Merge pull request #488 from broadinstitute/ks_mvn_serial_test_updates
Ks mvn serial test updates
This commit is contained in:
droazen
commit
b2b44c335f
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@ -33,6 +33,7 @@ for arg in "${@}" ; do
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elif [[ "${property_name}" == "test.debug.port" ]] ; then
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mvn_properties="${mvn_properties} -Dmaven.surefire.debug=\"-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${property_value}\""
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mvn_properties="${mvn_properties} -Dmaven.failsafe.debug=\"-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${property_value}\""
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elif [[ "${property_name}" == "test.default.maxmemory" ]] ; then
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mvn_properties="${mvn_properties} -Dtest.maxmemory=${property_value}"
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@ -98,18 +99,16 @@ for arg in "${@}" ; do
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elif [[ "${arg}" == "gatkfull.binary.release.tests" ]] ; then
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local_repo="sitetemprepo"
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mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
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mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo} -Dmaven.javadoc.skip=true"
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mvn_args="${mvn_args} -Dsting.generate-gatk-extensions.skipped=true"
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mvn_args="${mvn_args} -Dsting.jar.phase=none -Dsting.unpack.phase=none -Dsting.shade.phase=none"
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mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo}"
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mvn_args="${mvn_args} -Dsting.packagetests.enabled=true"
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mvn_args="${mvn_args} -Dsting.packagecommittests.skipped=false"
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# TODO: This runs only the pipeline tests (full, non-dry run), but not the commit tests for Queue.
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elif [[ "${arg}" == "queuefull.binary.release.tests" ]] ; then
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local_repo="sitetemprepo"
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mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
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mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo} -Dmaven.javadoc.skip=true"
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mvn_args="${mvn_args} -Dsting.generate-gatk-extensions.skipped=true"
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mvn_args="${mvn_args} -Dsting.jar.phase=none -Dsting.unpack.phase=none -Dsting.shade.phase=none"
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mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo}"
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mvn_args="${mvn_args} -Dsting.packagetests.enabled=true"
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mvn_args="${mvn_args} -Dsting.packagepipelinetests.skipped=false"
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mvn_args="${mvn_args} -Dsting.pipelinetests.run=true"
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92
pom.xml
92
pom.xml
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@ -32,13 +32,37 @@
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<resource.bundle.skip>false</resource.bundle.skip>
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<!-- TODO: Need a better a way to say "don't include hidden" by default -->
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<gatkdocs.include.hidden>-build-timestamp "${maven.build.timestamp}"</gatkdocs.include.hidden>
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<!--
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Phases of the build that may be disabled to speed up compilation.
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-->
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<sting.jar.phase>package</sting.jar.phase>
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<sting.test-utils.jar.phase>none</sting.test-utils.jar.phase>
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<sting.generate-resources.phase>generate-resources</sting.generate-resources.phase>
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<sting.process-resources.phase>process-resources</sting.process-resources.phase>
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<sting.process-test-resources.phase>process-test-resources</sting.process-test-resources.phase>
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<!--
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Package tests ensure the consistency of the packaged / shaded jars.
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It runs the tests where the monolithic jar is the only dependency on the classpath.
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-->
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<sting.packagecommittests.skipped>true</sting.packagecommittests.skipped>
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<sting.packageunittests.skipped>${sting.packagecommittests.skipped}</sting.packageunittests.skipped>
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<sting.packageintegrationtests.skipped>${sting.packagecommittests.skipped}</sting.packageintegrationtests.skipped>
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<sting.packagepipelinetests.skipped>${sting.packagecommittests.skipped}</sting.packagepipelinetests.skipped>
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<sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
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<!--
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Serial tests use the test jars to run tests, such that all tests are run from a single TestNG invocation.
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This is different that the invoker, that runs the test classes from the filesystem, but pointing at the packaged JAR files.
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TODO: Currently, all tests run within each package, since packages already collect dependencies for shading an uber jar.
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TODO: Should there be another level up of tests, possibly running "all tests" via this aggregator level?
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TODO: If that require the aggregator to be dependent on the child dependencies, perhaps a better approach might be another monolithic test project.
