Added a set of serial tests to gatk/queue packages, which runs all tests under their package in one TestNG execution.

New properties to disable regenerating example resources artifact when each parallel test runs under packagetest.
Moved collection of packagetest parameters from shell scripts into maven profiles.
Fixed necessity of test-utils jar by removing incorrect dependenciesToScan element during packagetests.
When building picard libraries, run clean first.
Fixed tools jar dependency in picard pom.
Integration tests properly use the ant-bridge.sh test.debug.port variable, like unit tests.

ant-bridge.sh

@@ -33,6 +33,7 @@ for arg in "${@}" ; do
 
         elif [[ "${property_name}" == "test.debug.port" ]] ; then
             mvn_properties="${mvn_properties} -Dmaven.surefire.debug=\"-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${property_value}\""
+            mvn_properties="${mvn_properties} -Dmaven.failsafe.debug=\"-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${property_value}\""
 
         elif [[ "${property_name}" == "test.default.maxmemory" ]] ; then
             mvn_properties="${mvn_properties} -Dtest.maxmemory=${property_value}"
@@ -98,18 +99,16 @@ for arg in "${@}" ; do
         elif [[ "${arg}" == "gatkfull.binary.release.tests" ]] ; then
             local_repo="sitetemprepo"
             mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
-            mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo} -Dmaven.javadoc.skip=true"
+            mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo}"
-            mvn_args="${mvn_args} -Dsting.generate-gatk-extensions.skipped=true"
+            mvn_args="${mvn_args} -Dsting.packagetests.enabled=true"
-            mvn_args="${mvn_args} -Dsting.jar.phase=none -Dsting.unpack.phase=none -Dsting.shade.phase=none"
             mvn_args="${mvn_args} -Dsting.packagecommittests.skipped=false"
 
         # TODO: This runs only the pipeline tests (full, non-dry run), but not the commit tests for Queue.
         elif [[ "${arg}" == "queuefull.binary.release.tests" ]] ; then
             local_repo="sitetemprepo"
             mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
-            mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo} -Dmaven.javadoc.skip=true"
+            mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo}"
-            mvn_args="${mvn_args} -Dsting.generate-gatk-extensions.skipped=true"
+            mvn_args="${mvn_args} -Dsting.packagetests.enabled=true"
-            mvn_args="${mvn_args} -Dsting.jar.phase=none -Dsting.unpack.phase=none -Dsting.shade.phase=none"
             mvn_args="${mvn_args} -Dsting.packagepipelinetests.skipped=false"
             mvn_args="${mvn_args} -Dsting.pipelinetests.run=true"
 

pom.xml

@@ -32,13 +32,37 @@
         <resource.bundle.skip>false</resource.bundle.skip>
         <!-- TODO: Need a better a way to say "don't include hidden" by default -->
         <gatkdocs.include.hidden>-build-timestamp "${maven.build.timestamp}"</gatkdocs.include.hidden>
+
+        <!--
+        Phases of the build that may be disabled to speed up compilation.
+        -->
         <sting.jar.phase>package</sting.jar.phase>
-        <sting.test-utils.jar.phase>none</sting.test-utils.jar.phase>
+        <sting.generate-resources.phase>generate-resources</sting.generate-resources.phase>
+        <sting.process-resources.phase>process-resources</sting.process-resources.phase>
+        <sting.process-test-resources.phase>process-test-resources</sting.process-test-resources.phase>
+
+        <!--
+        Package tests ensure the consistency of the packaged / shaded jars.
+        It runs the tests where the monolithic jar is the only dependency on the classpath.
+        -->
         <sting.packagecommittests.skipped>true</sting.packagecommittests.skipped>
         <sting.packageunittests.skipped>${sting.packagecommittests.skipped}</sting.packageunittests.skipped>
         <sting.packageintegrationtests.skipped>${sting.packagecommittests.skipped}</sting.packageintegrationtests.skipped>
         <sting.packagepipelinetests.skipped>${sting.packagecommittests.skipped}</sting.packagepipelinetests.skipped>
         <sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
+
+        <!--
+        Serial tests use the test jars to run tests, such that all tests are run from a single TestNG invocation.
+        This is different that the invoker, that runs the test classes from the filesystem, but pointing at the packaged JAR files.
+        TODO: Currently, all tests run within each package, since packages already collect dependencies for shading an uber jar.
+        TODO: Should there be another level up of tests, possibly running "all tests" via this aggregator level?
+        TODO: If that require the aggregator to be dependent on the child dependencies, perhaps a better approach might be another monolithic test project.
+        -->
+        <sting.serialcommittests.skipped>true</sting.serialcommittests.skipped>
+        <sting.serialunittests.skipped>${sting.serialcommittests.skipped}</sting.serialunittests.skipped>
+        <sting.serialintegrationtests.skipped>${sting.serialcommittests.skipped}</sting.serialintegrationtests.skipped>
+        <sting.serialpipelinetests.skipped>${sting.serialcommittests.skipped}</sting.serialpipelinetests.skipped>
+        <sting.seriallargescaletests.skipped>true</sting.seriallargescaletests.skipped>
     </properties>
 
