Fixed missing "mvn" command execution in ant-bridge.
Added pom.xml workarounds for duplicate classpath error, due to gatk-framework dependency containing required BaseTest, and jarred *UnitTest/*IntegrationTest classes that also exist as files under target/test-classes.
This commit is contained in:
Khalid Shakir
David Roazen
parent
caa76cdac4
commit
25aee7164e
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@ -87,7 +87,7 @@ for arg in "${@}" ; do
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# TODO: This runs *all* commit tests, including the few on Queue.
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elif [ "${arg}" = "gatkfull.binary.release.tests" ] ; then
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local_repo="sitetemprepo"
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mvn_args="install -Dmaven.repo.local=${local_repo} && verify"
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mvn_args="install -Dmaven.repo.local=${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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@ -96,7 +96,7 @@ for arg in "${@}" ; do
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# TODO: This runs only the pipeline tests (full, non-dry run), but not the commit tests for Queue.
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elif [ "${arg}" = "queuefull.binary.release.tests" ] ; then
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local_repo="sitetemprepo"
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mvn_args="install -Dmaven.repo.local=${local_repo} && verify"
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mvn_args="install -Dmaven.repo.local=${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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@ -153,6 +153,6 @@ if [ "${unknown_args}" != "" ]; then
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else
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echo "Equivalent maven command"
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echo "${mvn_cmd}${mvn_properties}${post_script}"
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sh -c "${mvn_cmd}${mvn_properties}${post_script}"
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# sh -c "${mvn_cmd}${mvn_properties}${post_script}"
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fi
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23
pom.xml
23
pom.xml
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@ -508,6 +508,9 @@
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</properties>
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</configuration>
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<executions>
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<!--
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TODO: see description of disable.gatk-framework.test.dependency in gatk-framework/pom.xml
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-->
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<execution>
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<id>package-unittests</id>
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<goals>
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@ -517,11 +520,10 @@
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<goals>
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<goal>test</goal>
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</goals>
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<profiles>
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<profile>unittests</profile>
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</profiles>
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<skipInvocation>${sting.packageunittests.skipped}</skipInvocation>
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<properties>
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<unittests.profile.enabled>true</unittests.profile.enabled>
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<disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
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<sting.packageunittests.skipped>${sting.packageunittests.skipped}</sting.packageunittests.skipped>
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</properties>
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</configuration>
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@ -536,11 +538,10 @@
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<goals>
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<goal>verify</goal>
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</goals>
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<profiles>
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<profile>integrationtests</profile>
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</profiles>
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<skipInvocation>${sting.packageintegrationtests.skipped}</skipInvocation>
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<properties>
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<integrationtests.profile.enabled>true</integrationtests.profile.enabled>
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<disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
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<sting.packageintegrationtests.skipped>${sting.packageintegrationtests.skipped}</sting.packageintegrationtests.skipped>
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</properties>
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</configuration>
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@ -555,11 +556,10 @@
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<goals>
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<goal>verify</goal>
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</goals>
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<profiles>
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<profile>integrationtests</profile>
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</profiles>
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<skipInvocation>${sting.packagepipelinetests.skipped}</skipInvocation>
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<properties>
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<integrationtests.profile.enabled>true</integrationtests.profile.enabled>
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<disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
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<sting.packagepipelinetests.skipped>${sting.packagepipelinetests.skipped}</sting.packagepipelinetests.skipped>
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</properties>
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</configuration>
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@ -574,11 +574,10 @@
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<goals>
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<goal>verify</goal>
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</goals>
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<profiles>
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<profile>integrationtests</profile>
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</profiles>
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<skipInvocation>${sting.packagelargescaletests.skipped}</skipInvocation>
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<properties>
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<integrationtests.profile.enabled>true</integrationtests.profile.enabled>
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<disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
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<sting.packagelargescaletests.skipped>${sting.packagelargescaletests.skipped}</sting.packagelargescaletests.skipped>
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</properties>
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</configuration>
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@ -211,11 +211,8 @@
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<configuration>
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<skip>false</skip>
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<includes>
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<include>**/*Test.class</include>
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<include>**/*UnitTest.class</include>
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</includes>
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<excludes>
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<exclude>**/*IntegrationTest.class</exclude>
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</excludes>
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</configuration>
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</execution>
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</executions>
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@ -88,21 +88,55 @@
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</execution>
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</executions>
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</plugin>
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<!--
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TODO: disable.gatk-framework.test.dependency is required because the the same test classes
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TODO: cannot be in both the gatk-framework 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: Move BaseTest and other non UnitTests into the sting-utils test jar/artifact.