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-->
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<sting.serialcommittests.skipped>true</sting.serialcommittests.skipped>
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<sting.serialunittests.skipped>${sting.serialcommittests.skipped}</sting.serialunittests.skipped>
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<sting.serialintegrationtests.skipped>${sting.serialcommittests.skipped}</sting.serialintegrationtests.skipped>
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<sting.serialpipelinetests.skipped>${sting.serialcommittests.skipped}</sting.serialpipelinetests.skipped>
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<sting.seriallargescaletests.skipped>true</sting.seriallargescaletests.skipped>
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</properties>
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<dependencies>
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@ -109,6 +133,20 @@
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-resources-plugin</artifactId>
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<executions>
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<execution>
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<id>default-resources</id>
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<goals>
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<goal>resources</goal>
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</goals>
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<phase>${sting.process-resources.phase}</phase>
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</execution>
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<execution>
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<id>default-testResources</id>
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<goals>
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<goal>testResources</goal>
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</goals>
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<phase>${sting.process-test-resources.phase}</phase>
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</execution>
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<execution>
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<id>copy-resource-bundle-log4j</id>
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<goals>
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@ -277,38 +315,13 @@
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<phase>${sting.jar.phase}</phase>
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</execution>
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<execution>
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<id>test-utils</id>
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<id>test-jar</id>
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<goals>
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<goal>jar</goal>
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<goal>test-jar</goal>
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</goals>
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<phase>${sting.test-utils-jar.phase}</phase>
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<phase>${sting.jar.phase}</phase>
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<configuration>
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<classesDirectory>${project.build.testOutputDirectory}</classesDirectory>
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<classifier>test-utils</classifier>
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<!--
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TODO: Excluding actual tests from tests-utils jar is required because the same test classes
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TODO: cannot be in both the test artifact AND the test classes directory.
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TODO: Otherwise maven throws an [ERROR] java.lang.RuntimeException: Duplicate test set
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TODO: This is due to AbstractSurefireMojo.scanForTestClasses() adding both scanDirectories() and scanDependencies().
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TODO: Pain to debug as exception is three maven invoker levels deep, outer maven, maven-inovker-plugin, then forked tests!
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TODO: See also: http://maven.apache.org/plugins/maven-jar-plugin/usage.html#The_preferred_way
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TODO: Then that dependency won't have test classes that will also run from the
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TODO: test classes directory during the invoked package test.
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-->
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<excludes>
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<exclude>**/*UnitTest.class</exclude>
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<exclude>**/*UnitTest$*.class</exclude>
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<exclude>**/*IntegrationTest.class</exclude>
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<exclude>**/*IntegrationTest$*.class</exclude>
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<exclude>**/*PipelineTest.class</exclude>
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<exclude>**/*PipelineTest$*.class</exclude>
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<exclude>**/*LargeScaleTest.class</exclude>
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<exclude>**/*LargeScaleTest.class</exclude>
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</excludes>
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<skipIfEmpty>true</skipIfEmpty>
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</configuration>
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</execution>
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</executions>
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@ -773,6 +786,25 @@
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<module>private</module>
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</modules>
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</profile>
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<!-- Collection of properties for use during package testing -->
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<profile>
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<id>packagetests-enabled</id>
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<activation>
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<property>
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<name>sting.packagetests.enabled</name>
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<value>true</value>
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</property>
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</activation>
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<properties>
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<maven.javadoc.skip>true</maven.javadoc.skip>
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<sting.generate-gatk-extensions.skipped>true</sting.generate-gatk-extensions.skipped>
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<sting.jar.phase>none</sting.jar.phase>
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<sting.generate-resources.phase>none</sting.generate-resources.phase>
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<sting.process-resources.phase>none</sting.process-resources.phase>
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<sting.process-test-resources.phase>none</sting.process-test-resources.phase>
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</properties>
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</profile>
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</profiles>
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</project>
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@ -40,20 +40,10 @@
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<artifactId>fastutil</artifactId>
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</dependency>
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>sting-utils</artifactId>
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<version>${project.version}</version>
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<classifier>test-utils</classifier>
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<type>test-jar</type>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-framework</artifactId>
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<version>${project.version}</version>
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<classifier>test-utils</classifier>
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<type>test-jar</type>
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<scope>test</scope>
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</dependency>
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@ -38,27 +38,10 @@
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<version>${sting.version}</version>
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</dependency>
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<!--
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Test dependencies are not transitive,
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so must include each explicit test artifact.
