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Merge pull request #504 from broadinstitute/dr_enable_kb_tests_in_maven 

Add ability to run *KnowledgeBaseTests to maven
This commit is contained in:
droazen 2014-02-11 15:32:24 -05:00
parent cc9a3b68fc 95e1402d21
commit 3cfcfa4fa0
9 changed files with 77 additions and 0 deletions
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3
ant-bridge.sh
View File

@ -127,6 +127,9 @@ for arg in "${@}" ; do
elif [[ "${arg}" == "largescaletest" ]] ; then elif [[ "${arg}" == "largescaletest" ]] ; then
mvn_args="verify -Dsting.largescaletests.skipped=false" mvn_args="verify -Dsting.largescaletests.skipped=false"
elif [[ "${arg}" == "knowledgebasetest" ]] ; then
mvn_args="verify -Dsting.knowledgebasetests.skipped=false"
elif [[ "${arg}" == "pipelinetest" ]] ; then elif [[ "${arg}" == "pipelinetest" ]] ; then
mvn_args="verify -Dsting.pipelinetests.skipped=false" mvn_args="verify -Dsting.pipelinetests.skipped=false"

21
pom.xml
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@ -50,6 +50,7 @@
<sting.packageintegrationtests.skipped>${sting.packagecommittests.skipped}</sting.packageintegrationtests.skipped> <sting.packageintegrationtests.skipped>${sting.packagecommittests.skipped}</sting.packageintegrationtests.skipped>
<sting.packagepipelinetests.skipped>${sting.packagecommittests.skipped}</sting.packagepipelinetests.skipped> <sting.packagepipelinetests.skipped>${sting.packagecommittests.skipped}</sting.packagepipelinetests.skipped>
<sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped> <sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
<sting.packageknowledgebasetests.skipped>true</sting.packageknowledgebasetests.skipped>
<!-- <!--
Serial tests use the test jars to run tests, such that all tests are run from a single TestNG invocation. Serial tests use the test jars to run tests, such that all tests are run from a single TestNG invocation.
@ -63,6 +64,7 @@
<sting.serialintegrationtests.skipped>${sting.serialcommittests.skipped}</sting.serialintegrationtests.skipped> <sting.serialintegrationtests.skipped>${sting.serialcommittests.skipped}</sting.serialintegrationtests.skipped>
<sting.serialpipelinetests.skipped>${sting.serialcommittests.skipped}</sting.serialpipelinetests.skipped> <sting.serialpipelinetests.skipped>${sting.serialcommittests.skipped}</sting.serialpipelinetests.skipped>
<sting.seriallargescaletests.skipped>true</sting.seriallargescaletests.skipped> <sting.seriallargescaletests.skipped>true</sting.seriallargescaletests.skipped>
<sting.serialknowledgebasetests.skipped>true</sting.serialknowledgebasetests.skipped>
</properties> </properties>
<dependencies> <dependencies>
@ -641,6 +643,25 @@
</properties> </properties>
</configuration> </configuration>
</execution> </execution>
<execution>
<id>package-knowledgebasetests</id>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
<configuration>
<goals>
<goal>verify</goal>
</goals>
<reportsDirectory>${project.build.directory}/invoker-reports/knowledgebase/${it.test}</reportsDirectory>
<skipInvocation>${sting.packageknowledgebasetests.skipped}</skipInvocation>
<properties>
<integrationtests.profile.enabled>true</integrationtests.profile.enabled>
<sting.packageknowledgebasetests.skipped>${sting.packageknowledgebasetests.skipped}</sting.packageknowledgebasetests.skipped>
<failsafe.summaryFile>${project.build.directory}/failsafe-reports/knowledgebase/failsafe-summary-${it.test}.xml</failsafe.summaryFile>
</properties>
</configuration>
</execution>
</executions> </executions>
</plugin> </plugin>
<plugin> <plugin>

3
protected/gatk-protected/pom.xml
View File

@ -95,6 +95,9 @@
<execution> <execution>
<id>package-largescaletests</id> <id>package-largescaletests</id>
</execution> </execution>
<execution>
<id>package-knowledgebasetests</id>
</execution>
<execution> <execution>
<id>package-pipelinetests</id> <id>package-pipelinetests</id>
</execution> </execution>

3
public/gatk-framework/pom.xml
View File

@ -82,6 +82,9 @@
<execution> <execution>
<id>package-largescaletests</id> <id>package-largescaletests</id>
</execution> </execution>
<execution>
<id>package-knowledgebasetests</id>
</execution>
<execution> <execution>
<id>package-pipelinetests</id> <id>package-pipelinetests</id>
</execution> </execution>

