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Merged bug fix from Stable into Unstable

This commit is contained in:
David Roazen 2011-10-14 03:26:35 -04:00
parent 4f01a742cb 442d33ba18
commit aad99563be
2 changed files with 116 additions and 50 deletions
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156
build.xml
View File

@ -67,6 +67,8 @@
<!-- If running the 'package' task, this property controls the name of the xml file to package --> <!-- If running the 'package' task, this property controls the name of the xml file to package -->
<property name="package.xml.dir" value="${public.dir}/packages" /> <property name="package.xml.dir" value="${public.dir}/packages" />
<property name="package.output.dir" value="${dist.dir}/packages" />
<property name="staging.dir" value="staging" />
<property name="executable" value="GenomeAnalysisTK" /> <property name="executable" value="GenomeAnalysisTK" />
<property environment="env"/> <property environment="env"/>
@ -118,6 +120,16 @@
</fileset> </fileset>
</path> </path>
<path id="testng.dependencies">
<fileset dir="${lib.dir}">
<include name="jcommander*.jar"/>
<include name="guice*.jar"/>
<include name="junit*.jar"/>
<include name="bsh*.jar"/>
<include name="snakeyaml*.jar"/>
</fileset>
</path>
<path id="build.results"> <path id="build.results">
<fileset dir="dist"> <fileset dir="dist">
<patternset refid="dependency.mask" /> <patternset refid="dependency.mask" />
@ -829,10 +841,54 @@
<target name="test.compile" depends="init.usecontracts,test.java.compile,test.scala.compile" /> <target name="test.compile" depends="init.usecontracts,test.java.compile,test.scala.compile" />
<path id="testng.default.classpath">
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
<pathelement location="${scala.classes}" />
<pathelement location="${java.contracts}" />
<pathelement location="${java.public.test.classes}" />
<pathelement location="${java.private.test.classes}" />
<pathelement location="${scala.public.test.classes}" />
<pathelement location="${scala.private.test.classes}" />
</path>
<path id="testng.gatk.releasetest.classpath">
<path refid="testng.dependencies" />
<path>
<fileset dir="${package.output.dir}">
<include name="**/${executable}.jar" />
</fileset>
</path>
<pathelement location="${java.contracts}" />
<pathelement location="${java.public.test.classes}" />
<pathelement location="${scala.public.test.classes}" />
<pathelement location="${scala.classes}" />
<path>
<fileset dir="${lib.dir}">
<include name="scala*.jar"/>
<include name="jna*.jar"/>
</fileset>
</path>
</path>
<path id="testng.queue.releasetest.classpath">
<path refid="testng.dependencies" />
<path>
<fileset dir="${package.output.dir}">
<include name="**/${executable}.jar" />
</fileset>
</path>
<pathelement location="${java.contracts}" />
<pathelement location="${java.public.test.classes}" />
<pathelement location="${scala.public.test.classes}" />
</path>
<!-- TEST --> <!-- TEST -->
<macrodef name="run-test"> <macrodef name="run-test">
<attribute name="testtype"/> <attribute name="testtype"/>
<attribute name="outputdir"/> <attribute name="outputdir"/>
<attribute name="classpath"/>
<attribute name="runfailed"/> <attribute name="runfailed"/>
<sequential> <sequential>
@ -853,6 +909,7 @@
<echo message="Sting: Running @{testtype} test cases!"/> <echo message="Sting: Running @{testtype} test cases!"/>
<taskdef resource="testngtasks" classpath="${testng.jar}"/> <taskdef resource="testngtasks" classpath="${testng.jar}"/>
<testng outputDir="@{outputdir}" <testng outputDir="@{outputdir}"
classpathref="@{classpath}"
haltOnFailure="false" failureProperty="test.failure" haltOnFailure="false" failureProperty="test.failure"
verbose="2" verbose="2"
workingDir="${basedir}" workingDir="${basedir}"
@ -865,16 +922,6 @@
<jvmarg line="${cofoja.jvm.args}"/> <jvmarg line="${cofoja.jvm.args}"/>
<!-- <jvmarg value="-Xdebug"/> --> <!-- <jvmarg value="-Xdebug"/> -->
<!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> --> <!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
<classpath>
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
<pathelement location="${scala.classes}" />
<pathelement location="${java.contracts}" />
<pathelement location="${java.public.test.classes}" />
