From e85e9a8cf5f76c3806116a1e8932339d8e3d9651 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 12 Apr 2012 14:42:40 -0400
Subject: [PATCH] More extensive testing of type of error thrown in
 multi-threaded walker test

-- Unfortunately the result of the multi-threaded test is non-deterministic so run the test 10x times to see if the right expection is always thrown
-- Now prints the stack trace and exception message of the caught exception of the wrong type, if this occurs
---
 .../org/broadinstitute/sting/WalkerTest.java     | 15 +++++++--------
 .../gatk/EngineFeaturesIntegrationTest.java      | 16 ++++++++++------
 2 files changed, 17 insertions(+), 14 deletions(-)

diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java
index 7f5212ba3..6e8689e82 100755
--- a/public/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -26,18 +26,17 @@
 package org.broadinstitute.sting;
 
 import org.apache.commons.lang.StringUtils;
-import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.Tribble;
 import org.broad.tribble.index.Index;
 import org.broad.tribble.index.IndexFactory;
-import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.gatk.CommandLineExecutable;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.testng.Assert;
 import org.testng.annotations.BeforeMethod;
@@ -315,9 +314,9 @@ public class WalkerTest extends BaseTest {
                     // it's the type we expected
                     System.out.println(String.format("  => %s PASSED", name));
                 } else {
-                    e.printStackTrace();
-                    Assert.fail(String.format("Test %s expected exception %s but got %s instead",
-                            name, expectedException, e.getClass()));
+                    e.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()));
                 }
             } 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 192c86fe3..68bd28d7a 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
@@ -86,13 +86,15 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
     // --------------------------------------------------------------------------------
 
     private class EngineErrorHandlingTestProvider extends TestDataProvider {
-        Class expectedException;
-        boolean multiThreaded;
+        final Class expectedException;
+        final boolean multiThreaded;
+        final int iterationsToTest;
 
         public EngineErrorHandlingTestProvider(Class exceptedException, final boolean multiThreaded) {
             super(EngineErrorHandlingTestProvider.class);
             this.expectedException = exceptedException;
             this.multiThreaded = multiThreaded;
+            this.iterationsToTest = multiThreaded ? 10 : 1;
             setName(String.format("Engine error handling: expected %s, is-multithreaded %b", exceptedException, multiThreaded));
         }
     }
@@ -113,9 +115,11 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
     //
     @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);
+        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();
+            WalkerTestSpec spec = new WalkerTestSpec(args, 0, cfg.expectedException);
+            executeTest(cfg.toString(), spec);
+        }
     }
 }
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