     <dependencies>
@@ -109,6 +133,20 @@
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-resources-plugin</artifactId>
                     <executions>
+                        <execution>
+                            <id>default-resources</id>
+                            <goals>
+                                <goal>resources</goal>
+                            </goals>
+                            <phase>${sting.process-resources.phase}</phase>
+                        </execution>
+                        <execution>
+                            <id>default-testResources</id>
+                            <goals>
+                                <goal>testResources</goal>
+                            </goals>
+                            <phase>${sting.process-test-resources.phase}</phase>
+                        </execution>
                         <execution>
                             <id>copy-resource-bundle-log4j</id>
                             <goals>
@@ -277,38 +315,13 @@
                             <phase>${sting.jar.phase}</phase>
                         </execution>
                         <execution>
-                            <id>test-utils</id>
+                            <id>test-jar</id>
                             <goals>
-                                <goal>jar</goal>
+                                <goal>test-jar</goal>
                             </goals>
-                            <phase>${sting.test-utils-jar.phase}</phase>
+                            <phase>${sting.jar.phase}</phase>
                             <configuration>
-                                <classesDirectory>${project.build.testOutputDirectory}</classesDirectory>
+                                <skipIfEmpty>true</skipIfEmpty>
-                                <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>
@@ -773,6 +786,25 @@
                 <module>private</module>
             </modules>
         </profile>
+
+        <!-- Collection of properties for use during package testing -->
+        <profile>
+            <id>packagetests-enabled</id>
+            <activation>
+                <property>
+                    <name>sting.packagetests.enabled</name>
+                    <value>true</value>
+                </property>
+            </activation>
+            <properties>
+                <maven.javadoc.skip>true</maven.javadoc.skip>
+                <sting.generate-gatk-extensions.skipped>true</sting.generate-gatk-extensions.skipped>
+                <sting.jar.phase>none</sting.jar.phase>
+                <sting.generate-resources.phase>none</sting.generate-resources.phase>
+                <sting.process-resources.phase>none</sting.process-resources.phase>
+                <sting.process-test-resources.phase>none</sting.process-test-resources.phase>
+            </properties>
+        </profile>
     </profiles>
 
 </project>

protected/gatk-protected/pom.xml

@@ -40,20 +40,10 @@
             <artifactId>fastutil</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>sting-utils</artifactId>
-            <version>${project.version}</version>
-            <classifier>test-utils</classifier>
-            <type>test-jar</type>
-            <scope>test</scope>
-        </dependency>
-
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
-            <classifier>test-utils</classifier>
             <type>test-jar</type>
             <scope>test</scope>
         </dependency>

public/external-example/pom.xml

@@ -38,27 +38,10 @@
             <version>${sting.version}</version>
         </dependency>
 