<pathelement location="${java.private.test.classes}" />
<pathelement location="${scala.public.test.classes}" />
<pathelement location="${scala.private.test.classes}" />
</classpath>
<classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/> <classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/>
<classfileset dir="${java.private.test.classes}" erroronmissingdir="false"> <classfileset dir="${java.private.test.classes}" erroronmissingdir="false">
@ -904,6 +951,10 @@
</sequential> </sequential>
</macrodef> </macrodef>
<target name="test.init">
<property name="testng.classpath" value="testng.default.classpath" />
</target>
<target name="alltests"> <target name="alltests">
<antcall target="test" inheritAll="false"/> <antcall target="test" inheritAll="false"/>
<antcall target="integrationtest" inheritAll="false"/> <antcall target="integrationtest" inheritAll="false"/>
@ -916,62 +967,81 @@
<antcall target="pipelinetest.public" inheritAll="false"/> <antcall target="pipelinetest.public" inheritAll="false"/>
</target> </target>
<target name="alltests.gatk.packagejar" depends="init.buildpublic,package">
<antcall target="test.public" inheritAll="false">
<param name="testng.classpath" value="testng.gatk.releasetest.classpath" />
</antcall>
<antcall target="integrationtest.public" inheritAll="false">
<param name="testng.classpath" value="testng.gatk.releasetest.classpath" />
</antcall>
</target>
<target name="alltests.queue.packagejar" depends="init.buildpublic,queue">
<antcall target="package" inheritAll="false">
<param name="executable" value="Queue" />
</antcall>
<antcall target="pipelinetest.public" inheritAll="false">
<param name="executable" value="Queue" />
<param name="testng.classpath" value="testng.queue.releasetest.classpath" />
</antcall>
</target>
<!-- Our four different test conditions: Test, IntegrationTest, PerformanceTest, PipelineTest --> <!-- Our four different test conditions: Test, IntegrationTest, PerformanceTest, PipelineTest -->
<target name="test" depends="init.buildall,test.compile,vcf.jar" description="Run unit tests"> <target name="test" depends="init.buildall,test.compile,vcf.jar,test.init" description="Run unit tests">
<condition property="ttype" value="*UnitTest" else="${single}"> <condition property="ttype" value="*UnitTest" else="${single}">
<not><isset property="single"/></not> <not><isset property="single"/></not>
</condition> </condition>
<run-test testtype="${ttype}" outputdir="${report}/${ttype}" runfailed="false"/> <run-test testtype="${ttype}" outputdir="${report}/${ttype}" classpath="${testng.classpath}" runfailed="false"/>
</target> </target>
<target name="test.public" depends="init.buildpublic,test"/> <target name="test.public" depends="init.buildpublic,test"/>
<target name="integrationtest" depends="init.buildall,test.compile" description="Run integration tests"> <target name="integrationtest" depends="init.buildall,test.compile,test.init" description="Run integration tests">
<condition property="itype" value="*IntegrationTest" else="${single}"> <condition property="itype" value="*IntegrationTest" else="${single}">
<not><isset property="single"/></not> <not><isset property="single"/></not>
</condition> </condition>
<run-test testtype="${itype}" outputdir="${report}/${itype}" runfailed="false"/> <run-test testtype="${itype}" outputdir="${report}/${itype}" classpath="${testng.classpath}" runfailed="false"/>
</target> </target>
<target name="integrationtest.public" depends="init.buildpublic,integrationtest"/> <target name="integrationtest.public" depends="init.buildpublic,integrationtest"/>
<target name="performancetest" depends="init.buildall,test.compile" description="Run performance tests"> <target name="performancetest" depends="init.buildall,test.compile,test.init" description="Run performance tests">
<condition property="ptype" value="*PerformanceTest" else="${single}"> <condition property="ptype" value="*PerformanceTest" else="${single}">
<not><isset property="single"/></not> <not><isset property="single"/></not>
</condition> </condition>
<run-test testtype="${ptype}" outputdir="${report}/${ptype}" runfailed="false"/> <run-test testtype="${ptype}" outputdir="${report}/${ptype}" classpath="${testng.classpath}" runfailed="false"/>
</target> </target>
