build.xml

<project name="public-tools" default="zip-nojre">

  <property name="min.ant.version" value="1.9.0" />
  <antversion property="this.ant.version" atleast="${min.ant.version}" />
  <fail message="The required minimum version of ant is ${min.ant.version}, you have ${ant.version}" unless="this.ant.version" />

  <dirname property="public.tools.basedir" file="${ant.file.public-tools}"/>
  <property name="tools.src.dir" location="${public.tools.basedir}/src"/>
  <property name="tools.src.lib.dir" location="${public.tools.basedir}/lib"/>
  <property name="tools.test.dir" location="${public.tools.basedir}/test"/>
  <property name="tools.test.lib.dir" location="${public.tools.basedir}/testLib"/>
  <property name="buildtools.dir" location="${public.tools.basedir}/buildLib"/> <!-- Libraries supporting the build process itself -->

  <property name="dist.dir" location="${public.tools.basedir}/dist"/>
  <property name="build.dir" location="${public.tools.basedir}/build"/>

  <property name="build.src" location="${build.dir}/src"/>
  <property name="build.test" location="${build.dir}/test"/>
  <property name="build.junit" location="${build.dir}/junit"/>
  <property name="build.text" location="${build.dir}/text"/>
  <property name="build.executable" location="${build.dir}/executable"/>
  <property name="build.misc" location="${build.dir}/misc"/>

  <property name="build.sysclasspath" value="ignore"/>
  <taskdef resource="net/sf/antcontrib/antlib.xml">
    <classpath>
      <pathelement location="${buildtools.dir}/ant-contrib-1.0b3.jar"/>
    </classpath>
  </taskdef>

  <property name="product" value="RTG Tools" />
  <property name="product.version" value="3.12.1" />
  <property name="product.repo" value="RealTimeGenomics/rtg-tools" />
  <property name="resources" value="tools" />
  <property name="main.class" value="com.rtg.RtgTools" />

  <property name="regression.update" value=""/> <!-- Empty means don't update nano-regression results -->

  <!-- This must currently be built from the RTG fork of htsjdk -->
  <property name="htsjdk.jar" value="sam-rtg-2.23.0.1.jar"/>


  <!-- Define resource collections for compilation, running, etc -->

  <!-- These jars are needed at run time -->
  <fileset id="tools.runtime.libs" dir="${tools.src.lib.dir}">
    <include name="${htsjdk.jar}" />
    <include name="gzipfix.jar" />
    <include name="RPlot.jar" />
    <include name="velocity-1.7.jar" />
    <include name="velocity-tools-generic.jar" />
    <include name="commons-collections-3.2.1.jar" />
    <include name="commons-lang-2.4.jar" />
    <include name="commons-compress-1.4.1.jar" />
    <include name="snappy-java-1.1.4.jar" />
    <include name="json-simple-1.1.1.jar" />
    <include name="js-20.2.0.jar" />
    <include name="js-scriptengine-20.2.0.jar" />
    <include name="graal-sdk-20.2.0.jar" />
    <include name="regex-20.2.0.jar" />
    <include name="truffle-api-20.2.0.jar" />
    <include name="icu4j-67.1.jar" />
  </fileset>

  <path id="tools.runtime.classpath">
    <pathelement path="${build.src}" />
    <pathelement path="${tools.src.dir}" />
    <resources refid="runtime.libs" />
  </path>

  <union id="tools.runtime.test.classpath">
    <resources refid="runtime.classpath"/>
    <path>
      <pathelement path="${build.test}" />
      <pathelement path="${tools.test.dir}" />
      <resources refid="runtime.test.libs" />
    </path>
  </union>

  <union id="tools.jar-src">
    <fileset dir="${build.misc}">
      <include name="com/rtg/**" />
    </fileset>
    <fileset dir="${build.src}" />
    <fileset dir="${tools.src.dir}">
      <include name="com/**/*.properties"/>
      <include name="com/rtg/simulation/variants/*.txt"/>
      <include name="com/rtg/reference/resources/**/*"/>
      <include name="com/rtg/report/resources/*"/>
      <include name="com/rtg/vcf/resources/*"/>
      <include name="com/rtg/mode/BLOSUM45" />
      <include name="com/rtg/mode/BLOSUM62" />
      <include name="com/rtg/mode/BLOSUM80" />
      <include name="com/rtg/graph/**/*.png"/>
    </fileset>
    <zipfileset src="${tools.src.lib.dir}/${htsjdk.jar}" excludes="META-INF/**"/>

