Fixed a number of issues, all revolving around VCell locking up under the right (wrong) conditions

debug_log4j2.xml

@@ -10,13 +10,13 @@
     </Appenders>
 
     <Loggers>
-        <Logger name="org.vcell" level="info" additivity="false">
+        <Logger name="org.vcell" level="debug" additivity="false">
             <AppenderRef ref="console"/>
         </Logger>
-        <Logger name="cbit" level="info" additivity="false">
+        <Logger name="cbit" level="debug" additivity="false">
             <AppenderRef ref="console"/>
         </Logger>
-        <Logger name="cbit" level="info" additivity="false">
+        <Logger name="cbit" level="debug" additivity="false">
             <AppenderRef ref="console"/>
         </Logger>
         <Logger name="org.apache.http" level="info" additivity="false">
@@ -28,7 +28,7 @@
         <Logger name = "io.jhdf" level="warn" additivity="false">
             <AppenderRef ref="console"/>
         </Logger>
-        <Root level="info">
+        <Root level="debug">
             <AppenderRef ref="console"/>
         </Root>
     </Loggers>

vcell-admin/src/test/java/cbit/vcell/client/ClientTaskDispatcherTest.java

@@ -10,6 +10,9 @@
 
 import java.awt.*;
 import java.util.Hashtable;
+import java.util.concurrent.Future;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.TimeoutException;
 
 import static cbit.vcell.client.task.AsynchClientTask.*;
 
@@ -40,6 +43,37 @@ public void sbNotLast( ) {
 			test(TASKTYPE_NONSWING_BLOCKING,TASKTYPE_NONSWING_BLOCKING, TASKTYPE_SWING_NONBLOCKING, TASKTYPE_NONSWING_BLOCKING);
 		});
 	}
+
+	@Test void blockingCheck(){
+		AsynchClientTask collatzConjecture = new AsynchClientTask(
+				"Collatz Conjecture", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
+
+			@Override
+			public void run(Hashtable<String, Object> hashTable) throws Exception {
+				for (long startingNum = 1; startingNum < Long.MAX_VALUE; startingNum++) {
+					long currentNum = startingNum;
+					long counter = 0;
+					while(true){
+						if (currentNum == 1 || currentNum == 2 || currentNum == 4) {
+							// We won't waste storage space
+							System.out.print(counter + ", ");
+							break;
+						}
+						counter++;
+						if (currentNum % 2 == 0) currentNum /= 2; // Even case
+						if (currentNum %2 == 1) currentNum = (3 * currentNum) + 1;
+					}
+				}
+			}
+		} ;
+		Assertions.assertThrows(TimeoutException.class, () -> {
+			Hashtable<String, Object> hashTable = new Hashtable<>();
+			Future<?> terribleFuture = ClientTaskDispatcher.dispatchWithFuture(null, hashTable,
+					new AsynchClientTask[]{collatzConjecture});
+			terribleFuture.get(2, TimeUnit.SECONDS); // Not expensive but significant timeout
+		});
+
+	}
 
 	private AsynchClientTask[] create(int ... types)  {
 		AsynchClientTask[] rval = new AsynchClientTask[types.length];

vcell-apiclient/src/main/java/org/vcell/api/client/VCellApiClient.java

@@ -61,6 +61,12 @@
 public class VCellApiClient implements AutoCloseable {
 
 	private static final Logger lg = LogManager.getLogger(VCellApiClient.class);
+	private static final boolean activeLogLevelIsSensitiveEnough;
+
+	static {
+		activeLogLevelIsSensitiveEnough = lg.isTraceEnabled();
+	}
+
 	private final HttpHost httpHost;
 	private final String pathPrefix_v0;
 	private final String clientID;
@@ -202,13 +208,13 @@ public SimulationTaskRepresentation[] getSimTasks(SimTasksQuerySpec simTasksQuer
 		HttpGet httpget = new HttpGet(getApiUrlPrefix() + "/simtask?" + simTasksQuerySpec.getQueryString());
 		httpget.addHeader("Authorization","Bearer "+httpClientContext.getUserToken(String.class));
 
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("Executing request to retrieve simulation tasks " + httpget.getRequestLine());
 		}
 
 		String responseBody = httpclient.execute(httpget, new VCellStringResponseHandler("getSimTasks()", httpget), httpClientContext);
 		String simTasksJson = responseBody;
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("returned: "+toStringTruncated(simTasksJson));
 		}
 
@@ -231,13 +237,13 @@ public BiomodelRepresentation[] getBioModels(BioModelsQuerySpec bioModelsQuerySp
 		HttpGet httpget = new HttpGet(getApiUrlPrefix()+"/biomodel?"+bioModelsQuerySpec.getQueryString());
 		httpget.addHeader("Authorization","Bearer "+httpClientContext.getUserToken(String.class));
 
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("Executing request to retrieve biomodels " + httpget.getRequestLine());
 		}
 
 		String responseBody = httpclient.execute(httpget, new VCellStringResponseHandler("getBioModels()", httpget), httpClientContext);
 		String bimodelsJson = responseBody;
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("returned: "+toStringTruncated(bimodelsJson));
 		}
 
@@ -251,13 +257,13 @@ public EventWrapper[] getEvents(long beginTimestamp) throws IOException {
 		HttpGet httpget = new HttpGet(getApiUrlPrefix()+"/events?beginTimestamp="+beginTimestamp);
 		httpget.addHeader("Authorization","Bearer "+httpClientContext.getUserToken(String.class));
 
