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Merge pull request #561 from broadinstitute/ks_package_classpath 

Updated package-tests classpath, and allowing javac -cp <package>.jar.
This commit is contained in:
droazen 2014-03-17 17:38:24 -04:00
parent 2e34ff7692 639247ab48
commit 6b3320f067
2 changed files with 24 additions and 1 deletions
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12
pom.xml
View File

@ -340,6 +340,18 @@
<exclude>org.broadinstitute.sting:*:tar.bz2:example-resources</exclude> <exclude>org.broadinstitute.sting:*:tar.bz2:example-resources</exclude>
</excludes> </excludes>
</artifactSet> </artifactSet>
<filters>
<!--
NOTE: Removing cofoja's annotation service to allow "javac -cp GenomeAnalysisTK.jar ..." without
needing an additional -proc:none argument. Using *:* to catch shaded GATK in Queue package.
-->
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/services/javax.annotation.processing.Processor</exclude>
</excludes>
</filter>
</filters>
<transformers> <transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer"> <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries> <manifestEntries>

13
public/package-tests/pom.xml
View File

@ -50,13 +50,15 @@
<!-- <!--
gatk-framework test-jar added for BaseTest gatk-framework test-jar added for BaseTest
TODO: Currently the <exclusion> isn't working 100%, so switched to using additionalClasspathElements
TODO: Uncomment below to use the explicitly bad "exclude *" to really test correct packaging, 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: 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. TODO: We only want the classes in the packaged jars tested, not the classes within the dependency jars too.
See also: See also:
http://stackoverflow.com/questions/547805/how-to-exclude-all-transitive-dependencies-of-a-maven-dependency 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 http://maven.apache.org/plugins/maven-jar-plugin/usage.html#The_preferred_way
-->
<dependency> <dependency>
<groupId>${project.groupId}</groupId> <groupId>${project.groupId}</groupId>
<artifactId>gatk-framework</artifactId> <artifactId>gatk-framework</artifactId>
@ -72,6 +74,7 @@
</exclusions> </exclusions>
</dependency> </dependency>
-->
<dependency> <dependency>
<groupId>org.testng</groupId> <groupId>org.testng</groupId>
@ -111,6 +114,10 @@
<workingDirectory>${sting.packagetests.basedir}</workingDirectory> <workingDirectory>${sting.packagetests.basedir}</workingDirectory>
<classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory> <classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory>
<testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory> <testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory>
<!-- TODO: Using additionalClasspathElement while debugging exclusion issue above -->
<additionalClasspathElements>
<additionalClasspathElement>${sting.basedir}/public/gatk-framework/target/gatk-framework-${project.version}-tests.jar</additionalClasspathElement>
</additionalClasspathElements>
</configuration> </configuration>
<executions> <executions>
<execution> <execution>
@ -148,6 +155,10 @@
<workingDirectory>${sting.packagetests.basedir}</workingDirectory> <workingDirectory>${sting.packagetests.basedir}</workingDirectory>
<classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory> <classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory>
<testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory> <testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory>
<!-- TODO: Using additionalClasspathElement while debugging exclusion issue above -->
<additionalClasspathElements>
<additionalClasspathElement>${sting.basedir}/public/gatk-framework/target/gatk-framework-${project.version}-tests.jar</additionalClasspathElement>
</additionalClasspathElements>
</configuration> </configuration>
<executions> <executions>
<execution> <execution>