<target name="performancetest.public" depends="init.buildpublic,performancetest" /> <target name="performancetest.public" depends="init.buildpublic,performancetest" />
<target name="pipelinetest" depends="init.buildall,test.compile" description="Run pipeline tests"> <target name="pipelinetest" depends="init.buildall,test.compile,test.init" description="Run pipeline tests">
<condition property="pipetype" value="*PipelineTest" else="${single}"> <condition property="pipetype" value="*PipelineTest" else="${single}">
<not><isset property="single"/></not> <not><isset property="single"/></not>
</condition> </condition>
<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/> <run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" classpath="${testng.classpath}" runfailed="false"/>
</target> </target>
<target name="pipelinetest.public" depends="init.buildpublic,pipelinetest" /> <target name="pipelinetest.public" depends="init.buildpublic,pipelinetest" />
<target name="pipelinetestrun" depends="init.buildall,test.compile" description="Run pipeline tests"> <target name="pipelinetestrun" depends="init.buildall,test.compile,test.init" description="Run pipeline tests">
<property name="pipeline.run" value="run"/> <property name="pipeline.run" value="run"/>
<condition property="pipetype" value="*PipelineTest" else="${single}"> <condition property="pipetype" value="*PipelineTest" else="${single}">
<not><isset property="single"/></not> <not><isset property="single"/></not>
</condition> </condition>
<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/> <run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" classpath="${testng.classpath}" runfailed="false"/>
</target> </target>
<target name="pipelinetestrun.public" depends="init.buildpublic,pipelinetestrun" /> <target name="pipelinetestrun.public" depends="init.buildpublic,pipelinetestrun" />
<target name="failed-test" depends="init.buildall,test.compile"> <target name="failed-test" depends="init.buildall,test.compile,test.init">
<run-test testtype="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/> <run-test testtype="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
</target> </target>
<target name="failed-integration" depends="init.buildall,test.compile"> <target name="failed-integration" depends="init.buildall,test.compile,test.init">
<run-test testtype="${report}/*IntegrationTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/> <run-test testtype="${report}/*IntegrationTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
</target> </target>
<target name="failed-performance" depends="init.buildall,test.compile"> <target name="failed-performance" depends="init.buildall,test.compile,test.init">
<run-test testtype="${report}/*PerformanceTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/> <run-test testtype="${report}/*PerformanceTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
</target> </target>
<target name="failed-pipeline" depends="init.buildall,test.compile"> <target name="failed-pipeline" depends="init.buildall,test.compile,test.init">
<run-test testtype="${report}/*PipelineTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/> <run-test testtype="${report}/*PipelineTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
</target> </target>
<!-- ******************************************************************************** --> <!-- ******************************************************************************** -->
@ -1029,14 +1099,14 @@
<!-- Unzip all classes from their current locations and assemble them in a staging directory --> <!-- Unzip all classes from their current locations and assemble them in a staging directory -->
<target name="stage" description="stage files for distribution"> <target name="stage" description="stage files for distribution">
<mkdir dir="staging"/> <mkdir dir="${staging.dir}"/>
<!-- <!--
HACK: Create the edu directory before EDU on case-insensitive mac filesystems. HACK: Create the edu directory before EDU on case-insensitive mac filesystems.
The ivy dependency colt -> concurrent contains an EDU.oswego package which The ivy dependency colt -> concurrent contains an EDU.oswego package which
BCEL doesn't even pull in but messes up edu.mit.broad. BCEL doesn't even pull in but messes up edu.mit.broad.