-		if (lg.isInfoEnabled()) {
+		if (lg.isTraceEnabled()) {
 			lg.info("Executing request to retrieve user events " + httpget.getRequestLine());
 		}
 
 		String responseBody = httpclient.execute(httpget, new VCellStringResponseHandler("getEvents()", httpget), httpClientContext);
 		String eventWrappersJson = responseBody;
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("returned: "+toStringTruncated(eventWrappersJson));
 		}
 
@@ -271,13 +277,13 @@ public BiomodelRepresentation getBioModel(String bmId) throws IOException {
 		HttpGet httpget = new HttpGet(getApiUrlPrefix()+"/biomodel/"+bmId);
 		httpget.addHeader("Authorization","Bearer "+httpClientContext.getUserToken(String.class));
 
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("Executing request to retrieve biomodel " + httpget.getRequestLine());
 		}
 
 		String responseBody = httpclient.execute(httpget, new VCellStringResponseHandler("getBioModel()", httpget), httpClientContext);
 		String bimodelsJson = responseBody;
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("returned: "+toStringTruncated(bimodelsJson));
 		}
 
@@ -291,7 +297,7 @@ public String getBioModelVCML(String bmId) throws IOException {
 		HttpGet httpget = new HttpGet(getApiUrlPrefix()+"/biomodel/"+bmId+"/biomodel.vcml");
 		httpget.addHeader("Authorization","Bearer "+httpClientContext.getUserToken(String.class));
 
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("Executing request to retrieve biomodel " + httpget.getRequestLine());
 		}
 
@@ -306,13 +312,13 @@ public SimulationRepresentation getSimulation(String bmId, String simKey) throws
 		HttpGet httpget = new HttpGet(getApiUrlPrefix()+"/biomodel/"+bmId+"/simulation/"+simKey);
 		httpget.addHeader("Authorization","Bearer "+httpClientContext.getUserToken(String.class));
 
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("Executing request to retrieve simulation " + httpget.getRequestLine());
 		}
 
 		String responseBody = httpclient.execute(httpget, new VCellStringResponseHandler("getSimulation()", httpget), httpClientContext);
 		String simulationJson = responseBody;
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("returned: "+toStringTruncated(simulationJson));
 		}
 
@@ -326,12 +332,12 @@ public String getOptRunJson(String optimizationId,boolean bStop) throws IOExcept
 		HttpGet httpget = new HttpGet(getApiUrlPrefix()+"/optimization/"+optimizationId+"?bStop="+bStop);
 		httpget.addHeader("Authorization","Bearer "+httpClientContext.getUserToken(String.class));
 
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("Executing request to retrieve optimization run " + httpget.getRequestLine());
 		}
 
 		String responseBody = httpclient.execute(httpget, new VCellStringResponseHandler("getOptRunJson()", httpget), httpClientContext);
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("returned: "+toStringTruncated(responseBody));
 		}
 		return responseBody;
@@ -429,7 +435,7 @@ public SimulationTaskRepresentation[] startSimulation(String bmId, String simKey
 		HttpPost httppost = new HttpPost(getApiUrlPrefix()+"/biomodel/"+bmId+"/simulation/"+simKey+"/startSimulation");
 		httppost.addHeader("Authorization", "Bearer "+httpClientContext.getUserToken(String.class));
 
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("Executing request to retrieve simulation " + httppost.getRequestLine());
 		}
 
@@ -453,13 +459,13 @@ public SimulationTaskRepresentation[] stopSimulation(String bmId, String simKey)
 		HttpPost httppost = new HttpPost(getApiUrlPrefix()+"/biomodel/"+bmId+"/simulation/"+simKey+"/stopSimulation");
 		httppost.addHeader("Authorization", "Bearer "+httpClientContext.getUserToken(String.class));
 
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("Executing request to retrieve simulation " + httppost.getRequestLine());
 		}
 
 		String responseBody = httpclient.execute(httppost, new VCellStringResponseHandler("stopSimulation()", httppost), httpClientContext);
 		String simTaskReps = responseBody;
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("returned: "+toStringTruncated(simTaskReps));
 		}
 
@@ -826,7 +832,7 @@ public String getServerSoftwareVersion() throws ClientProtocolException, IOExcep
 
 		HttpGet httpget = new HttpGet(getApiUrlPrefix()+"/swversion");
 
-		if (lg.isInfoEnabled()) {
+		if (activeLogLevelIsSensitiveEnough) {
 			lg.info("Executing request to retrieve server software version " + httpget.getRequestLine());
 		}
 

vcell-client/src/main/java/cbit/gui/graph/gui/CartoonTool.java

@@ -48,11 +48,13 @@
 import cbit.gui.graph.actions.CartoonToolSaveAsImageActions;
 import cbit.gui.graph.actions.GraphViewAction;
 import cbit.gui.graph.groups.VCGroupManager;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.vcell.util.gui.GeneralGuiUtils;
 
 public abstract class CartoonTool implements GraphView, MouseListener,
 		MouseMotionListener, ActionListener, KeyListener {
-
+	private static final Logger lg = LogManager.getLogger(CartoonTool.class);
 	public static final boolean GROUPS_ARE_ENABLED = false;
 
 	private GraphPane graphPane = null;
@@ -359,7 +361,7 @@ public final void updateButtonGroup(ButtonGroup buttonGroup,
 				return;
 			}
 		}
-		System.out.println("ERROR: button with actionCommand " + actionCommand + " not found");
+        lg.warn("ERROR: button with actionCommand {} not found", actionCommand);
 		return;
 	}