Update task cancellation.

broadinstitute · Aug 10, 2021 · a3b36b1 · a3b36b1
1 parent 5e1d98f
commit a3b36b1
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Showing 2 changed files with 1 addition and 5 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/runtime/AsynchronousStreamWriter.java b/src/main/java/org/broadinstitute/hellbender/utils/runtime/AsynchronousStreamWriter.java
@@ -106,7 +106,7 @@ public Future<Integer> waitForPreviousBatchCompletion() {
      */
     public boolean terminate() {
         boolean isCancelled = true;
-        if (previousBatch != null) {
+        if (previousBatch != null && !previousBatch.isDone()) {
             logger.warn("Cancelling outstanding asynchronous writing");
             isCancelled = previousBatch.cancel(true);
         }

diff --git a/...ava/org/broadinstitute/hellbender/utils/python/StreamingPythonScriptExecutorUnitTest.java b/...ava/org/broadinstitute/hellbender/utils/python/StreamingPythonScriptExecutorUnitTest.java
@@ -261,8 +261,6 @@ public void testRaiseAsynchronousPythonException(final PythonScriptExecutor.Pyth
         try {
             streamingPythonExecutor.sendAsynchronousCommand("raise Exception" + NL);
             streamingPythonExecutor.waitForAck();
-        } catch (PythonScriptExecutorException e) {
-            throw e;
         } finally {
             streamingPythonExecutor.terminate();
             Assert.assertFalse(streamingPythonExecutor.getProcess().isAlive());
@@ -287,8 +285,6 @@ public void testRaiseAsynchronousBatchWritePythonException(final PythonScriptExe
                     BATCH_SIZE);
             streamingPythonExecutor.startBatchWrite(batchCommand, batchList);
             streamingPythonExecutor.waitForPreviousBatchCompletion();
-        } catch (PythonScriptExecutorException e) {
-            throw e;
         } finally {
             streamingPythonExecutor.terminate();
             Assert.assertFalse(streamingPythonExecutor.getProcess().isAlive());