From de13f41fc3a78b9b21432b2cb914e047db01bf37 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Fri, 31 Jan 2014 20:25:58 +0800
Subject: [PATCH] One step closer to a proper test-utils artifact. Using the
 maven-jar-plugin to create a test classifer, excluding actual tests, until we
 can properly separate the classes into separate artifacts/modules.

---
 ant-bridge.sh                    |  2 +-
 pom.xml                          | 43 ++++++++++++++++++++++++++-----
 protected/gatk-protected/pom.xml |  4 +--
 public/external-example/pom.xml  |  7 +++--
 public/gatk-framework/pom.xml    | 44 +++-----------------------------
 public/package-tests/pom.xml     | 29 ++++++---------------
 public/queue-framework/pom.xml   | 14 ++--------
 public/sting-utils/pom.xml       | 12 +--------
 8 files changed, 59 insertions(+), 96 deletions(-)

diff --git a/ant-bridge.sh b/ant-bridge.sh
index e9af3e749..07498c8f3 100755
--- a/ant-bridge.sh
+++ b/ant-bridge.sh
@@ -153,6 +153,6 @@ if [ "${unknown_args}" != "" ]; then
 else
     echo "Equivalent maven command"
     echo "${mvn_cmd}${mvn_properties}${post_script}"
-#    sh -c "${mvn_cmd}${mvn_properties}${post_script}"
+    sh -c "${mvn_cmd}${mvn_properties}${post_script}"
 
 fi
diff --git a/pom.xml b/pom.xml
index 2100556ed..5474b5dfc 100644
--- a/pom.xml
+++ b/pom.xml
@@ -33,6 +33,7 @@
         <!-- TODO: Need a better a way to say "don't include hidden" by default -->
         <gatkdocs.include.hidden>-build-timestamp "${maven.build.timestamp}"</gatkdocs.include.hidden>
         <sting.jar.phase>package</sting.jar.phase>
+        <sting.test-utils.jar.phase>none</sting.test-utils.jar.phase>
         <sting.packagecommittests.skipped>true</sting.packagecommittests.skipped>
         <sting.packageunittests.skipped>${sting.packagecommittests.skipped}</sting.packageunittests.skipped>
         <sting.packageintegrationtests.skipped>${sting.packagecommittests.skipped}</sting.packageintegrationtests.skipped>
@@ -275,6 +276,41 @@
                             <id>default-jar</id>
                             <phase>${sting.jar.phase}</phase>
                         </execution>
+                        <execution>
+                            <id>test-utils</id>
+                            <goals>
+                                <goal>jar</goal>
+                            </goals>
+                            <phase>${sting.test-utils-jar.phase}</phase>
+                            <configuration>
+                                <classesDirectory>${project.build.testOutputDirectory}</classesDirectory>
+                                <classifier>test-utils</classifier>
+                                <!--
+                                TODO: Excluding actual tests from tests-utils jar is required because the same test classes
+                                TODO: cannot be in both the test artifact AND the test classes directory.
+
+                                TODO: Otherwise maven throws an [ERROR] java.lang.RuntimeException: Duplicate test set
+
+                                TODO: This is due to AbstractSurefireMojo.scanForTestClasses() adding both scanDirectories() and scanDependencies().
+                                TODO: Pain to debug as exception is three maven invoker levels deep, outer maven, maven-inovker-plugin, then forked tests!
+
+                                TODO: See also: http://maven.apache.org/plugins/maven-jar-plugin/usage.html#The_preferred_way
+
+                                TODO: Then that dependency won't have test classes that will also run from the
+                                TODO: test classes directory during the invoked package test.
+                                -->
+                                <excludes>
+                                    <exclude>**/*UnitTest.class</exclude>
+                                    <exclude>**/*UnitTest$*.class</exclude>
+                                    <exclude>**/*IntegrationTest.class</exclude>
+                                    <exclude>**/*IntegrationTest$*.class</exclude>
+                                    <exclude>**/*PipelineTest.class</exclude>
+                                    <exclude>**/*PipelineTest$*.class</exclude>
+                                    <exclude>**/*LargeScaleTest.class</exclude>
+                                    <exclude>**/*LargeScaleTest.class</exclude>
+                                </excludes>
+                            </configuration>
+                        </execution>
                     </executions>
                 </plugin>
 