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TODO: switch from test-utils classifier to a tests-utils artifact
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TODO: see also http://maven.apache.org/plugins/maven-jar-plugin/usage.html#The_preferred_way
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-->
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<dependency>
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<groupId>org.broadinstitute.sting</groupId>
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<artifactId>sting-utils</artifactId>
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<version>${sting.version}</version>
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<classifier>test-utils</classifier>
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<type>test-jar</type>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.broadinstitute.sting</groupId>
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<artifactId>gatk-framework</artifactId>
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<version>${sting.version}</version>
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<classifier>test-utils</classifier>
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<type>test-jar</type>
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<scope>test</scope>
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</dependency>
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@ -208,7 +191,6 @@
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<phase>none</phase>
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</execution>
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<execution>
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<!-- run all non integration tests -->
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<id>unit-tests</id>
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<goals>
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<goal>test</goal>
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@ -16,7 +16,6 @@
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<properties>
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<sting.basedir>${project.basedir}/../..</sting.basedir>
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<sting.packagetests.artifactId>gatk-package</sting.packagetests.artifactId>
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<sting.test-utils-jar.phase>${sting.jar.phase}</sting.test-utils-jar.phase>
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</properties>
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<dependencies>
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@ -26,15 +25,6 @@
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>sting-utils</artifactId>
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<version>${project.version}</version>
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<classifier>test-utils</classifier>
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<type>test-jar</type>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.testng</groupId>
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<artifactId>testng</artifactId>
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@ -55,7 +45,7 @@
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<executions>
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<execution>
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<id>example-resources</id>
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<phase>generate-resources</phase>
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<phase>${sting.generate-resources.phase}</phase>
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</execution>
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</executions>
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</plugin>
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@ -79,14 +69,6 @@
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</execution>
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</executions>
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</plugin>
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<!--
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<executions>
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</executions>
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</plugin>
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-->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-invoker-plugin</artifactId>
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@ -51,10 +51,79 @@
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<classifier>example-resources</classifier>
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<type>tar.bz2</type>
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</dependency>
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-framework</artifactId>
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<version>${project.version}</version>
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<type>test-jar</type>
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</dependency>
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<dependency>
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<groupId>org.testng</groupId>
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<artifactId>testng</artifactId>
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<scope>test</scope>
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</dependency>
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|
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<dependency>
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<groupId>com.google.caliper</groupId>
|
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<artifactId>caliper</artifactId>
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<scope>test</scope>
|
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</dependency>
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</dependencies>
|
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<build>
|
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
|
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<artifactId>maven-surefire-plugin</artifactId>
|
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<executions>
|
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<execution>
|
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<id>unit-tests</id>
|
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<configuration>
|
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<skip>${sting.serialunittests.skipped}</skip>
|
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<dependenciesToScan>
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<scan>org.broadinstitute.sting:.*</scan>
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</dependenciesToScan>
|
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</configuration>
|
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</execution>
|
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</executions>
|
||||
</plugin>
|
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|
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<plugin>
|
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<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-failsafe-plugin</artifactId>
|
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<executions>
|
||||
<execution>
|
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<id>integration-tests</id>
|
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<configuration>
|
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<skip>${sting.serialintegrationtests.skipped}</skip>
|
||||
<dependenciesToScan>
|
||||
<scan>org.broadinstitute.sting:.*</scan>
|
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</dependenciesToScan>
|
||||
</configuration>
|
||||
</execution>
|
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<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>${project.version}</version>
|
||||
<type>test-jar</type>
|
||||
<scope>test</scope>
|
||||
<optional>true</optional>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
</profile>
|
||||
<profile>
|
||||
|
|
@ -148,7 +225,47 @@
|
|||
<version>${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>
|
||||
<build>
|
||||
<plugins>
|
||||
<!-- TODO: All tests require access to private. For now. -->
|
||||
<plugin>
|
||||
<groupId>com.pyx4j</groupId>
|
||||
<artifactId>maven-junction-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>link-private-testdata</id>
|
||||
<phase>process-test-resources</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>unlink-private-testdata</id>
|
||||
<phase>clean</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</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>
|
||||
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@
|
|||
<goals>
|
||||
<goal>single</goal>
|
||||
</goals>
|
||||
<phase>generate-resources</phase>
|
||||
<phase>${sting.generate-resources.phase}</phase>
|
||||
<configuration>
|
||||
<appendAssemblyId>false</appendAssemblyId>
|
||||
<descriptors>
|
||||
|
|
|
|||
|
|
@ -48,13 +48,29 @@
|
|||
<artifactId>cofoja</artifactId>
|
||||
</dependency>
|
||||
|
||||
<!--
|
||||
gatk-framework test-jar added for BaseTest
|
||||
TODO: Uncomment below to use the explicitly bad "exclude *" to really test correct packaging,
|
||||
TODO: until we can separate BaseTest and other utilities into their own sting-test-utils artifact.