--> -->
<mkdir dir="staging/edu"/> <mkdir dir="${staging.dir}/edu"/>
<unjar dest="staging" overwrite="false"> <unjar dest="${staging.dir}" overwrite="false">
<fileset dir="${dist.dir}"> <fileset dir="${dist.dir}">
<patternset refid="dependency.mask" /> <patternset refid="dependency.mask" />
</fileset> </fileset>
@ -1045,8 +1115,8 @@
<!-- Build a package consisting of all supporting files --> <!-- Build a package consisting of all supporting files -->
<target name="package" depends="dist,stage" description="bundle up an executable for distribution"> <target name="package" depends="dist,stage" description="bundle up an executable for distribution">
<mkdir dir="dist/packages" /> <mkdir dir="${package.output.dir}" />
<xslt destdir="dist/packages" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false"> <xslt destdir="${package.output.dir}" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false">
<flattenmapper/> <flattenmapper/>
<fileset dir="${package.xml.dir}"> <fileset dir="${package.xml.dir}">
<include name="${executable}.xml" /> <include name="${executable}.xml" />
@ -1057,11 +1127,11 @@
</fileset> </fileset>
</xslt> </xslt>
<ant antfile="${dist.dir}/packages/${executable}.xml" target="package" /> <ant antfile="${package.output.dir}/${executable}.xml" target="package" />
</target> </target>
<target name="release" depends="package" description="release a build, putting each file in a location specified by the package"> <target name="release" depends="package" description="release a build, putting each file in a location specified by the package">
<ant antfile="${dist.dir}/packages/${executable}.xml" target="release" /> <ant antfile="${package.output.dir}/${executable}.xml" target="release" />
</target> </target>
<!-- Build a subset of picard with only those classes we need by completely abusing the packaging system --> <!-- Build a subset of picard with only those classes we need by completely abusing the packaging system -->
@ -1070,7 +1140,7 @@
<!-- Build out a classpath --> <!-- Build out a classpath -->
<pathconvert property="required.picard.jars" pathsep=":"> <pathconvert property="required.picard.jars" pathsep=":">
<fileset dir="${basedir}"> <fileset dir="${basedir}">
<include name="staging" /> <include name="${staging.dir}" />
<include name="${lib.dir}/picard-*.*.*.jar" /> <include name="${lib.dir}/picard-*.*.*.jar" />
<include name="${lib.dir}/sam-*.jar" /> <include name="${lib.dir}/sam-*.jar" />
</fileset> </fileset>
@ -1078,14 +1148,14 @@
<echo message="required.picard.jars=${required.picard.jars}" /> <echo message="required.picard.jars=${required.picard.jars}" />
<!-- Stage picard-private --> <!-- Stage picard-private -->
<delete dir="staging" /> <delete dir="${staging.dir}" />
<mkdir dir="staging" /> <mkdir dir="${staging.dir}" />
<unjar src="${picard.dist.dir}/picard-private.jar" dest="staging" overwrite="true" /> <unjar src="${picard.dist.dir}/picard-private.jar" dest="${staging.dir}" overwrite="true" />
<!-- Use the packaging system to extract parts of picard-private we need --> <!-- Use the packaging system to extract parts of picard-private we need -->
<mkdir dir="${dist.dir}/packages" /> <mkdir dir="${package.output.dir}" />
<xslt in="${package.xml.dir}/PicardPrivate.xml" out="${dist.dir}/packages/BuildPicardPrivate.xml" style="${package.xml.dir}/CreatePackager.xsl" /> <xslt in="${package.xml.dir}/PicardPrivate.xml" out="${package.output.dir}/BuildPicardPrivate.xml" style="${package.xml.dir}/CreatePackager.xsl" />
<ant antfile="${dist.dir}/packages/BuildPicardPrivate.xml"> <ant antfile="${package.output.dir}/BuildPicardPrivate.xml">
<property name="additional.jars" value="${required.picard.jars}" /> <property name="additional.jars" value="${required.picard.jars}" />
</ant> </ant>
</target> </target>
@ -1121,7 +1191,7 @@
<delete dir="${build.dir}"/> <delete dir="${build.dir}"/>
<delete dir="${lib.dir}"/> <delete dir="${lib.dir}"/>
<delete dir="dump"/> <delete dir="dump"/>
<delete dir="staging"/> <delete dir="${staging.dir}"/>
<delete dir="${dist.dir}"/> <delete dir="${dist.dir}"/>
<delete dir="pipelinetests"/> <delete dir="pipelinetests"/>
</target> </target>

10
public/packages/GATKEngine.xml
View File

@ -26,14 +26,10 @@
<package name="GATKEngine"> <package name="GATKEngine">
<executable name="GATKEngine"> <executable name="GATKEngine">
<dependencies> <dependencies>
<!-- Core walkers --> <!-- Package everything in org.broadinstitute.sting -->
<package name="org.broadinstitute.sting.gatk.walkers.**" /> <package name="org.broadinstitute.sting.**" />
<!-- All non-oneoff GATK-specific RODs -->
<package name="org.broadinstitute.sting.utils.codecs.**" />
<!-- Filters -->
<package name="org.broadinstitute.sting.gatk.filters" />
<!-- Tribble codecs --> <!-- Tribble codecs -->
<package name="org.broad.tribble.*" /> <package name="org.broad.tribble.**" />
<!-- Workaround - depend on the logger impl required by JEXL --> <!-- Workaround - depend on the logger impl required by JEXL -->
<package name="org.apache.commons.logging.impl" /> <package name="org.apache.commons.logging.impl" />
</dependencies> </dependencies>