@@ -508,9 +544,6 @@
                         </properties>
                     </configuration>
                     <executions>
-                        <!--
-                        TODO: see description of disable.gatk-framework.test.dependency in gatk-framework/pom.xml
-                        -->
                         <execution>
                             <id>package-unittests</id>
                             <goals>
@@ -523,7 +556,6 @@
                                 <skipInvocation>${sting.packageunittests.skipped}</skipInvocation>
                                 <properties>
                                     <unittests.profile.enabled>true</unittests.profile.enabled>
-                                    <disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
                                     <sting.packageunittests.skipped>${sting.packageunittests.skipped}</sting.packageunittests.skipped>
                                 </properties>
                             </configuration>
@@ -541,7 +573,6 @@
                                 <skipInvocation>${sting.packageintegrationtests.skipped}</skipInvocation>
                                 <properties>
                                     <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
-                                    <disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
                                     <sting.packageintegrationtests.skipped>${sting.packageintegrationtests.skipped}</sting.packageintegrationtests.skipped>
                                 </properties>
                             </configuration>
@@ -559,7 +590,6 @@
                                 <skipInvocation>${sting.packagepipelinetests.skipped}</skipInvocation>
                                 <properties>
                                     <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
-                                    <disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
                                     <sting.packagepipelinetests.skipped>${sting.packagepipelinetests.skipped}</sting.packagepipelinetests.skipped>
                                 </properties>
                             </configuration>
@@ -577,7 +607,6 @@
                                 <skipInvocation>${sting.packagelargescaletests.skipped}</skipInvocation>
                                 <properties>
                                     <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
-                                    <disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
                                     <sting.packagelargescaletests.skipped>${sting.packagelargescaletests.skipped}</sting.packagelargescaletests.skipped>
                                 </properties>
                             </configuration>
diff --git a/protected/gatk-protected/pom.xml b/protected/gatk-protected/pom.xml
index d3e50eec9..14774def7 100644
--- a/protected/gatk-protected/pom.xml
+++ b/protected/gatk-protected/pom.xml
@@ -44,7 +44,7 @@
             <groupId>${project.groupId}</groupId>
             <artifactId>sting-utils</artifactId>
             <version>${project.version}</version>
-            <type>test-jar</type>
+            <classifier>test-utils</classifier>
             <scope>test</scope>
         </dependency>
 
@@ -52,7 +52,7 @@
             <groupId>${project.groupId}</groupId>
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
-            <type>test-jar</type>
+            <classifier>test-utils</classifier>
             <scope>test</scope>
         </dependency>
 
diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml
index 5aba7ab26..d51e5a6f5 100644
--- a/public/external-example/pom.xml
+++ b/public/external-example/pom.xml
@@ -41,12 +41,15 @@
         <!--
         Test dependencies are not transitive,
         so must include each explicit test artifact.
+
+        TODO: switch from test-utils classifier to a tests-utils artifact
+        TODO: see also http://maven.apache.org/plugins/maven-jar-plugin/usage.html#The_preferred_way
         -->
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>sting-utils</artifactId>
             <version>${sting.version}</version>
-            <type>test-jar</type>
+            <classifier>test-utils</classifier>
             <scope>test</scope>
         </dependency>
 
@@ -54,7 +57,7 @@
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>gatk-framework</artifactId>
             <version>${sting.version}</version>
-            <type>test-jar</type>
+            <classifier>test-utils</classifier>
             <scope>test</scope>
         </dependency>
 
diff --git a/public/gatk-framework/pom.xml b/public/gatk-framework/pom.xml
index 1443c7037..e8b2f7c71 100644
--- a/public/gatk-framework/pom.xml
+++ b/public/gatk-framework/pom.xml
@@ -16,6 +16,7 @@
     <properties>
         <sting.basedir>${project.basedir}/../..</sting.basedir>
         <sting.packagetests.artifactId>gatk-package</sting.packagetests.artifactId>
+        <sting.test-utils-jar.phase>${sting.jar.phase}</sting.test-utils-jar.phase>
     </properties>
 
     <dependencies>
@@ -29,7 +30,7 @@
             <groupId>${project.groupId}</groupId>
             <artifactId>sting-utils</artifactId>
             <version>${project.version}</version>
-            <type>test-jar</type>
+            <classifier>test-utils</classifier>
             <scope>test</scope>
         </dependency>
 