9
public/gatk-package/pom.xml
View File

@ -121,6 +121,15 @@
</dependenciesToScan> </dependenciesToScan>
</configuration> </configuration>
</execution> </execution>
<execution>
<id>knowledge-base-tests</id>
<configuration>
<skip>${sting.serialknowledgebasetests.skipped}</skip>
<dependenciesToScan>
<scan>org.broadinstitute.sting:.*</scan>
</dependenciesToScan>
</configuration>
</execution>
</executions> </executions>
</plugin> </plugin>

11
public/package-tests/pom.xml
View File

@ -23,6 +23,7 @@
<sting.packageintegrationtests.skipped>true</sting.packageintegrationtests.skipped> <sting.packageintegrationtests.skipped>true</sting.packageintegrationtests.skipped>
<sting.packagepipelinetests.skipped>true</sting.packagepipelinetests.skipped> <sting.packagepipelinetests.skipped>true</sting.packagepipelinetests.skipped>
<sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped> <sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
<sting.packageknowledgebasetests.skipped>true</sting.packageknowledgebasetests.skipped>
<failsafe.summaryFile>${project.build.directory}/failsafe-reports/failsafe-summary.xml</failsafe.summaryFile> <failsafe.summaryFile>${project.build.directory}/failsafe-reports/failsafe-summary.xml</failsafe.summaryFile>
</properties> </properties>
@ -181,6 +182,16 @@
<skip>${sting.packagelargescaletests.skipped}</skip> <skip>${sting.packagelargescaletests.skipped}</skip>
</configuration> </configuration>
</execution> </execution>
<execution>
<id>knowledge-base-tests</id>
<goals>
<goal>verify</goal>
</goals>
<!-- run knowledge base tests -->
<configuration>
<skip>${sting.packageknowledgebasetests.skipped}</skip>
</configuration>
</execution>
</executions> </executions>
</plugin> </plugin>
</plugins> </plugins>

3
public/queue-framework/pom.xml
View File

@ -183,6 +183,9 @@
<execution> <execution>
<id>package-largescaletests</id> <id>package-largescaletests</id>
</execution> </execution>
<execution>
<id>package-knowledgebasetests</id>
</execution>
<execution> <execution>
<id>package-pipelinetests</id> <id>package-pipelinetests</id>
</execution> </execution>

9
public/queue-package/pom.xml
View File

@ -159,6 +159,15 @@
</dependenciesToScan> </dependenciesToScan>
</configuration> </configuration>
</execution> </execution>
<execution>
<id>knowledge-base-tests</id>
<configuration>
<skip>${sting.serialknowledgebasetests.skipped}</skip>
<dependenciesToScan>
<scan>org.broadinstitute.sting:.*</scan>
</dependenciesToScan>
</configuration>
</execution>
</executions> </executions>
</plugin> </plugin>

15
public/sting-root/pom.xml
View File

@ -33,6 +33,7 @@
<sting.integrationtests.skipped>${sting.committests.skipped}</sting.integrationtests.skipped> <sting.integrationtests.skipped>${sting.committests.skipped}</sting.integrationtests.skipped>
<sting.pipelinetests.skipped>${sting.committests.skipped}</sting.pipelinetests.skipped> <sting.pipelinetests.skipped>${sting.committests.skipped}</sting.pipelinetests.skipped>
<sting.largescaletests.skipped>true</sting.largescaletests.skipped> <sting.largescaletests.skipped>true</sting.largescaletests.skipped>
<sting.knowledgebasetests.skipped>true</sting.knowledgebasetests.skipped>
<sting.pipelinetests.run>false</sting.pipelinetests.run> <sting.pipelinetests.run>false</sting.pipelinetests.run>
<scala.maxmemory>1g</scala.maxmemory> <scala.maxmemory>1g</scala.maxmemory>
<test.maxmemory>4g</test.maxmemory> <test.maxmemory>4g</test.maxmemory>
@ -456,6 +457,20 @@
</includes> </includes>
</configuration> </configuration>
</execution> </execution>
<execution>
<id>knowledge-base-tests</id>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
<!-- run knowledge base tests -->
<configuration>
<skip>${sting.knowledgebasetests.skipped}</skip>
<includes>
<include>**/*KnowledgeBaseTest.class</include>
</includes>
</configuration>
</execution>
</executions> </executions>
</plugin> </plugin>