Merged bug fix from Stable into Unstable

public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java

@@ -47,7 +47,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
     /**
      * An exception that's occurred in this traversal.  If null, no exception has occurred.
      */
-    private Throwable error = null;
+    private RuntimeException error = null;
 
     /**
      * Queue of incoming shards.
@@ -345,22 +345,22 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
         return error != null;
     }
 
-    private synchronized StingException getTraversalError() {
+    private synchronized RuntimeException getTraversalError() {
         if(!hasTraversalErrorOccurred())
             throw new ReviewedStingException("User has attempted to retrieve a traversal error when none exists");
-
+        return error;
-        // If the error is already a StingException, pass it along as is.  Otherwise, wrap it.
-        if(error instanceof StingException)
-            return (StingException)error;
-        else
-            return new ReviewedStingException("An error occurred during the traversal.",error);
     }
 
     /**
      * Allows other threads to notify of an error during traversal.
      */
     protected synchronized void notifyOfTraversalError(Throwable error) {
-        this.error = error;    
+        // If the error is already a Runtime, pass it along as is.  Otherwise, wrap it.
+        if (error instanceof RuntimeException)
+            this.error = (RuntimeException)error;
+        else
+            this.error = new ReviewedStingException("An error occurred during the traversal.", error);
+
     }
 
 

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowingWalker.java

@@ -0,0 +1,72 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.qc;
+
+import org.broadinstitute.sting.commandline.Input;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.gatk.walkers.TreeReducible;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+
+/**
+ * a walker that simply throws errors.  Allows us to test that the engine is behaving as expected with error handling
+ */
+public class ErrorThrowingWalker extends RodWalker<Integer,Integer> implements TreeReducible<Integer> {
+    @Input(fullName="exception", shortName = "E", doc="Java class of exception to throw", required=true)
+    public String exceptionToThrow;
+
+    //
+    // Template code to allow us to build the walker, doesn't actually do anything
+    //
+    @Override
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( exceptionToThrow.equals("UserException") ) {
+            throw new UserException("UserException");
+        } else if ( exceptionToThrow.equals("NullPointerException") ) {
+            throw new NullPointerException();
+        } else if ( exceptionToThrow.equals("ReviewedStingException") ) {
+            throw new ReviewedStingException("ReviewedStingException");
+        } else {
+            throw new UserException.BadArgumentValue("exception", "exception isn't a recognized value " + exceptionToThrow);
+        }
+    }
+
+    @Override
+    public Integer reduceInit() {
+        return 0;
+    }
+
+    @Override
+    public Integer reduce(Integer value, Integer sum) {
+        return value + sum;
+    }
+
+    public Integer treeReduce(final Integer lhs, final Integer rhs) {
+        return lhs + rhs;
+    }
+}

public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java

@@ -25,9 +25,13 @@
 package org.broadinstitute.sting.gatk;
 
 import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
+import java.util.Arrays;
+
 /**
  *
  */
@@ -73,4 +77,45 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
     @Test() private void testMissingInterval() {
         testMissingFile("missing interval", "-T UnifiedGenotyper -L missing.interval_list -I " + b37GoodBAM);
     }
+
+
+    // --------------------------------------------------------------------------------
+    //
+    // Test that our exceptions are coming back as we expect
+    //
+    // --------------------------------------------------------------------------------
+
+    private class EngineErrorHandlingTestProvider extends TestDataProvider {
+        Class expectedException;
+        boolean multiThreaded;
+
+        public EngineErrorHandlingTestProvider(Class exceptedException, final boolean multiThreaded) {
+            super(EngineErrorHandlingTestProvider.class);
+            this.expectedException = exceptedException;
+            this.multiThreaded = multiThreaded;
+            setName(String.format("Engine error handling: expected %s, is-multithreaded %b", exceptedException, multiThreaded));
+        }
+    }
+
+    @DataProvider(name = "EngineErrorHandlingTestProvider")
+    public Object[][] makeEngineErrorHandlingTestProvider() {
+        for ( final boolean multiThreaded : Arrays.asList(true, false)) {
+            new EngineErrorHandlingTestProvider(NullPointerException.class, multiThreaded);
+            new EngineErrorHandlingTestProvider(UserException.class, multiThreaded);
+            new EngineErrorHandlingTestProvider(ReviewedStingException.class, multiThreaded);
+        }
+
+        return EngineErrorHandlingTestProvider.getTests(EngineErrorHandlingTestProvider.class);
+    }
+
+    //
+    // Loop over errors to throw, make sure they are the errors we get back from the engine, regardless of NT type
+    //
+    @Test(dataProvider = "EngineErrorHandlingTestProvider")
+    public void testEngineErrorHandlingTestProvider(EngineErrorHandlingTestProvider cfg) {
+        final String root = "-T ErrorThrowing -R " + b37KGReference;
+        final String args = root + (cfg.multiThreaded ? " -nt 2" : "") + " -E " + cfg.expectedException.getSimpleName();
+        WalkerTestSpec spec = new WalkerTestSpec(args, 0, cfg.expectedException);
+        executeTest(cfg.toString(), spec);
+    }
 }