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TODO: Then that dependency won't have test classes that will also run from the gatk-framework
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TODO: test classes directory during the invoked package test.
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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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<executions>
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<execution>
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<id>package-unittests</id>
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<configuration>
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<properties>
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<disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
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</properties>
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</configuration>
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</execution>
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<execution>
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<id>package-integrationtests</id>
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<configuration>
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<properties>
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<disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
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</properties>
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</configuration>
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</execution>
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<execution>
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<id>package-largescaletests</id>
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<configuration>
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<properties>
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<disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
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</properties>
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</configuration>
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</execution>
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<execution>
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<id>package-pipelinetests</id>
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<configuration>
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<properties>
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<disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
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</properties>
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</configuration>
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</execution>
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</executions>
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</plugin>
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@ -2,6 +2,10 @@
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<!--
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Run during package testing by the maven invoker plugin in the sting-aggregator /pom.xml
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-->
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<parent>
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<groupId>org.broadinstitute.sting</groupId>
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<artifactId>sting-root</artifactId>
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@ -15,6 +19,10 @@
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<properties>
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<sting.basedir>${project.basedir}/../..</sting.basedir>
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<sting.packageunittests.skipped>true</sting.packageunittests.skipped>
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<sting.packageintegrationtests.skipped>true</sting.packageintegrationtests.skipped>
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<sting.packagepipelinetests.skipped>true</sting.packagepipelinetests.skipped>
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<sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
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</properties>
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<!-- Dependency configuration (versions, etc.) -->
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@ -39,14 +47,6 @@
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<artifactId>cofoja</artifactId>
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</dependency>
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-framework</artifactId>
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<version>${project.version}</version>
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<type>test-jar</type>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.testng</groupId>
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<artifactId>testng</artifactId>
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@ -65,8 +65,36 @@
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</build>
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<profiles>
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<!--
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TODO: see description of disable.gatk-framework.test.dependency in gatk-framework/pom.xml
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-->
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<profile>
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<id>include-gatk-framework-tests</id>
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<activation>
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<property>
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<name>disable.gatk-framework.test.dependency</name>
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<value>false</value>
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</property>
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</activation>
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<dependencies>
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<dependency>
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<groupId>${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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<scope>test</scope>
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</dependency>
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</dependencies>
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</profile>
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<profile>
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<id>unittests</id>
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<activation>
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<activeByDefault>false</activeByDefault>
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<property>
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<name>unittests.profile.enabled</name>
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<value>true</value>
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</property>
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</activation>
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<build>
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<!-- Plugin configuration -->
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<plugins>
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@ -101,6 +129,13 @@
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<profile>
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<id>integrationtests</id>
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<activation>
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<activeByDefault>false</activeByDefault>
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<property>
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<name>integrationtests.profile.enabled</name>
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<value>true</value>
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</property>
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</activation>
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<build>
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<!-- Plugin configuration -->
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<plugins>
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@ -389,13 +389,8 @@
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<!-- TODO: Re-enable unit tests by default? -->
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<skip>${sting.unittests.skipped}</skip>
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<includes>
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<include>**/*Test.class</include>
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<include>**/*UnitTest.class</include>
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</includes>
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<excludes>
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<exclude>**/*IntegrationTest.class</exclude>
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<exclude>**/*PipelineTest.class</exclude>
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<exclude>**/*LargeScaleTest.class</exclude>
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</excludes>
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</configuration>
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</execution>
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</executions>
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