().getOwner(), sim.getJobCount());
 				// get initial status from database
 				SimulationStatus simStatus = simulationDatabaseDirect.getSimulationStatus(vcSimId.getSimulationKey());
 

vcell-cli/src/main/java/org/vcell/cli/run/SolverHandler.java

@@ -243,7 +243,7 @@ public void initialize(List<BioModel> bioModelList, SedML sedml) throws Expressi
 			AbstractTask topTask = entry.getKey();
 			Task actualTask = topTaskToBaseTask.get(topTask.getId());
 			TempSimulation tempSimulation = taskToTempSimulationMap.get(topTask);
-			int scanCount = tempSimulation.getScanCount();
+			int scanCount = tempSimulation.getScanCount_2();
 
 			if(scanCount > 1) {        // we know that topTask is a RepeatedTask
 //				assert task instanceof RepeatedTask;
@@ -383,7 +383,7 @@ public void simulateAllTasks(ExternalDocInfo externalDocInfo, SedML sedml, CLIRe
 						tempSimulation.getMeshSpecification().setSamplingSize(newSize);
 					}
 
-					int scanCount = tempSimulation.getScanCount();
+					int scanCount = tempSimulation.getScanCount_2();
 					for (int i = 0; i < scanCount; i++) {
 						TempSimulationJob simJob = new TempSimulationJob(tempSimulation, i, null);
 						simJobsList.add(simJob);

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

@@ -485,7 +485,7 @@ public void simStatusChanged(SimStatusEvent simStatusEvent) {
 	// if failed, notify
 	if (simStatusEvent.isNewFailureEvent()) {
 		String qualifier = "";
-		if (simulation.getScanCount() > 1) {
+		if (simulation.getJobCount() > 1) {
 			qualifier += "One job from ";
 		}
 		PopupGenerator.showErrorDialog(this, qualifier + "Simulation '" + simulation.getName() + "' failed\n" + simStatus.getDetails());

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

@@ -4381,7 +4381,7 @@ public void run(Hashtable<String, Object> hashTable) throws Exception {
 								// check for running once more... directly from job status
 								SimulationStatus serverSimulationStatus = getServerSimulationStatus(simInfo);
 								if (serverSimulationStatus != null
-										&& serverSimulationStatus.numberOfJobsDone() < simulations[i].getScanCount()) {
+										&& serverSimulationStatus.numberOfJobsDone() < simulations[i].getJobCount()) {
 									SimulationStatus simStatus = getClientServerManager().getJobManager()
 											.stopSimulation(simInfo.getAuthoritativeVCSimulationIdentifier());
 									// updateStatus
@@ -4460,7 +4460,7 @@ public OpenModelInfoHolder[] getOpenDesktopDocumentInfos(boolean bIncludeSimulat
 							}
 							Simulation[] sims = simContexts[i].getSimulations();
 							for (int j = 0; j < sims.length; j += 1) {
-								for (int k = 0; k < sims[j].getScanCount(); k += 1) {
+								for (int k = 0; k < sims[j].getJobCount(); k += 1) {
 									FieldDataWindowManager.OpenModelInfoHolder simInfoHolder = new FieldDataWindowManager.FDSimBioModelInfo(
 											sims[j].getName(), bioModel.getVersion(), simContexts[i],
 											sims[j].getSimulationInfo(), k,
@@ -4488,7 +4488,7 @@ public OpenModelInfoHolder[] getOpenDesktopDocumentInfos(boolean bIncludeSimulat
 						}
 						Simulation[] sims = mathModel.getSimulations();
 						for (int i = 0; i < sims.length; i += 1) {
-							for (int k = 0; k < sims[i].getScanCount(); k += 1) {
+							for (int k = 0; k < sims[i].getJobCount(); k += 1) {
 								FieldDataWindowManager.OpenModelInfoHolder simInfoHolder = new FieldDataWindowManager.FDSimMathModelInfo(
 										sims[i].getName(), mathModel.getVersion(), mathModel.getMathDescription(),
 										sims[i].getSimulationInfo(), k,