    <zipfileset src="${tools.src.lib.dir}/velocity-1.7.jar" excludes="META-INF/**" />

    <zipfileset src="${tools.src.lib.dir}/velocity-tools-generic.jar" excludes="META-INF/**" />
    <zipfileset src="${tools.src.lib.dir}/commons-collections-3.2.1.jar" excludes="META-INF/**" />
    <zipfileset src="${tools.src.lib.dir}/commons-lang-2.4.jar" excludes="META-INF/**" />
    <zipfileset src="${tools.src.lib.dir}/commons-compress-1.4.1.jar" excludes="META-INF/**" />
    <zipfileset src="${tools.src.lib.dir}/snappy-java-1.1.4.jar" excludes="META-INF/**" includes="**/*.class" />
    <zipfileset src="${tools.src.lib.dir}/json-simple-1.1.1.jar" excludes="META-INF/**" />

    <zipfileset src="${tools.src.lib.dir}/RPlot.jar" excludes="META-INF/**"/>
    <zipfileset src="${tools.src.lib.dir}/gzipfix.jar">
      <include name="com/rtg/util/gzip/WorkingGzipInputStream.class" />
    </zipfileset>
  </union>

  <union id="tools.jar-test">
    <resources refid="jar-src"/>
    <fileset dir="${build.test}">
      <include name="**/*.class"/>
    </fileset>
    <fileset dir="${tools.test.dir}">
      <include name="com/**/*.txt"/>
      <include name="com/**/*.properties"/>
      <include name="com/rtg/**/resources/**/*"/>
      <include name="com/rtg/mode/BLOSUM*" />
      <include name="com/rtg/util/testFile"/>
      <include name="com/rtg/util/cli/spell.*"/>
    </fileset>
    <zipfileset src="${tools.test.lib.dir}/spelling.jar"/>
    <zipfileset src="${tools.test.lib.dir}/junit.jar" excludes="META-INF/**"/>
    <zipfileset src="${tools.test.lib.dir}/hamcrest-core-1.3.jar" excludes="META-INF/**"/>
  </union>


  <!-- These jars are only needed at compile time -->
  <fileset id="compiletime.libs" dir="${tools.src.lib.dir}">
    <include name="jumble-annotations.jar" />
    <include name="findbugs-annotations.jar" />
    <include name="findbugs-jsr305.jar" />
  </fileset>

  <union id="runtime.libs">
    <resources refid="tools.runtime.libs"/>
  </union>

  <!-- These jars are needed at test run time -->
  <fileset id="runtime.test.libs" dir="${tools.test.lib.dir}" includes="*.jar"/>

  <path id="src.path">
    <pathelement path="${tools.src.dir}" />
  </path>

  <path id="test.path">
    <pathelement path="${tools.test.dir}" />
  </path>

  <union id="runtime.classpath">
    <resources refid="tools.runtime.classpath"/>
  </union>

  <union id="runtime.test.classpath">
    <resources refid="tools.runtime.test.classpath"/>
  </union>

  <union id="jar-src">
    <resources refid="tools.jar-src"/>
  </union>

  <union id="jar-test">
    <resources refid="jar-src"/>
    <resources refid="tools.jar-test"/>
  </union>

  <fileset id="common-resources" dir="${public.tools.basedir}/installer/resources/common"/>

  <union id="tools-resources">
    <fileset refid="common-resources" />
    <fileset dir="${public.tools.basedir}/installer/resources/tools"/>
  </union>


  <!-- Targets -->

  <target name="clean">
    <delete dir="${dist.dir}"/>
    <delete dir="${build.dir}"/>
  </target>