|
||||
TODO: We only want the classes in the packaged jars tested, not the classes within the dependency jars too.
|
||||
See also:
|
||||
http://stackoverflow.com/questions/547805/how-to-exclude-all-transitive-dependencies-of-a-maven-dependency
|
||||
http://maven.apache.org/plugins/maven-jar-plugin/usage.html#The_preferred_way
|
||||
-->
|
||||
<dependency>
|
||||
<groupId>${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>${failsafe.summaryFile}</summaryFile>
|
||||
<dependenciesToScan>
|
||||
<scan>org.broadinstitute.sting:.*</scan>
|
||||
</dependenciesToScan>
|
||||
</configuration>
|
||||
<executions>
|
||||
<execution>
|
||||
|
|
|
|||
|
|
@ -18,7 +18,6 @@
|
|||
<gatk.extensions.sources>${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>
|
||||
|
|
|
|||
|
|
@ -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>
|
||||
|
|
@ -163,7 +239,55 @@
|
|||
<version>${project.version}</version>
|
||||
<optional>true</optional>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>${project.groupId}</groupId>
|
||||
<artifactId>queue-private</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<type>test-jar</type>
|
||||
<scope>test</scope>
|
||||
<optional>true</optional>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
<build>
|
||||
<plugins>
|
||||
<!-- TODO: All tests require access to private. For now. -->
|
||||
<plugin>
|
||||
<groupId>com.pyx4j</groupId>
|
||||
<artifactId>maven-junction-plugin</artifactId>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>link-private-testdata</id>
|
||||
<phase>process-test-resources</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>unlink-private-testdata</id>
|
||||
<phase>clean</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>link-private-qscript</id>
|
||||
<phase>process-test-resources</phase>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>unlink-private-qscript</id>
|
||||
<phase>clean</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</profile>
|
||||
<profile>
|
||||
<id>packagetests-enabled</id>
|
||||
<activation>
|
||||
<property>
|
||||
<name>sting.packagetests.enabled</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
</activation>
|
||||
<properties>
|
||||
<sting.unpack.phase>none</sting.unpack.phase>
|
||||
<sting.shade.phase>none</sting.shade.phase>
|
||||
</properties>
|
||||
</profile>
|
||||
</profiles>
|
||||
|
||||
|
|
|
|||
|
|
@ -37,8 +37,8 @@
|
|||
<groupId>com.sun</groupId>
|
||||
<artifactId>tools.jar</artifactId>
|
||||
<version>1.5</version>
|
||||
<classifier>system</classifier>
|
||||
<systemPath>${java.home}../lib/tools.jar</systemPath>
|
||||
<scope>system</scope>
|
||||
<systemPath>${java.home}/../lib/tools.jar</systemPath>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
</project>
|
||||
|
|
|
|||
|
|
@ -17,7 +17,6 @@
|
|||
<sting.basedir>${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>
|
||||
|
|
|
|||
Loading…
Reference in New Issue