-        <!--
-        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>${sting.version}</version>
-            <classifier>test-utils</classifier>
-            <type>test-jar</type>
-            <scope>test</scope>
-        </dependency>
-
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>gatk-framework</artifactId>
             <version>${sting.version}</version>
-            <classifier>test-utils</classifier>
             <type>test-jar</type>
             <scope>test</scope>
         </dependency>
@@ -208,7 +191,6 @@
                         <phase>none</phase>
                     </execution>
                     <execution>
-                        <!-- run all non integration tests -->
                         <id>unit-tests</id>
                         <goals>
                             <goal>test</goal>

public/gatk-framework/pom.xml

@@ -16,7 +16,6 @@
     <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>
@@ -26,15 +25,6 @@
             <version>${project.version}</version>
         </dependency>
 
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>sting-utils</artifactId>
-            <version>${project.version}</version>
-            <classifier>test-utils</classifier>
-            <type>test-jar</type>
-            <scope>test</scope>
-        </dependency>
-
         <dependency>
             <groupId>org.testng</groupId>
             <artifactId>testng</artifactId>
@@ -55,7 +45,7 @@
                 <executions>
                     <execution>
                         <id>example-resources</id>
-                        <phase>generate-resources</phase>
+                        <phase>${sting.generate-resources.phase}</phase>
                     </execution>
                 </executions>
             </plugin>
@@ -79,14 +69,6 @@
                     </execution>
                 </executions>
             </plugin>
-            <!--
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <executions>
-                </executions>
-            </plugin>
--->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-invoker-plugin</artifactId>

public/gatk-package/pom.xml

@@ -51,10 +51,79 @@
             <classifier>example-resources</classifier>
             <type>tar.bz2</type>
         </dependency>
+
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+            <type>test-jar</type>
+        </dependency>
+
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>com.google.caliper</groupId>
+            <artifactId>caliper</artifactId>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>
         <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>unit-tests</id>
+                        <configuration>
+                            <skip>${sting.serialunittests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-failsafe-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>integration-tests</id>
+                        <configuration>
+                            <skip>${sting.serialintegrationtests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>pipeline-tests</id>
+                        <configuration>
+                            <skip>${sting.serialpipelinetests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>large-scale-tests</id>
+                        <configuration>
+                            <skip>${sting.seriallargescaletests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-dependency-plugin</artifactId>
@@ -132,6 +201,14 @@
                     <version>${project.version}</version>
                     <optional>true</optional>
                 </dependency>
+                <dependency>
+                    <groupId>${project.groupId}</groupId>
+                    <artifactId>gatk-protected</artifactId>
+                    <version>${project.version}</version>
+                    <type>test-jar</type>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
             </dependencies>
         </profile>
         <profile>
@@ -148,8 +225,29 @@
                     <version>${project.version}</version>
                     <optional>true</optional>
                 </dependency>
+                <dependency>
+                    <groupId>${project.groupId}</groupId>
+                    <artifactId>gatk-private</artifactId>
+                    <version>${project.version}</version>
+                    <type>test-jar</type>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
             </dependencies>
         </profile>
+        <profile>
+            <id>packagetests-enabled</id>
+            <activation>
+                <property>
+                    <name>sting.packagetests.enabled</name>
+                    <value>true</value>
+                </property>
+            </activation>
+            <properties>
+                <sting.unpack.phase>none</sting.unpack.phase>
+                <sting.shade.phase>none</sting.shade.phase>
+            </properties>
+        </profile>
     </profiles>
 
 </project>

public/gsalib/pom.xml

@@ -30,7 +30,7 @@
                         <goals>
                             <goal>single</goal>
                         </goals>
-                        <phase>generate-resources</phase>
+                        <phase>${sting.generate-resources.phase}</phase>
                         <configuration>
                             <appendAssemblyId>false</appendAssemblyId>
                             <descriptors>

public/package-tests/pom.xml

@@ -48,13 +48,29 @@
             <artifactId>cofoja</artifactId>
         </dependency>
 