  <target name="init">
    <mkdir dir="${dist.dir}"/>
    <mkdir dir="${build.dir}"/>
    <mkdir dir="${build.src}"/>
    <mkdir dir="${build.test}"/>
    <mkdir dir="${build.text}"/>
    <mkdir dir="${build.executable}"/>
    <mkdir dir="${build.junit}"/>
    <mkdir dir="${build.misc}"/>
  </target>

  <property name="vcs.info.cmd" value="git"/>
  <property name="vcs.info.args" value="rev-list --abbrev-commit -n 1 HEAD"/>

  <target name="rtg-vcs-info" depends="init" unless="rtg.vcs.commit.revision">
    <exec executable="${vcs.info.cmd}" outputproperty="vcs.cmd.out" resultproperty="vcs.cmd.rc" dir="${public.tools.basedir}">
      <arg line="${vcs.info.args}"/>
    </exec>
    <condition property="rtg.vcs.commit.revision"
               value="unknown"
               else="${vcs.cmd.out}">
      <isfailure code="${vcs.cmd.rc}"/>
    </condition>
    <echo message="Current build revision is ${rtg.vcs.commit.revision}"/>
  </target>


  <target name="compile-src" depends="init" description="Compiles all code in src.">
    <property name="src.path" refid="src.path" />
    <javac destdir="${build.src}"  debug="true"
           sourcepath="" srcdir="${src.path}">
      <compilerarg value="-Xlint" />
      <compilerarg value="-Xlint:-serial" />
      <compilerarg value="-proc:none" />
      <classpath>
        <resources refid="runtime.libs"/>
        <resources refid="compiletime.libs"/>
      </classpath>
    </javac>
  </target>

  <target name="compile-test" depends="compile-src" description="Compiles all code in test.">
    <property name="test.path" refid="test.path" />
    <javac destdir="${build.test}" debug="true"
           sourcepath="" srcdir="${test.path}">
      <compilerarg value="-Xlint" />
      <compilerarg value="-Xlint:-serial" />
      <compilerarg value="-proc:none" />
      <classpath>
        <pathelement path="${build.src}"/>
        <resources refid="runtime.libs"/>
        <resources refid="compiletime.libs"/>
        <resources refid="runtime.test.libs" />
      </classpath>
    </javac>
  </target>

  <target name="compile" depends="compile-test" description="Compile all Java source code."/>

  <!--
       This definition puts a property value into a file, but only if it
       is different to the value that is already there, in order to
       prevent the triggering of expensive targets multiple times.
  -->
  <macrodef name="set-version-file">
    <attribute name="file"/>
    <attribute name="value"/>
    <attribute name="strict" default="false"/>
    <sequential>
      <local name="old-value"/>
      <loadfile property="old-value" srcFile="@{file}" failonerror="false" quiet="true"/>
      <fail message="Need to clean first. (last='${old-value}' current='@{value}')">
        <condition>
          <and>
            <istrue value="@{strict}"/>
            <available file="@{file}"/>
            <not>
              <equals arg1="${old-value}" arg2="@{value}"/>
            </not>
          </and>
        </condition>
      </fail>
      <if>
        <not>
          <equals arg1="${old-value}" arg2="@{value}"/>
        </not>
        <then>
          <echo message="Setting @{file} to @{value}"/>
          <echo file="@{file}" message="@{value}"/>
        </then>
      </if>
    </sequential>
  </macrodef>

  <target name="set-rtg-build-version" depends="init,rtg-vcs-info">
    <tstamp> <format property="build.time" pattern="yyyy-MM-dd" /></tstamp>
    <set-version-file file="${build.src}/com/rtg/build.version" value="${rtg.vcs.commit.revision}"/>
    <set-version-file file="${build.src}/com/rtg/build.time" value="${build.time}"/>
  </target>

  <target name="set-rtg-build-product">
    <set-version-file file="${build.misc}/com/rtg/product.version" value="${product.version}"/>
    <set-version-file file="${build.misc}/com/rtg/product.name" value="${product}" strict="true"/>
    <set-version-file file="${build.misc}/com/rtg/product.repo" value="${product.repo}"/>
  </target>


