build.xml

<project name="DomainAnnotation" default="compile" basedir=".">

  <description>
      Build JAR and WAR files for DomainAnnotation 
  </description>

  <!-- set global properties for this build -->
  <property name="src" location="lib/src"/>
  <property name="test.src" location="test/src"/>
  <property name="dist" location="dist"/>
  <property name="classes" location="classes"/>
  <property name="bin" location="bin"/>
  <property name="jar.file" value="DomainAnnotation.jar"/>
  <property name="jars.dir" value="/kb/deployment/lib/jars"/>
  <property name="war.file" value="DomainAnnotation.war"/>
  <property name="scripts" location="scripts"/>
  <property name="web.xml" location="${scripts}/web.xml"/>
  <property name="exec.cmd.file" value="run_DomainAnnotation_async_job.sh"/>
  <property name="startup.cmd.file" value="start_server.sh"/>

  <fileset dir="${jars.dir}" id="lib">
    <include name="ini4j/ini4j-0.5.2.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="jetty/jetty-all-7.0.0.jar"/>
    <include name="jna/jna-3.4.0.jar"/>
    <include name="joda/joda-time-2.2.jar"/>
    <include name="junit/junit-4.9.jar"/>
    <include name="kbase/auth/kbase-auth-0.3.1.jar"/>
    <include name="kbase/common/kbase-common-0.0.17.jar"/>
    <include name="logback/logback-core-1.1.2.jar"/>
    <include name="logback/logback-classic-1.1.2.jar"/>
    <include name="servlet/servlet-api-2.5.jar"/>
    <include name="slf4j/slf4j-api-1.7.7.jar"/>
    <include name="syslog4j/syslog4j-0.9.46.jar"/>
    <include name="kbase/workspace/WorkspaceClient-0.2.0.jar"/>
    <include name="kbase/shock/shock-client-0.0.10.jar" />
    <include name="kbase/genomes/kbase-genomes-20140411.jar"/>
    <include name="strbio/strbio-1.3.jar"/>
    <include name="apache_commons/http/httpclient-4.3.1.jar"/>
    <include name="apache_commons/http/httpcore-4.3.jar"/>
    <include name="apache_commons/http/httpmime-4.3.1.jar"/>
    <include name="apache_commons/commons-logging-1.1.1.jar"/>
    <include name="apache_commons/commons-codec-1.8.jar"/>
    <include name="apache_commons/commons-io-2.4.jar"/>
    <include name="apache_commons/commons-lang3-3.1.jar"/>
  </fileset>

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

  <path id="src.path">
    <pathelement location="${src}" />
    <pathelement location="${test.src}" />
  </path>

  <target name="compile" description="compile the source">
    <mkdir dir="${classes}"/>
    <mkdir dir="${dist}"/>
    <exec executable="git" outputproperty="git.url"><arg line="config --get remote.origin.url"/></exec>
    <exec executable="git" outputproperty="git.branch"><arg line="rev-parse --abbrev-ref HEAD"/></exec>
    <exec executable="git" outputproperty="git.commit"><arg line="rev-parse HEAD"/></exec>
    <echo file="${src}/git.properties">giturl=${git.url}
branch=${git.branch}
commit=${git.commit}</echo>
    <!-- Compile class files-->
    <javac destdir="${classes}" includeantruntime="false" target="1.7" source="1.7" debug="true" classpathref="compile.classpath">
      <src refid="src.path"/>
    </javac>
    <!-- Copy resource files-->
    <copy todir="${classes}">
      <fileset dir="${src}">
      </fileset>
    </copy>
    <!-- Copy dependencies-->
    <unzip dest="${classes}">
        <fileset refid="lib"/>
    </unzip>
    <jar destfile="${dist}/${jar.file}" basedir="${classes}">
      <manifest>
        <attribute name="Main-Class" value="domainannotation.DomainModelLibPreparation"/>
      </manifest>
    </jar>
    <delete dir="${classes}"/>
  </target>

  <target name="war" depends="compile" description="build the WAR file. Assumes compile has been run">
    <!-- make the war file for the server-->
    <mkdir dir="${dist}/lib"/>
    <copy todir="${dist}/lib/" flatten="true">
      <fileset refid="lib"/>
      <resources>
        <file file="${dist}/${jar.file}"/>
      </resources>
    </copy>
    <war destfile="${dist}/${war.file}" webxml="${web.xml}">
      <lib dir="${dist}/lib/"/>
    </war>
    <delete dir="${dist}/lib"/>
    <mkdir dir="${scripts}/webapps"/>
    <copy file="${dist}/${war.file}" tofile="${scripts}/webapps/root.war"/>
  </target>

  <target name="build-executable-script" description="create command-line script">
    <mkdir dir="${bin}"/>
    <property name="jar.absolute.path" location="${dist}/${jar.file}"/>
    <pathconvert targetos="unix" property="lib.classpath" refid="compile.classpath"/>
    <echo file="${bin}/${exec.cmd.file}">#!/bin/bash
java -cp ${jar.absolute.path}:${lib.classpath} domainannotation.DomainAnnotationServer $1 $2 $3
    </echo>
    <chmod file="${bin}/${exec.cmd.file}" perm="a+x"/>
  </target>
  
  <target name="test" description="run all tests">
    <junit printsummary="yes" haltonfailure="yes" fork="true">
      <classpath>
        <pathelement location="${dist}/${jar.file}"/>
        <path refid="compile.classpath"/>
      </classpath>
      <formatter type="plain" usefile="false" />
      <batchtest>
        <fileset dir="${test.src}">
          <include name="**/test/**Test.java"/>
        </fileset>
      </batchtest>
    </junit>
  </target>
</project>