Fixed threading locations

virtualcell · Jan 30, 2025 · 60079af · 60079af
1 parent 69d66f2
commit 60079af
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Showing 3 changed files with 25 additions and 25 deletions.
diff --git a/vcell-cli/src/main/java/org/vcell/cli/commands/TimeLimitedCommand.java b/vcell-cli/src/main/java/org/vcell/cli/commands/TimeLimitedCommand.java
@@ -24,7 +24,7 @@ public abstract class TimeLimitedCommand implements Callable<Integer> {
      * Perform the desired command
      * @return return code of the command
      */
-    protected abstract Integer executeCommand();
+    protected abstract Integer executeCommand() throws Exception;
 
     protected long getTimeout() {return this.timeout;}
 

diff --git a/vcell-cli/src/main/java/org/vcell/cli/commands/execution/ExecuteOmexCommand.java b/vcell-cli/src/main/java/org/vcell/cli/commands/execution/ExecuteOmexCommand.java
@@ -64,27 +64,10 @@ public class ExecuteOmexCommand extends ExecutionBasedCommand {
     @Override
     public Integer call() throws Exception {
         if (!this.executionShouldContinue()) return 0;
-        CLIRecordable cliTracer = new CliTracer();
         ExecutorService executor = Executors.newSingleThreadExecutor();
         Future<Integer> futureResult = executor.submit(this::executeCommand);
         long startTime_ms = System.currentTimeMillis();
-
         try {
-            File tmpDirExec = Files.createTempDirectory("VCell_CLI_" + Long.toHexString(new Date().getTime())).toFile();
-            File tmpDirConv = Files.createTempDirectory("VCell_CLI_" + Long.toHexString(new Date().getTime())).toFile();
-            Tracer.clearTraceEvents();
-
-            startTime_ms = System.currentTimeMillis();
-            boolean needsNoConversion = !this.inputFilePath.getName().endsWith(".vcml");
-            File inFile = needsNoConversion ? this.inputFilePath : ExecuteOmexCommand.performInputFileConversion(this.inputFilePath, tmpDirConv);
-
-            if (inFile != null)
-                ExecuteImpl.singleMode(inFile, tmpDirExec, cliTracer,
-                        this.bKeepTempFiles, this.bExactMatchOnly, this.bEncapsulateOutput, this.bSmallMeshOverride);
-
-
-            FileUtils.copyDirectoryContents(tmpDirExec, this.outputFilePath, true, null);
-            Integer ignored;
             try { // This try is explicitly for timeouts
                 if (this.getTimeout() == 0) {
                     futureResult.get();
@@ -94,6 +77,7 @@ public Integer call() throws Exception {
             } catch (TimeoutException e) {
                 // In the event of timeout, we want to log like we're talking from the command in question
                 // We'll leave an in-log reference to the actual class and method
+                futureResult.cancel(true);
                 String debugSnipIt = logger.getLevel().isInRange(Level.TRACE, Level.DEBUG) ? "(TimeLimitedCommand::call) " : "";
                 String msg = String.format("%sTask too too long, exceeding %s %s.", debugSnipIt, this.getTimeout(), this.getTimeUnit().toString().toLowerCase());
                 LogManager.getLogger(this.getClass()).error(msg);
@@ -171,8 +155,23 @@ protected boolean executionShouldContinue() {
      * @return return code of the command
      */
     @Override
-    protected Integer executeCommand() {
-        return 0;
+    protected Integer executeCommand() throws Exception {
+            File tmpDirExec = Files.createTempDirectory("VCell_CLI_" + Long.toHexString(new Date().getTime())).toFile();
+            File tmpDirConv = Files.createTempDirectory("VCell_CLI_" + Long.toHexString(new Date().getTime())).toFile();
+            Tracer.clearTraceEvents();
+
+            boolean needsNoConversion = !this.inputFilePath.getName().endsWith(".vcml");
+            File inFile = needsNoConversion ? this.inputFilePath : ExecuteOmexCommand.performInputFileConversion(this.inputFilePath, tmpDirConv);
+
+            CLIRecordable cliTracer = new CliTracer();
+            if (inFile != null)
+                ExecuteImpl.singleMode(inFile, tmpDirExec, cliTracer,
+                        this.bKeepTempFiles, this.bExactMatchOnly, this.bEncapsulateOutput, this.bSmallMeshOverride);
+
+
+            FileUtils.copyDirectoryContents(tmpDirExec, this.outputFilePath, true, null);
+            return 0;
+
     }
 
     private static File performInputFileConversion(File inputFile, File outputDir) {

diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteImpl.java b/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteImpl.java
@@ -4,6 +4,7 @@
 import cbit.vcell.solver.ode.ODESolverResultSet;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.jlibsedml.XMLException;
 import org.vcell.cli.messaging.CLIRecordable;
 import org.vcell.cli.exceptions.ExecutionException;
 import org.vcell.cli.run.hdf5.BiosimulationsHdfWriterException;
@@ -118,14 +119,14 @@ private static void runSingleExecOmex(File inputFile, File outputDir, CLIRecorda
 
     public static void singleMode(File inputFile, File rootOutputDir, CLIRecordable cliLogger,
                                   boolean bKeepTempFiles, boolean bExactMatchOnly, boolean bEncapsulateOutput,
-                                  boolean bSmallMeshOverride) throws Exception{
+                                  boolean bSmallMeshOverride) throws IOException, BiosimulationsHdfWriterException, ExecutionException, XMLException {
         ExecuteImpl.singleMode(inputFile, rootOutputDir, cliLogger, bKeepTempFiles, bExactMatchOnly,
                 bEncapsulateOutput, bSmallMeshOverride, false);
     }
 
     public static void singleMode(File inputFile, File rootOutputDir, CLIRecordable cliLogger,
             boolean bKeepTempFiles, boolean bExactMatchOnly, boolean bEncapsulateOutput,
-          boolean bSmallMeshOverride, boolean bBioSimMode) throws Exception {
+          boolean bSmallMeshOverride, boolean bBioSimMode) throws IOException, BiosimulationsHdfWriterException, ExecutionException, XMLException {
         // Build statuses
         String bioModelBaseName = FileUtils.getBaseName(inputFile.getName()); // bioModelBaseName = input file without the path
         String outputBaseDir = rootOutputDir.getAbsolutePath(); 
@@ -209,13 +210,13 @@ public static void singleExecVcml(File vcmlFile, File outputDir, CLIRecordable c
             somethingFailed = somethingDidFail();
         } catch (ExpressionException e) {
             Tracer.failure(e, "ExpressionException while processing VCML " + vcmlFile.getName());
-            logger.error("InterruptedException while creating results CSV from VCML " + vcmlFile.getName(), e);
+            logger.error("ExpressionException while creating results CSV from VCML " + vcmlFile.getName(), e);
             somethingFailed = somethingDidFail();
-        } catch (InterruptedException e) {
+        } /*catch (InterruptedException e) {
             Tracer.failure(e, "InterruptedException while processing VCML " + vcmlFile.getName());
             logger.error("InterruptedException while transposing CSV from VCML " + vcmlFile.getName(), e);
             somethingFailed = somethingDidFail();
-        } catch (Exception e) {
+        }*/ catch (Exception e) {
             Tracer.failure(e, "Unexpected exception while processing VCML " + vcmlFile.getName());
             String errorMessage = String.format("Unexpected exception while transposing CSV from VCML <%s>\n%s", vcmlFile.getName(), e.toString());
             logger.error(errorMessage, e);