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

@@ -117,7 +117,7 @@ public SimulationStatus getSimulationStatus(Simulation simulation) {
 	SimulationStatus cachedSimStatus = simHash.getSimulationStatus(simulation);
 	if (cachedSimStatus!=null){
 		if (simulation.getIsDirty()) {
-			return SimulationStatus.newNotSaved(simulation.getScanCount());
+			return SimulationStatus.newNotSaved(simulation.getJobCount());
 		} else {
 			return cachedSimStatus;
 		}
@@ -151,7 +151,7 @@ private void initHash(Simulation[] simulations) {
 				if (simStatus != null) {
 					simHash.setSimulationStatus(simulations[i], simStatus);
 				} else {
-					simHash.setSimulationStatus(simulations[i], SimulationStatus.newNeverRan(simulations[i].getScanCount()));
+					simHash.setSimulationStatus(simulations[i], SimulationStatus.newNeverRan(simulations[i].getJobCount()));
 				}
 			}
 		}
@@ -498,7 +498,7 @@ void updateStatusFromServer(Simulation simulation) {
 	SimulationStatus serverStatus = getDocumentWindowManager().getRequestManager().getServerSimulationStatus(simulation.getSimulationInfo());
 
 	SimulationStatus newStatus = null;
-	if (oldStatus.isStopRequested() && serverStatus.numberOfJobsDone() < simulation.getScanCount()) {
+	if (oldStatus.isStopRequested() && serverStatus.numberOfJobsDone() < simulation.getJobCount()) {
 		// if stop requested but still going, get updated server info but adjust status
 		newStatus = SimulationStatus.newStopRequest(serverStatus);
 	} else {
@@ -622,7 +622,7 @@ public void runQuickSimulation(final Simulation originalSimulation, ViewerType v
 	}
 	//Let user tell how many simultaneous processes to run if this is local paramscan
 	final int[] simultaneousSimsSetting = new int[] {1};
-	if(originalSimulation.getScanCount() > 1) {
+	if(originalSimulation.getJobCount() > 1) {
 		try {
 			String simultaneousSims = DialogUtils.showInputDialog0(getDocumentWindowManager().getComponent(), "Local multi-scan simulation, enter maximum simulataneous sims to run at once", "1");
 			simultaneousSimsSetting[0] = Integer.parseInt(simultaneousSims);
@@ -741,7 +741,7 @@ public void solverAborted(SolverEvent event) {
 		taskList.add(task);
 	}
 
-	AsynchClientTask runOthers = new AsynchClientTask("running scans", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
+	AsynchClientTask runOthers = new AsynchClientTask("running scans/trials", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
 		@Override
 		public void run(Hashtable<String, Object> hashTable) throws Exception {
 			if (getClientTaskStatusSupport().isInterrupted()) {
@@ -750,7 +750,7 @@ public void run(Hashtable<String, Object> hashTable) throws Exception {
 			Simulation[] sims = (Simulation[])hashTable.get("simsArray");
 			Simulation simulation = sims[0];
 			//Run param scans to generate data for scansnum > 0
-			if(simulation.getScanCount() > 1) {
+			if(simulation.getJobCount() > 1) {
 				//Start master thread so clientdispatcher modal dialog can end
 				new Thread(new Runnable() {
 					@Override
@@ -772,7 +772,7 @@ public void windowClosing(WindowEvent e) {
 						//Counter of how many simultaneous param scan threads are running (decremented when scan thread finishes)
 						final int[] currentlyRunningCountHolder = new int[] {0};
 						//Run other scans starting at 1 (scan 0 is already done if we got here)
-						for (int i = 1; i < simulation.getScanCount(); i++) {
+						for (int i = 1; i < simulation.getJobCount(); i++) {
 							//Check if we can start another new param scan thread
 							while(currentlyRunningCountHolder[0] >= simultaneousSimsSetting[0]) {
 								try {
@@ -785,15 +785,15 @@ public void windowClosing(WindowEvent e) {
 									e.printStackTrace();
 								}
 							}
-							final int scanNum = i;
+							final int jobIndex = i;
 							//increment the concurrent running counter
 							currentlyRunningCountHolder[0]+= 1;
 							//Start new param scan thread
 							new Thread(new Runnable() {
 								@Override
 								public void run() {
 									try {
-										SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, scanNum, null), 0);
+										SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, jobIndex, null), 0);
 										Solver solver = createQuickRunSolver(localSimDataDir, simTask);
 										solver.startSolver();
 										while(true) {
@@ -835,8 +835,8 @@ public void run() {
 										//decrement the concurrent running counter
 										currentlyRunningCountHolder[0]-= 1;
 										//Set progress on dataviewer
-										if(((SimResultsViewer)haveSimulationWindow.getDataViewer()).getLocalScanProgress() < (scanNum+1)) {
-											((SimResultsViewer)haveSimulationWindow.getDataViewer()).setLocalScanProgress(scanNum+1);
+										if(((SimResultsViewer)haveSimulationWindow.getDataViewer()).getLocalJobProgress() < (jobIndex+1)) {
+											((SimResultsViewer)haveSimulationWindow.getDataViewer()).setLocalScanProgress(jobIndex+1);
 										}
 									}
 								}}).start();

