45bf45d5deac830c90a6c382ed3a2f53fff251b6 braney Mon Oct 1 14:25:16 2018 -0700 stop special casing jtidy (fixes TrackCheck problem ) diff --git java/build.xml java/build.xml index 33d9b5f..d76f692 100644 --- java/build.xml +++ java/build.xml @@ -1,217 +1,215 @@ <?xml version="1.0"?> <!-- Build file for genome.ucsc.edu QA library directory --> <project name="qa" default="baseBuild" basedir="."> <target name="init"> <!-- directories --> <property environment="env"/> <!-- N.B. use MACHTYPE due since scripts ref files that maybe in diff locations on diff OSs --> <property name="bin.dir" value="${env.HOME}/bin/${env.MACHTYPE}"/> <property name="build.dir" value="."/> <property name="src.dir" value="src"/> <property name="doc.dir" value="/usr/local/apache/htdocs/qa"/> <property name="classes.dir" value="${build.dir}/classes"/> <!-- compile props --> <property name="build.debug" value="on" /> <property name="build.optimize" value="off" /> <property name="build.compiler" value="modern" /> <property name="build.includes" value="**/*.java"/> <property name="build.excludes" value="edu/ucsc/genome/qa/cgiCheck/HGNearCheck.java,edu/ucsc/genome/qa/lib/ErrorFile.java"/> <!-- javadoc props --> <property name="javadoc.packages" value="*"/> <property name="javadoc.dir" value="${doc.dir}/api"/> <!-- classpath fun --> <property name="httpunit.jar" value="/usr/share/java/httpunit.jar"/> - <property name="jtidy.jar" value="/cluster/bin/java/jtidy.jar"/> <property name="rhino.jar" value="/usr/share/java/rhino.jar"/> <property name="mysql.jar" value="/cluster/bin/java/mysql-connector-java-3.0.16-ga-bin.jar"/> <path id="qa.classpath"> <pathelement location="${classes.dir}"/> <pathelement path="${httpunit.jar}"/> - <pathelement path="${jtidy.jar}"/> <pathelement path="${rhino.jar}"/> <pathelement path="${mysql.jar}"/> <pathelement path="${java.class.path}/"/> </path> </target> <target name="build" depends="compile, generateWrappers, javaDoc, quickTest"/> <target name="baseBuild" depends="compile, generateWrappers"/> <target name="compile" depends="init" description="Compile the source files"> <mkdir dir="${classes.dir}" /> <javac srcdir="${src.dir}" destdir="${classes.dir}" debug="${build.debug}" optimize="${build.optimize}" deprecation="${build.deprecation}" includes="${build.includes}" excludes="${build.excludes}" classpathref="qa.classpath"> </javac> </target> <target name="javaDoc" depends="init" description="Build the API documentation"> <mkdir dir="${javadoc.dir}"/> <javadoc destdir="${javadoc.dir}" package="true" packagenames="${javadoc.packages}" classpathref="qa.classpath" > <sourcepath> <pathelement path="${src.dir}"/> </sourcepath> </javadoc> </target> <target name="setQuickTest"> <property name="test.props" value="src/edu/ucsc/genome/qa/cgiCheck/quick.props" /> </target> <target name="setHourTest"> <property name="test.props" value="src/edu/ucsc/genome/qa/cgiCheck/hour.props" /> </target> <target name="setFullTest"> <property name="test.props" value="src/edu/ucsc/genome/qa/cgiCheck/full.props" /> </target> <target name="someTest"> <java classname="edu.ucsc.genome.qa.cgiCheck.TrackCheck" classpathref="qa.classpath"> <arg value="${test.props}"/> </java> <java classname="edu.ucsc.genome.qa.cgiCheck.HGGeneCheck" classpathref="qa.classpath"> <arg value="${test.props}"/> </java> <java classname="edu.ucsc.genome.qa.cgiCheck.PBGeneCheck" classpathref="qa.classpath"> <arg value="${test.props}"/> </java> </target> <target name="quickTest" depends="init,setQuickTest,someTest" description="Quick test of the tests"> </target> <target name="hourTest" depends="init,setHourTest,someTest" description="Roughly hour long test of site"> </target> <target name="fullTest" depends="init,setFullTest,someTest" description="Overnight automated test of site."> </target> <target name="generateWrappers" depends="init" description="Generate wrapper scripts for program classes."> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.qa.cgiCheck"/> <param name="progClass" value="HGGeneCheck"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.qa.cgiCheck"/> <param name="progClass" value="HGNearCheck"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.qa.cgiCheck"/> <param name="progClass" value="PBGeneCheck"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.qa.cgiCheck"/> <param name="progClass" value="TrackCheck"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.qa.linkCheck"/> <param name="progClass" value="LinkCheck"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.qa.monitor"/> <param name="progClass" value="ApacheMonitor"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.qa.monitor"/> <param name="progClass" value="ApacheReport"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.qa.monitor"/> <param name="progClass" value="DatabaseMonitor"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.qa.monitor"/> <param name="progClass" value="FileCheck"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.qa.filter"/> <param name="progClass" value="ScoreFilter"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.util"/> <param name="progClass" value="GetMaxCoord"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.util"/> <param name="progClass" value="LoadQuality"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.util"/> <param name="progClass" value="ScaffoldQuality"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.util"/> <param name="progClass" value="LiftOverTest"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.util"/> <param name="progClass" value="LiftOverRescue"/> </antcall> <antcall target="generateWrapper" inheritAll="yes" inheritRefs="yes"> <param name="progPkg" value="edu.ucsc.genome.util"/> <param name="progClass" value="SequenceCheck"/> </antcall> </target> <target name="clean" depends="init"> <delete dir="${classes.dir}" quiet="yes"/> <delete dir="${javadoc.dir}" quiet="yes"/> </target> <!-- target to generate a run script for one of the program classes. - call with `progPkg parameter set to package name and 'progClass' - set to the class name, which is also the name of the of the - wrapper to generate --> <target name="generateWrapper" description="Generate a wrapper script for a class."> <property name="run.classpath" refid="qa.classpath"/> <property name="wrapper" value="${bin.dir}/${progClass}"/> <dependset> <!-- rebuild if template or build.xml changes --> <srcfilelist dir="misc" files="runTemplate.sh,build.xml"/> <srcfilelist dir="." files=""/> <targetfilelist dir="${bin.dir}" files="${progClass}"/> </dependset> <!-- should be able specify a filterset inside of the copy - instead of seperately, however this didn't work - in ant 1.5.4 --> <copy file="misc/runTemplate.sh" tofile="${wrapper}" overwrite="yes"/> <replace file="${wrapper}" token="@JAVA_HOME@" value="${java.home}"/> <replace file="${wrapper}" token="@CLASSPATH@" value="${run.classpath}"/> <replace file="${wrapper}" token="@PROG_CLASS@" value="${progPkg}.${progClass}"/> <chmod file="${wrapper}" perm="a+x"/> </target> </project>