defs.xml

<!--
  ~ The MIT License
  ~
  ~ Copyright (c) 2018 The Broad Institute
  ~
  ~ Permission is hereby granted, free of charge, to any person obtaining a copy
  ~ of this software and associated documentation files (the "Software"), to deal
  ~ in the Software without restriction, including without limitation the rights
  ~ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  ~ copies of the Software, and to permit persons to whom the Software is
  ~ furnished to do so, subject to the following conditions:
  ~
  ~ The above copyright notice and this permission notice shall be included in
  ~ all copies or substantial portions of the Software.
  ~
  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  ~ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  ~ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  ~ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  ~ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  ~ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  ~ THE SOFTWARE.
  -->

<!-- To be included in build.xml -->
<!-- Get GIT hash, if available, otherwise leave it blank.  -->
<exec executable="git" outputproperty="repository.revision" failifexecutionfails="true" errorproperty="">
    <arg value="log"/>
    <arg value="-1"/>
    <arg value="--pretty=format:%h_%at"/>
</exec>
<property name="repository.revision" value=""/>


<property name="Drop-seq.version" value="2.4.0"/>
<property name="zip.label" value="Drop-seq_tools-${Drop-seq.version}"/>
<property name="javac.debug" value="true"/>
<property name="javac.target" value="1.8"/>
<property name="testng.verbosity" value="2"/>
<property name="jdk.url" value="http://docs.oracle.com/javase/8/docs/api/"/>

<property environment="env"/>
<property name="env.TMPDIR" value="/tmp"/>


<macrodef name="compile">
    <attribute name="destdir"/>
    <attribute name="src"/>
    <attribute name="classpathrefid"/>
    <sequential>
        <mkdir dir="@{destdir}"/>
        <javac destdir="@{destdir}"
               optimize="${javac.opt}"
               includes ="org/broadinstitute/dropseqrna/**/*.*"
               debug="${javac.debug}"
               includeantruntime="false">
            <src path="@{src}"/>
            <classpath refid="@{classpathrefid}"/>
        </javac>
    </sequential>
</macrodef>

<!-- TEST -->
<taskdef resource="testngtasks" classpathref="test.classpath"/>
<macrodef name="test">
    <attribute name="destdir"/>
    <attribute name="classpathrefid"/>
    <attribute name="classes"/>
    <sequential>
        <testng suitename="Drop-seq-tests" classpathref="@{classpathrefid}" outputdir="@{destdir}"
                failureproperty="tests.failed" excludedgroups="slow" workingDir="${basedir}"
                verbose="${testng.verbosity}">
            <classpath>
                <pathelement path="@{classes}"/>
            </classpath>
            <classfileset dir="@{classes}">
                <include name="**/Test*.class"/>
                <include name="**/*Test.class"/>
            </classfileset>
            <jvmarg value="-Xmx1G"/>
            <jvmarg value="-Djava.io.tmpdir=${env.TMPDIR}"/>
        </testng>
        <fail if="tests.failed" message="There were failed unit tests"/>
    </sequential>
</macrodef>

<macrodef name="single-test">
    <attribute name="destdir"/>
    <attribute name="classpathrefid"/>
    <attribute name="classes"/>
    <sequential>
        <fail unless="test.name" message="Please provide input test: -Dtest.name=..." />
        <testng suitename="Drop-seq-tests" classpathref="@{classpathrefid}" outputdir="@{destdir}"
                failureproperty="tests.failed" excludedgroups="slow" workingDir="${basedir}"
                verbose="${testng.verbosity}">
            <classpath>
                <pathelement path="@{classes}"/>
            </classpath>
            <classfileset dir="@{classes}">
                <include name="**/Test*.class"/>
                <include name="**/${test.name}.class"/>
            </classfileset>
            <jvmarg value="-Xmx1G"/>
            <jvmarg value="-Djava.io.tmpdir=${env.TMPDIR}"/>
        </testng>
        <fail if="tests.failed" message="There were failed unit tests"/>
    </sequential>
</macrodef>

        <!-- Create script to invoke the given main program. -->
<macrodef name="package-command">
    <attribute name="title"/>
    <attribute name="visibility"/>
    <sequential>
        <!-- Copy template for script, and then replace slugs with appropriate values -->
        <copy file="src/scripts/@{visibility}_clp_template.sh" tofile="${dist}/scripts/@{title}"/>
        <replace file="${dist}/scripts/@{title}">
            <replacefilter token="__PROGNAME__" value="@{title}"/>
        </replace>
        <chmod perm="ug+rx" file="${dist}/@{title}"/>
    </sequential>
</macrodef>

<!-- jacoco stuff
 public.dir must be defined before this file is included.
 Add this:
 xmlns:jacoco="antlib:org.jacoco.ant"
 to the <project> element in the file where this file is included.
 -->
<property name="jacoco.dir" location="jacoco_reports"/>
<property name="jacoco.binary" location="${jacoco.dir}/jacoco.exec"/>

<taskdef uri="antlib:org.jacoco.ant" resource="org/jacoco/ant/antlib.xml">
    <classpath path="${public.dir}/lib/test/jacocoant.jar"/>
</taskdef>

<!-- Unfortunately can't invoke a macro from inside <jacoco:coverage>, so testng invocation is duplicated -->
<target name="coverage" depends="compile-tests">
<jacoco:coverage destfile="${jacoco.binary}">
    <testng suitename="Drop-seq-tests" classpathref="test.classpath" outputdir="${test.output}"
            failureproperty="tests.failed" excludedgroups="slow" workingDir="${basedir}"
            verbose="${testng.verbosity}">
        <classpath>
            <pathelement path="${classes.test}"/>
        </classpath>
        <classfileset dir="${classes.test}">
            <include name="**/Test*.class"/>
            <include name="**/*Test.class"/>
        </classfileset>
        <jvmarg value="-Xmx1G"/>
    </testng>
</jacoco:coverage>
</target>

<target name="coverage-report">
<jacoco:report>

    <executiondata>
        <file file="${jacoco.binary}"/>
    </executiondata>

    <structure name="Drop-seq">
        <classfiles>
            <fileset dir="${classes}"/>
        </classfiles>
        <sourcefiles encoding="UTF-8">
            <fileset dir="src"/>
        </sourcefiles>
    </structure>

    <xml destfile="${jacoco.dir}/jacoco.xml"/>
    <html destdir="${jacoco.dir}"/>

</jacoco:report>
</target>

<target name="coverage-and-report" depends="coverage, coverage-report"
        description="Run unit test suite with coverage and generate report"/>