+        <!--
+        gatk-framework test-jar added for BaseTest
+        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>${project.groupId}</groupId>
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
-            <classifier>test-utils</classifier>
             <type>test-jar</type>
             <scope>test</scope>
+            <!--
+            <exclusions>
+                <exclusion>
+                    <groupId>*</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+            </exclusions>
+            -->
         </dependency>
 
         <dependency>
@@ -95,13 +111,9 @@
                             <workingDirectory>${sting.packagetests.basedir}</workingDirectory>
                             <classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory>
                             <testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory>
-                            <dependenciesToScan>
-                                <scan>org.broadinstitute.sting:.*</scan>
-                            </dependenciesToScan>
                         </configuration>
                         <executions>
                             <execution>
-                                <!-- run all non integration tests -->
                                 <id>unit-tests</id>
                                 <goals>
                                     <goal>test</goal>
@@ -137,9 +149,6 @@
                             <classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory>
                             <testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory>
                             <summaryFile>${failsafe.summaryFile}</summaryFile>
-                            <dependenciesToScan>
-                                <scan>org.broadinstitute.sting:.*</scan>
-                            </dependenciesToScan>
                         </configuration>
                         <executions>
                             <execution>

public/queue-framework/pom.xml

@@ -18,7 +18,6 @@
         <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>
@@ -66,7 +65,6 @@
             <groupId>${project.groupId}</groupId>
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
-            <classifier>test-utils</classifier>
             <type>test-jar</type>
             <scope>test</scope>
         </dependency>
@@ -130,7 +128,7 @@
                 <executions>
                     <execution>
                         <id>example-resources</id>
-                        <phase>generate-resources</phase>
+                        <phase>${sting.generate-resources.phase}</phase>
                     </execution>
                 </executions>
             </plugin>

public/queue-package/pom.xml

@@ -82,10 +82,86 @@
             <classifier>example-resources</classifier>
             <type>tar.bz2</type>
         </dependency>
+
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>queue-framework</artifactId>
+            <version>${project.version}</version>
+            <type>test-jar</type>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+            <type>test-jar</type>
+        </dependency>
+
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>com.google.caliper</groupId>
+            <artifactId>caliper</artifactId>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>
         <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>unit-tests</id>
+                        <configuration>
+                            <skip>${sting.serialunittests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-failsafe-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>integration-tests</id>
+                        <configuration>
+                            <skip>${sting.serialintegrationtests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>pipeline-tests</id>
+                        <configuration>
+                            <skip>${sting.serialpipelinetests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>large-scale-tests</id>
+                        <configuration>
+                            <skip>${sting.seriallargescaletests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-dependency-plugin</artifactId>
@@ -163,8 +239,29 @@
                     <version>${project.version}</version>
                     <optional>true</optional>
                 </dependency>
+                <dependency>
+                    <groupId>${project.groupId}</groupId>
+                    <artifactId>queue-private</artifactId>
+                    <version>${project.version}</version>
+                    <type>test-jar</type>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
             </dependencies>
         </profile>
+        <profile>
+            <id>packagetests-enabled</id>
+            <activation>
+                <property>
+                    <name>sting.packagetests.enabled</name>
+                    <value>true</value>
+                </property>
+            </activation>
+            <properties>
+                <sting.unpack.phase>none</sting.unpack.phase>
+                <sting.shade.phase>none</sting.shade.phase>
+            </properties>
+        </profile>
     </profiles>
 
 </project>

public/repo/net/sf/picard/1.107.1676/picard-1.107.1676.pom

@@ -37,8 +37,8 @@
             <groupId>com.sun</groupId>
             <artifactId>tools.jar</artifactId>
             <version>1.5</version>
-            <classifier>system</classifier>
+            <scope>system</scope>
-            <systemPath>${java.home}../lib/tools.jar</systemPath>
+            <systemPath>${java.home}/../lib/tools.jar</systemPath>
         </dependency>
     </dependencies>
 </project>

public/sting-utils/pom.xml

@@ -17,7 +17,6 @@
         <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>