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

@@ -392,7 +392,7 @@ public void simStatusChanged(SimStatusEvent simStatusEvent) {
 	// if failed, notify
 	if (simStatusEvent.isNewFailureEvent()) {
 		String qualifier = "";
-		if (simulation.getScanCount() > 1) {
+		if (simulation.getJobCount() > 1) {
 			qualifier += "One job from ";
 		}
 		PopupGenerator.showErrorDialog(this, qualifier + "Simulation '" + simulation.getName() + "' failed\n" + simStatus.getDetails());

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

@@ -45,7 +45,7 @@ public void changeSimulationInstances(Simulation[] newSimulations) {
 			// look in list for existing status
 			//
 			if (newSimulations[i].getKey()==null || newSimulations[i].getIsDirty()){
-				newHash.put(newSimulations[i],SimulationStatus.newNotSaved(newSimulations[i].getScanCount()));
+				newHash.put(newSimulations[i],SimulationStatus.newNotSaved(newSimulations[i].getJobCount()));
 			// 
 			// try to find status for previous instance of this simulation
 			// 
@@ -72,7 +72,7 @@ public void changeSimulationInstances(Simulation[] newSimulations) {
 				if (newSimStatus!=null){
 					newHash.put(newSimulations[i],newSimStatus);
 				}else{
-					newHash.put(newSimulations[i],SimulationStatus.newUnknown(newSimulations[i].getScanCount())); // unknown status
+					newHash.put(newSimulations[i],SimulationStatus.newUnknown(newSimulations[i].getJobCount())); // unknown status
 				}
 			}
 		}

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

@@ -1178,8 +1178,8 @@ private DataInfoProvider getDataInfoProvider(VCDocument document, PDEDataContext
      */
     private String generateTestCriteriaReport(TestCaseNew testCase, TestCriteriaNew testCriteria, Simulation testSim, TFGenerateReport.VCDocumentAndSimInfo userSelectedRefSimInfo/*,VCDocument refDoc,VCDocument testDocument*/) {
 
-        if (testSim.getScanCount() != 1) {
-            throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
+        if (testSim.getJobCount() != 1) {
+            throw new RuntimeException("paramater scans and trials are not supported in Math Testing Framework");
         }
         SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(testSim, MathOverrides.ScanIndex.ZERO);
 
@@ -1310,8 +1310,8 @@ private String generateTestCriteriaReport(TestCaseNew testCase, TestCriteriaNew
                             VCDataIdentifier refVcdID = new VCSimulationDataIdentifier(refVCDocumentAndSimInfo.getSimInfo().getAuthoritativeVCSimulationIdentifier(), 0);
                             PDEDataManager refDataManager = (PDEDataManager) getRequestManager().getDataManager(null, refVcdID, refSim.isSpatial());
 