  <macrodef name="rtg-jar">
    <attribute name="main"/>
    <attribute name="file"/>
    <attribute name="refid"/>
    <sequential>
      <jar destfile="@{file}" duplicate="fail">
        <manifest>
          <attribute name="Main-Class" value="@{main}"/>
          <attribute name="Implementation-Title" value="RTG"/>
          <attribute name="Implementation-Vendor" value="Real Time Genomics"/>
          <attribute name="Class-Path" value="."/>
        </manifest>
        <resources refid="@{refid}"/>
      </jar>
    </sequential>
  </macrodef>

  <target name="rtg-tools.jar" depends="compile-src,set-rtg-build-version,set-rtg-build-product" description="Tools jar.">
    <rtg-jar main="com.rtg.RtgTools" file="${build.dir}/rtg-tools.jar" refid="jar-src"/>
  </target>

  <target name="rtg-all.jar" depends="compile,set-rtg-build-version,set-rtg-build-product" description="Create jar including tests.">
    <rtg-jar main="RtgTestEntry" file="${build.dir}/rtg-all.jar" refid="jar-test"/>
  </target>

  <target name="javadoc" depends="compile-src" description="Build javadocs">
    <javadoc sourcepath="${src.path}" destdir="${build.dir}/javadocs" source="1.8"
             Author="true" Version="true" Package="true"
             useexternalfile="true" additionalparam="-quiet" docfilessubdirs="true">
      <tag name="has" enabled="false"/>
      <tag name="assoc" enabled="false"/>
      <tag name="depend" enabled="false"/>
      <tag name="composed" enabled="false"/>
      <tag name="minOccurs" enabled="false"/>
      <tag name="maxOccurs" enabled="false"/>
      <tag name="nillable" enabled="false"/>
      <tag name="nillableContainer" enabled="false"/>
      <tag name="minOccursContainer" enabled="false"/>
      <tag name="length" enabled="false"/>
      <tag name="minLength" enabled="false"/>
      <tag name="maxLength" enabled="false"/>
      <tag name="enumeration" enabled="false"/>
      <tag name="pattern" enabled="false"/>
      <tag name="minExclusive" enabled="false"/>
      <tag name="maxExclusive" enabled="false"/>
      <tag name="minInclusive" enabled="false"/>
      <tag name="maxInclusive" enabled="false"/>
      <classpath>
        <resources refid="runtime.libs" />
        <resources refid="compiletime.libs" />
      </classpath>
    </javadoc>
  </target>

  <scriptdef language="javascript" name="lowercase">
    <attribute name="value" />
    <attribute name="name" />
    project.setProperty(attributes.get("name"), attributes.get("value").toLowerCase());
  </scriptdef>

  <target name="zip-init" depends="rtg-vcs-info"> <!-- set up properties -->
    <tstamp> <format property="build.tstamp" pattern="yyyyMMddHHmm" /></tstamp>
    <propertyregex property="almostproductfilename" input="${product}" regexp="\s+" global="true" replace="-" />
    <property name="almostproductfilename" value="${product}" />
    <lowercase name="productfilename" value="${almostproductfilename}" />
    <condition property="zipversion"
               value="${productfilename}-${product.version}"
               else="${productfilename}-${product.version}-${rtg.vcs.commit.revision}">
      <istrue value="${release.build}"/>
    </condition>

    <property name="zipfile.base" location="${build.dir}/${zipversion}-base.zip" />
    <property name="zipfile.nojre" location="${dist.dir}/${zipversion}-nojre.zip" />
    <property name="zipfile" value="${zipfile.nojre}" /> <!-- Default when running smoketest -->
    <property name="rtg-jar-for-zip" value="rtg-${resources}.jar"/>
  </target>

  <target name="zip-jars">
    <antcall>
      <target name="${rtg-jar-for-zip}"/>
    </antcall>
  </target>

  <resources id="tools.zip.text">
    <file file="${public.tools.basedir}/installer/README.txt"/>
    <file file="${public.tools.basedir}/installer/ReleaseNotes.txt"/>
  </resources>
  <union id="zip.text">
    <resources refid="tools.zip.text"/>
    <file file="${public.tools.basedir}/LICENSE.txt"/>
  </union>
  <target name="zip-text">
    <copy todir="${build.text}">
      <resources refid="zip.text"/>
      <filterchain>
        <replaceregex pattern="RTG.VERSION" replace="${product}" />
        <fixcrlf eol="crlf" />
      </filterchain>
    </copy>
  </target>

