From 9242f63a4d1185ef0a146b7fb354d2450752390b Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Wed, 25 Jul 2012 22:11:10 -0400
Subject: [PATCH] On the way to really sorting out HMS error handling

-- Better error message when a traveral error occurs (a real bug)
-- EngineFeaturesIntegrationTest runs the multi-threaded error testing routines 50x times
-- A bit of cleanup in WalkerTest
---
 .../executive/HierarchicalMicroScheduler.java  |  2 +-
 .../org/broadinstitute/sting/WalkerTest.java   | 18 ++++++++++--------
 .../gatk/EngineFeaturesIntegrationTest.java    |  4 ++--
 3 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
index 1fe2b840f..3dc36dda2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
@@ -358,7 +358,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
         if (error instanceof RuntimeException)
             this.error = (RuntimeException)error;
         else
-            this.error = new ReviewedStingException("An error occurred during the traversal.", error);
+            this.error = new ReviewedStingException("An error occurred during the traversal.  Message=" + error.getMessage(), error);
 
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java
index a997385d6..7e38c00f3 100755
--- a/public/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -169,7 +169,6 @@ public class WalkerTest extends BaseTest {
         Class expectedException = null;
         boolean includeImplicitArgs = true;
         boolean includeShadowBCF = true;
-        boolean repairHeader = false;
 
         // the default output path for the integration test
         private File outputFileLocation = null;
@@ -211,8 +210,6 @@ public class WalkerTest extends BaseTest {
                         String.format(" -et %s -K %s ", GATKRunReport.PhoneHomeOption.NO_ET, gatkKeyFile));
                 if ( includeShadowBCF && GENERATE_SHADOW_BCF )
                     args = args + " --generateShadowBCF ";
-                if ( repairHeader )
-                    args = args + " --repairVCFHeader public/data/vcfHeaderForRepairs.vcf ";
             }
 
             return args;
@@ -224,7 +221,6 @@ public class WalkerTest extends BaseTest {
          * which will ultimately blow up...
          */
         public void disableShadowBCF() { this.includeShadowBCF = false; }
-        public void repairHeaders() { this.repairHeader = true; }
         public void setOutputFileLocation(File outputFileLocation) {
             this.outputFileLocation = outputFileLocation;
         }        
@@ -367,10 +363,16 @@ public class WalkerTest extends BaseTest {
                     // it's the type we expected
                     //System.out.println(String.format("  => %s PASSED", name));
                 } else {
-                    if ( e.getCause() != null )
-                        e.getCause().printStackTrace(System.out);  // must print to stdout to see the message
-                    Assert.fail(String.format("Test %s expected exception %s but instead got %s with error message %s",
-                            name, expectedException, e.getClass(), e.getMessage()));
+                    final String message = String.format("Test %s expected exception %s but instead got %s with error message %s",
+                            name, expectedException, e.getClass(), e.getMessage());
+                    if ( e.getCause() != null ) {
+                        final ByteArrayOutputStream baos = new ByteArrayOutputStream();
+                        final PrintStream ps = new PrintStream(baos);
+                        e.getCause().printStackTrace(ps);
+                        BaseTest.log(message);
+                        BaseTest.log(baos.toString());
+                    }
+                    Assert.fail(message);
                 }
             } else {
                 // we didn't expect an exception but we got one :-(
diff --git a/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
index 01af55ca3..f1acfda20 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
@@ -90,7 +90,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
             super(EngineErrorHandlingTestProvider.class);
             this.expectedException = exceptedException;
             this.multiThreaded = multiThreaded;
-            this.iterationsToTest = multiThreaded ? 10 : 1;
+            this.iterationsToTest = multiThreaded ? 50 : 1;
             setName(String.format("Engine error handling: expected %s, is-multithreaded %b", exceptedException, multiThreaded));
         }
     }
@@ -110,7 +110,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
     // 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) {
+    public void testEngineErrorHandlingTestProvider(final EngineErrorHandlingTestProvider cfg) {
         for ( int i = 0; i < cfg.iterationsToTest; i++ ) {
             final String root = "-T ErrorThrowing -R " + b37KGReference;
             final String args = root + (cfg.multiThreaded ? " -nt 2" : "") + " -E " + cfg.expectedException.getSimpleName();