-                            if (refSim.getScanCount() != 1) {
-                                throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
+                            if (refSim.getJobCount() != 1) {
+                                throw new RuntimeException("paramater scans and trials are not supported in Math Testing Framework");
                             }
                             SimulationSymbolTable refSimSymbolTable = new SimulationSymbolTable(refSim, MathOverrides.ScanIndex.ZERO);
 
@@ -1407,8 +1407,8 @@ private String generateTestCriteriaReport(TestCaseNew testCase, TestCriteriaNew
                             }
                         } else if (testCase.getType().equals(TestCaseNew.REGRESSION)) {
                             Simulation refSim = ((ClientDocumentManager) getRequestManager().getDocumentManager()).getSimulation(testCriteria.getRegressionSimInfo());
-                            if (refSim.getScanCount() != 1) {
-                                throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
+                            if (refSim.getJobCount() != 1) {
+                                throw new RuntimeException("paramater scans and trials are not supported in Math Testing Framework");
                             }
                             SimulationSymbolTable refSimSymbolTable = new SimulationSymbolTable(refSim, MathOverrides.ScanIndex.ZERO);
 

vcell-client/src/main/java/cbit/vcell/client/data/ODETimePlotMultipleScansPanel.java

@@ -84,8 +84,11 @@ public PlotPane getPlotPane() {
 private void initialize()  {
 
 	setLayout(new BorderLayout());
-	int scanCount = simulation.getScanCount();
+	int scanCount = simulation.getScanCount_2();
 	int trialCount = simulation.getNumTrials();
+	if (trialCount > 1){
+		throw new RuntimeException("trials are not yet supported in ODETimePlotMultipleScansPanel");
+	}
 
 	plotPane = new PlotPane();
 	plotPane.getPlot2DDataPanel1().setXVarName(xVarColumnName);

vcell-client/src/main/java/cbit/vcell/client/data/SimResultsViewer.java

@@ -173,17 +173,17 @@ private Simulation getSimulation() {
 }
 
 private JLabel label = new JLabel("<html><b>Choose Parameter Values</b></html>");
-private int localScanProgress;
-public void setLocalScanProgress(int localScanProgress) {
-	this.localScanProgress = localScanProgress;
+private int localJobProgress;
+public void setLocalScanProgress(int localJobProgress) {
+	this.localJobProgress = localJobProgress;
 	SwingUtilities.invokeLater(new Runnable() {
 	@Override
 	public void run() {
-		label.setText("<html><b>Choose Parameter Values progress:("+(localScanProgress)+"/"+getSimulation().getScanCount()+")</b></html>");
+		label.setText("<html><b>Choose Parameter Values/Trials progress:("+(localJobProgress)+"/"+getSimulation().getJobCount()+")</b></html>");
 	}});
 }
-public int getLocalScanProgress() {
-	return localScanProgress;
+public int getLocalJobProgress() {
+	return localJobProgress;
 }
 /**
  * Insert the method's description here.
@@ -216,7 +216,7 @@ public void propertyChange(java.beans.PropertyChangeEvent evt) {
 
 
 	// if necessarry, create parameter choices panel and wire it up
-	if (getSimulation().getScanCount() > 1) {
+	if (getSimulation().getScanCount_2() > 1) {
 		JPanel panel = new JPanel();
 		panel.setLayout(new BorderLayout(5, 0));
 		panel.setBorder(BorderFactory.createEtchedBorder());
@@ -321,7 +321,7 @@ public void actionPerformed(ActionEvent e) {
 	// put things together
 	setLayout(new java.awt.BorderLayout());
 	add(getMainViewer(), java.awt.BorderLayout.CENTER);
-	if (getSimulation().getScanCount() > 1) {
+	if (getSimulation().getScanCount_2() > 1) {
 		add(getParamChoicesPanel(), java.awt.BorderLayout.SOUTH);
 	}
 }