build.xml

<project name="Genbank genome uploader" default="compile" basedir=".">

  <description>
      Build jar-file for genome uploader in genbank format
  </description>

  <!-- set global properties for this build -->
  <property name="src" location="src"/>
  <property name="dst" location="lib/jars"/>
  <property name="classes" location="classes"/>
  <property name="jar.file" value="kbase_transform_deps.jar"/>
  <property name="jarsdir" value="../jars/lib/jars"/>
  <property name="doc" location="docs/javadoc"/>
  <property name="dst.jar.dir" value="lib/jars/kbase/transform/"/>
  <property name="tempunpack" location="unpackedjars"/>
  <property name="war.file" value="KBaseDataImport.war"/>
  <property name="war.dir" value="war"/>

  <fileset dir="${jarsdir}" id="lib">
    <include name="apache_commons/commons-codec-1.8.jar"/>
    <include name="apache_commons/commons-io-2.4.jar"/>
    <include name="apache_commons/commons-fileupload-1.2.2.jar"/>
    <include name="apache_commons/commons-cli-1.2.jar"/>
    <include name="apache_commons/commons-lang3-3.1.jar"/>
    <include name="jackson/jackson-annotations-2.2.3.jar"/>
    <include name="jackson/jackson-core-2.2.3.jar"/>
    <include name="jackson/jackson-databind-2.2.3.jar"/>
    <include name="google/guava-14.0.1.jar"/>
    <include name="kbase/genomes/kbase-genomes-20140411.jar"/>
    <include name="kbase/auth/kbase-auth-1398468950-3552bb2.jar"/>
    <include name="kbase/genomes/kbase-genomes-20140411.jar"/>
    <include name="kbase/common/kbase-common-0.0.7.jar"/>
    <include name="kbase/workspace/WorkspaceClient-0.2.0.jar"/>
    <include name="kbase/workspace/WorkspaceService-0.2.0.jar"/>
    <include name="ini4j/ini4j-0.5.2.jar"/>
    <include name="junit/junit-4.9.jar"/>
    <include name="strbio/strbio-1.3.jar"/>
    <!-- Might not need the following jars (may need refactoring code) -->
    <include name="kbase/kidl/kbase-kidl-parser2.jar"/>
    <include name="servlet/servlet-api-2.5.jar"/>
    <include name="jetty/jetty-all-7.0.0.jar"/>
  </fileset>

  <path id="compile.classpath">
    <fileset refid="lib"/>
  </path>

  <path id="test.classpath">
    <path refid="compile.classpath"/>
    <pathelement path="${classes}"/>
  </path>

  <target name="init" description="make directories">
    <!-- Create the output directory structure-->
    <mkdir dir="${classes}"/>
    <mkdir dir="${dst}"/>
    <mkdir dir="${dst.jar.dir}"/>
  </target>

  <target name="compile" depends="init" description="compile the source">
    <!-- Compile class files-->
    <javac destdir="${classes}" includeantruntime="false" target="1.7" source="1.7" debug="true" classpathref="compile.classpath">
      <src path="${src}"/>
    </javac>
    <!-- Copy resource files-->
    <copy todir="${classes}">
      <fileset dir="${src}">
      </fileset>
    </copy>
    <unzip dest="${classes}">
        <fileset refid="lib"/>
    </unzip>
    <jar destfile="${dst.jar.dir}/${jar.file}" basedir="${classes}"/>
  </target>

  <target name="javadoc" description="build javadocs">
    <unzip dest="${tempunpack}">
      <fileset refid="lib"/>
    </unzip>
    <javadoc access="protected" author="false" classpathref="compile.classpath"
      destdir="${doc}" nodeprecated="false" nodeprecatedlist="false"
      noindex="false" nonavbar="false" notree="false"
      source="1.7" splitindex="true" use="true" version="true">
      <link href="http://download.oracle.com/javase/7/docs/api/"/>
      <link href="http://fasterxml.github.io/jackson-core/javadoc/2.2.0/"/>
      <link href="http://fasterxml.github.io/jackson-databind/javadoc/2.2.0/"/>
      <fileset refid="client-jdoc-files"/>
      <fileset refid="sources-jdoc-files"/>
    </javadoc>
    <delete dir="${tempunpack}"/>
  </target>

  <target name="preparejunitreportdir" if="env.JENKINS_REPORT_DIR">
    <delete dir="${env.JENKINS_REPORT_DIR}"/>
    <mkdir dir="${env.JENKINS_REPORT_DIR}"/>
  </target>
  
  <target name="test" depends="compile, preparejunitreportdir" description="Testing genbank uploader">
    <junit fork="yes" maxmemory="3G" haltonfailure="yes">
      <classpath refid="test.classpath"/>
      <formatter type="plain" usefile="false" />
      <formatter type="xml" usefile="true" if="env.JENKINS_REPORT_DIR"/>
      <batchtest todir="${env.JENKINS_REPORT_DIR}">
        <fileset dir="${src}">
          <include name="**/test/**/**Test.java"/>
        </fileset>
      </batchtest>
    </junit>
    <fail message="Test failure detected, check test results." if="test.failed" />
  </target>

  <target name="clean" description="clean up" >
    <!-- Clean up internal temporary files and folders-->
    <delete dir="${classes}"/>
    <delete dir="${dst}"/>
  </target>
</project>