@@ -77,66 +78,29 @@
                     </execution>
                 </executions>
             </plugin>
+            <!--
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
                 <executions>
-                    <execution>
-                        <goals>
-                            <goal>test-jar</goal>
-                        </goals>
-                    </execution>
                 </executions>
             </plugin>
-            <!--
-            TODO: disable.gatk-framework.test.dependency is required because the the same test classes
-            TODO: cannot be in both the gatk-framework test artifact AND the test classes directory.
-
-            TODO: Otherwise maven throws an [ERROR] java.lang.RuntimeException: Duplicate test set
-
-            TODO: This is due to AbstractSurefireMojo.scanForTestClasses() adding both scanDirectories() and scanDependencies().
-            TODO: Pain to debug as exception is three maven invoker levels deep, outer maven, maven-inovker-plugin, then forked tests!
-
-            TODO: Move BaseTest and other non UnitTests into the sting-utils test jar/artifact.
-
-            TODO: Then that dependency won't have test classes that will also run from the gatk-framework
-            TODO: test classes directory during the invoked package test.
-            -->
+-->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-invoker-plugin</artifactId>
                 <executions>
                     <execution>
                         <id>package-unittests</id>
-                        <configuration>
-                            <properties>
-                                <disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
-                            </properties>
-                        </configuration>
                     </execution>
                     <execution>
                         <id>package-integrationtests</id>
-                        <configuration>
-                            <properties>
-                                <disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
-                            </properties>
-                        </configuration>
                     </execution>
                     <execution>
                         <id>package-largescaletests</id>
-                        <configuration>
-                            <properties>
-                                <disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
-                            </properties>
-                        </configuration>
                     </execution>
                     <execution>
                         <id>package-pipelinetests</id>
-                        <configuration>
-                            <properties>
-                                <disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
-                            </properties>
-                        </configuration>
                     </execution>
                 </executions>
             </plugin>
diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml
index 3483f4da3..f10518d7d 100644
--- a/public/package-tests/pom.xml
+++ b/public/package-tests/pom.xml
@@ -47,6 +47,14 @@
             <artifactId>cofoja</artifactId>
         </dependency>
 
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+            <classifier>test-utils</classifier>
+            <scope>test</scope>
+        </dependency>
+
         <dependency>
             <groupId>org.testng</groupId>
             <artifactId>testng</artifactId>
@@ -65,27 +73,6 @@
     </build>
 
     <profiles>
-        <!--
-        TODO: see description of disable.gatk-framework.test.dependency in gatk-framework/pom.xml
-        -->
-        <profile>
-            <id>include-gatk-framework-tests</id>
-            <activation>
-                <property>
-                    <name>disable.gatk-framework.test.dependency</name>
-                    <value>false</value>
-                </property>
-            </activation>
-            <dependencies>
-                <dependency>
-                    <groupId>${project.groupId}</groupId>
-                    <artifactId>gatk-framework</artifactId>
-                    <version>${project.version}</version>
-                    <type>test-jar</type>
-                    <scope>test</scope>
-                </dependency>
-            </dependencies>
-        </profile>
         <profile>
             <id>unittests</id>
             <activation>
diff --git a/public/queue-framework/pom.xml b/public/queue-framework/pom.xml
index 8ccc7f351..4dd3c188e 100644
--- a/public/queue-framework/pom.xml
+++ b/public/queue-framework/pom.xml
@@ -18,6 +18,7 @@
         <gatk.extensions.sources>${project.build.directory}/generated-sources/gatk-extensions</gatk.extensions.sources>
         <sting.generate-gatk-extensions.skipped>false</sting.generate-gatk-extensions.skipped>
         <sting.packagetests.artifactId>queue-package</sting.packagetests.artifactId>
+        <sting.test-utils-jar.phase>${sting.jar.phase}</sting.test-utils-jar.phase>
     </properties>
 
     <dependencies>
@@ -65,7 +66,7 @@
             <groupId>${project.groupId}</groupId>
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
-            <type>test-jar</type>
+            <classifier>test-utils</classifier>
             <scope>test</scope>
         </dependency>
 
@@ -170,17 +171,6 @@
                     </execution>
                 </executions>
             </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <executions>
-                    <execution>
-                        <goals>
-                            <goal>test-jar</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-invoker-plugin</artifactId>
diff --git a/public/sting-utils/pom.xml b/public/sting-utils/pom.xml
index 7e68cf740..54734efac 100644
--- a/public/sting-utils/pom.xml
+++ b/public/sting-utils/pom.xml
@@ -17,6 +17,7 @@
         <sting.basedir>${project.basedir}/../..</sting.basedir>
         <gsalib.packagedir>org/broadinstitute/sting/utils/R</gsalib.packagedir>
         <gsalib.filename>gsalib.tar.gz</gsalib.filename>
+        <sting.test-utils-jar.phase>${sting.jar.phase}</sting.test-utils-jar.phase>
     </properties>
 
     <dependencies>
@@ -154,17 +155,6 @@
                     </execution>
                 </executions>
             </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <executions>
-                    <execution>
-                        <goals>
-                            <goal>test-jar</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
         </plugins>
     </build>
 </project>