From 4ac50c89ad31177fae71d46cf01e7cbfc3c98f64 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 14 Feb 2013 22:02:30 -0500
Subject: [PATCH] Updating TestNG to the latest version

-- changed SkipException constructors that are now private in TestNG
-- Updated build.xml to use the latest testng
-- Added guice dependency to ivy
-- Fixed broken SampleDBUnitTest

The SampleDBUnitTest was only passing before because the map comparison in the old TestNG was broken. It was comparing two DIFFERENT samples and testing for "equals"

GSA-695 #resolve
---
 build.xml                                                      | 2 +-
 ivy.xml                                                        | 3 ++-
 .../broadinstitute/sting/gatk/samples/SampleDBUnitTest.java    | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/build.xml b/build.xml
index 482fe70be..bb02c1ff1 100644
--- a/build.xml
+++ b/build.xml
@@ -1073,7 +1073,7 @@
     <property name="report" value="${build.dir}/report"/>
     <property name="iwww.report.dir" value="${user.home}/private_html/report"/>
     <property name="test.output" value="${dist.dir}/test"/>
-    <property name="testng.jar" value="${lib.dir}/testng-5.14.1.jar"/>
+    <property name="testng.jar" value="${lib.dir}/testng-6.8.jar"/>
 
     <path id="java.test.source.path">
         <dirset dir="${basedir}">
diff --git a/ivy.xml b/ivy.xml
index 13ecfa2d2..4bd6ad7b8 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -84,9 +84,10 @@
         <dependency org="org.scala-lang" name="scala-library" rev="2.9.2"/>
 
         <!-- testing and evaluation dependencies -->
-        <dependency org="org.testng" name="testng" rev="5.14.1"/>
+        <dependency org="org.testng" name="testng" rev="6.8"/>
         <dependency org="org.uncommons" name="reportng" rev="1.1.2"/>
         <dependency org="com.google.caliper" name="caliper" rev="0.5-rc1"/>
+		<dependency org="com.google.inject" name="guice" rev="3.0"/>
 
         <!-- Contracts for Java and dependencies -->
         <dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-r139"/>
diff --git a/public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java
index a4e5b6d78..295b31203 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java
@@ -60,7 +60,7 @@ public class SampleDBUnitTest extends BaseTest {
 
     private static final Set<Sample> testPEDFamilyF3 = new HashSet<Sample>(Arrays.asList(
             new Sample("s1", "fam3", "d1", "m1", Gender.FEMALE, Affection.AFFECTED),
-            new Sample("d1", "fam3", null, null, Gender.FEMALE, Affection.UNKNOWN),
+            new Sample("d1", "fam3", null, null, Gender.MALE, Affection.UNKNOWN),
             new Sample("m1", "fam3", null, null, Gender.FEMALE, Affection.UNKNOWN)
             ));