From 639247ab48324d20d094098af8f17a84d2412ff7 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Mon, 17 Mar 2014 05:47:59 -0400
Subject: [PATCH] Updated package-tests classpath, and allowing javac -cp
 <package>.jar. Package tests now hard coding just the gatk-framework tests
 jar, to include ONLY BaseTest, until the exclusions may be debugged. Removing
 cofoja's annotation service from the package jars, to allow javac -cp
 <package>.jar.

---
 pom.xml                      | 12 ++++++++++++
 public/package-tests/pom.xml | 13 ++++++++++++-
 2 files changed, 24 insertions(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index eb3ace24f..5c5c1eb5e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -340,6 +340,18 @@
                                         <exclude>org.broadinstitute.sting:*:tar.bz2:example-resources</exclude>
                                     </excludes>
                                 </artifactSet>
+                                <filters>
+                                    <!--
+                                    NOTE: Removing cofoja's annotation service to allow "javac -cp GenomeAnalysisTK.jar ..." without
+                                    needing an additional -proc:none argument. Using *:* to catch shaded GATK in Queue package.
+                                    -->
+                                    <filter>
+                                        <artifact>*:*</artifact>
+                                        <excludes>
+                                            <exclude>META-INF/services/javax.annotation.processing.Processor</exclude>
+                                        </excludes>
+                                    </filter>
+                                </filters>
                                 <transformers>
                                     <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                         <manifestEntries>
diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml
index f53e7e02e..54bb8c0ac 100644
--- a/public/package-tests/pom.xml
+++ b/public/package-tests/pom.xml
@@ -50,13 +50,15 @@
 
         <!--
         gatk-framework test-jar added for BaseTest
+
+        TODO: Currently the <exclusion> isn't working 100%, so switched to using additionalClasspathElements
+
         TODO: Uncomment below to use the explicitly bad "exclude *" to really test correct packaging,
         TODO: until we can separate BaseTest and other utilities into their own sting-test-utils artifact.
         TODO: We only want the classes in the packaged jars tested, not the classes within the dependency jars too.
         See also:
           http://stackoverflow.com/questions/547805/how-to-exclude-all-transitive-dependencies-of-a-maven-dependency
           http://maven.apache.org/plugins/maven-jar-plugin/usage.html#The_preferred_way
-        -->
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>gatk-framework</artifactId>
@@ -72,6 +74,7 @@
             </exclusions>
 
         </dependency>
+        -->
 
         <dependency>
             <groupId>org.testng</groupId>
@@ -111,6 +114,10 @@
                             <workingDirectory>${sting.packagetests.basedir}</workingDirectory>
                             <classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory>
                             <testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory>
+                            <!-- TODO: Using additionalClasspathElement while debugging exclusion issue above -->
+                            <additionalClasspathElements>
+                                <additionalClasspathElement>${sting.basedir}/public/gatk-framework/target/gatk-framework-${project.version}-tests.jar</additionalClasspathElement>
+                            </additionalClasspathElements>
                         </configuration>
                         <executions>
                             <execution>
@@ -148,6 +155,10 @@
                             <workingDirectory>${sting.packagetests.basedir}</workingDirectory>
                             <classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory>
                             <testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory>
+                            <!-- TODO: Using additionalClasspathElement while debugging exclusion issue above -->
+                            <additionalClasspathElements>
+                                <additionalClasspathElement>${sting.basedir}/public/gatk-framework/target/gatk-framework-${project.version}-tests.jar</additionalClasspathElement>
+                            </additionalClasspathElements>
                         </configuration>
                         <executions>
                             <execution>