  <target name="zip-exes">
    <union id="executable-resources">
      <fileset dir="${public.tools.basedir}/installer" includes="rtg"/>
      <restrict>
        <resources refid="${resources}-resources"/>
        <rsel:name xmlns:rsel="antlib:org.apache.tools.ant.types.resources.selectors" name="**/*.sh"/>
      </restrict>
    </union>
    <union id="non-executable-resources">
      <fileset dir="${public.tools.basedir}/installer" includes="rtg.bat"/>
      <restrict>
        <resources refid="${resources}-resources"/>
        <rsel:not xmlns:rsel="antlib:org.apache.tools.ant.types.resources.selectors">
          <rsel:name name="**/*.sh"/>
        </rsel:not>
      </restrict>
    </union>
    <copy todir="${build.executable}">
      <resources refid="executable-resources"/>
    </copy>
  </target>

  <target name="zip-base" depends="zip-init,zip-jars,zip-text,zip-exes">
    <zip destfile="${zipfile.base}" duplicate="fail">
      <mappedresources>
        <resources refid="non-executable-resources"/>
        <globmapper from="*" to="${zipversion}/*"/>
      </mappedresources>
      <zipfileset prefix="${zipversion}" dir="${build.text}" includes="*.txt" />
      <zipfileset prefix="${zipversion}" dir="${build.executable}" filemode="755"/>
      <zipfileset fullpath="${zipversion}/RTG.jar" dir="${build.dir}" includes="${rtg-jar-for-zip}"/>
      <zipfileset fullpath="${zipversion}/third-party/gzipfix.jar" dir="${tools.src.lib.dir}" includes="gzipfix.jar" />
    </zip>
  </target>

  <target name="zip-nojre" depends="zip-base" description="Create the distributable zip file without JRE.">
    <copy file="${zipfile.base}" tofile="${zipfile.nojre}"/>
  </target>


  <!--
     Targets that exist to make things bearable for developers running
     stuff from Windows command-line.
    -->

  <property name="run.args" value=""/>

  <target name="run" depends="compile-src" description="Run any class. -Drun.class=xxx -Drun.args=xxx">
    <java classname="${run.class}" fork="true">
      <arg line="${run.args}" />
      <classpath>
        <resources refid="runtime.classpath" />
      </classpath>
    </java>
  </target>

  <target name="runrtg" description="Run RTG. -Drun.args=xxx">
    <antcall target="run">
      <param name="run.class" value="${main.class}"/>
    </antcall>
  </target>


  <property name="test.jvm.args" value="" />
  <property name="junit.jar" value="${tools.test.lib.dir}/junit.jar"/>
  <property name="junit.runner" value="RtgTestEntry" />

  <target name="runtest" depends="compile-src,compile-test" description="Run a unit test class. -Dtest.class=xxx">
    <fail unless="test.class" message="test.class property must be set"/>
    <property name="regression.root" refid="test.path" />
    <java classname="${junit.runner}" fork="true" failonerror="true" dir="${build.junit}">
      <arg line="${test.class}" />
      <jvmarg value="-server" />
      <jvmarg value="-ea" />
      <jvmarg value="-Duser.language=US" />
      <jvmarg value="-Duser.country=US" />
      <jvmarg value="-Djava.awt.headless=true" />
      <jvmarg value="-Drtg.developer=true" />
      <jvmarg value="-Djunit.printFailures=true" />
      <jvmarg value="-Dregression.root=${regression.root}" />
      <jvmarg value="-Dregression.update=${regression.update}" />
      <jvmarg value="-javaagent:${buildtools.dir}/handlechecker.jar" />
      <jvmarg line="${test.jvm.args}" />
      <classpath>
        <pathelement path="${junit.jar}"/>
        <resources refid="runtime.test.classpath" />
      </classpath>
    </java>
  </target>

  <target name="runalltests" description="Run all unit tests">
    <antcall target="runtest">
      <param name="test.class" value="AllTests"/>
    </antcall>
  </target>
</project>