build.xml

<?xml version="1.0" encoding="UTF-8"?>
<project name="ZFIN" default="usage" basedir=".">

    <property name="build.sysclasspath" value="ignore"/>

    <property name="buildfiles.dir" value="buildfiles"/>


    <import file="${buildfiles.dir}/base-properties.xml"/>

    <taskdef resource="net/sf/antcontrib/antlib.xml">
        <classpath>
            <pathelement location="lib/Java/ant-contrib-0.3.jar"/>
        </classpath>
    </taskdef>

    <property name="commons.dir" value="${basedir}/commons/env"/>

    <property environment="env"/>


    <!--If INSTANCE system property is not defined,-->
    <!--then define from the environment.-->
    <condition property="instance.env.defined">
        <not>
            <equals arg1="${env.INSTANCE}" arg2=""/>
        </not>
    </condition>

    <fail unless="instance.env.defined"
          message="INSTANCE must be defined in the environment even if overriden by -DINSTANCE."/>

    <!--If INSTANCE system property is not defined,-->
    <!--then define from the environment.-->
    <condition property="instance.overridden">
        <and>
            <not>
                <equals arg1="${INSTANCE}" arg2="$${INSTANCE}"/>
            </not>
            <not>
                <equals arg1="${env.INSTANCE}" arg2="${INSTANCE}"/>
            </not>
        </and>
    </condition>

    <property name="classes.dir.target" value="${env.TARGETROOT}/home/WEB-INF/classes"/>
    <property name="lib.dir.target" value="${env.TARGETROOT}/home/WEB-INF/lib"/>
    <!--If the INSTANCE variable is not already set (this code gets run for every target, I believe)-->
    <!--the we check if it is defined in the system as OVERRIDE_INSTANCE-->
    <if>
        <equals arg1="${instance.overridden}" arg2="true"/>
        <then>
            <echo message="!!!!!!!"/>
            <echo message="Instance IS system defined and set to '${INSTANCE}'."/>
            <echo message="Instance IS defined in environment as '${env.INSTANCE}'."/>
            <echo message="!!!!!!!"/>
        </then>
        <else>
            <property name="INSTANCE" value="${env.INSTANCE}"/>
            <echo message="INSTANCE = ${INSTANCE}"/>
        </else>
    </if>


    <!--Define property file.-->
    <property name="property.file" value="${basedir}/home/WEB-INF/zfin.properties"/>
    <property name="log4j.file" value="${commons.dir}/${INSTANCE}.log4j.xml"/>

    <!--If the property file is not defined then fail.-->
    <!--
        <echo message="property file=${property.file}"/>
    -->

    <!-- Load properties into Ant for build-time use -->
    <property file="${property.file}"/>

    <!-- ensure git is looking in the source tree directory for hooks -->
    <exec executable="git">
        <arg value="config" />
        <arg value="core.hooksPath" />
        <arg value=".githooks" />
    </exec>


    <!-- Load filters directly from zfin.properties instead of generated allfilter.xml -->
    <filterset id="allfilters">
        <filtersfile file="${property.file}"/>
    </filterset>
    <import file="${buildfiles.dir}/properties.xml"/>
    <import file="${buildfiles.dir}/gwt.xml"/>
    <import file="${buildfiles.dir}/test.xml"/>
    <import file="${buildfiles.dir}/performance.xml"/>
    <import file="${buildfiles.dir}/tomcat.xml"/>
    <import file="${buildfiles.dir}/usage.xml"/>
    <import file="${buildfiles.dir}/serialization.xml"/>
    <import file="${buildfiles.dir}/warehouse.xml"/>
    <import file="${buildfiles.dir}/utilities.xml"/>
    <import file="${buildfiles.dir}/jenkins.xml"/>
    <import file="${buildfiles.dir}/solr-ant.xml"/>
    <import file="${buildfiles.dir}/shipper.xml"/>
    <import file="${buildfiles.dir}/base-properties.xml"/>
    <!--
        <echo message="property file=${LOG4J_FILE}"/>
    -->

    <!-- ====================================================================== -->
    <!-- COMPILE TASKS                                                          -->
    <!-- ====================================================================== -->

    <target name="prepare" depends="hibernate-available" description="Prepares directories for compilation">
        <mkdir dir="${classbin.dir}"/>
        <mkdir dir="${classbin.dir}/resources"/>
        <copy file="${conf.dir}/hibernate.cfg.xml" todir="${classbin.dir}"/>
        <copy file="${conf.dir}/mchange-log.properties" todir="${classbin.dir}"/>

        <copy file="${commons.dir}/${LOG4J_FILE}" tofile="${web-inf.dir}/classes/log4j2.xml" failonerror="false">
            <filterset>
                <filter token="DEFAULT_EMAIL" value="${DEFAULT_EMAIL}"/>
            </filterset>
        </copy>

        <copy todir="${classbin.dir}/org/zfin">
            <fileset dir="${hibernate.conf.dir}">
                <include name="*.hbm.xml"/>
            </fileset>
        </copy>
        <copy todir="${classbin.dir}">
            <fileset dir="${source.dir}">
                <include name="**/*.properties"/>
            </fileset>
        </copy>

        <if>
            <equals arg1="${hibernate.exists}" arg2="true"/>
            <then>
                <echo message="Hibernate configuration file hibernate.properties found"/>
                <copy file="${conf.dir}/hibernate.properties" tofile="${classbin.dir}/hibernate.properties"
                      failonerror="false"/>
            </then>
        </if>
        <!--
                <copy file="${conf.dir}/application.properties" todir="${classbin.dir}/resources"/>
        -->
        <copy file="${conf.dir}/zfin-messages.properties" tofile="${classbin.dir}/zfin-messages.properties"/>
    </target>


    <target name="do"
            depends="cleanClasses, compile, prepare-properties"
            description="Everything to compile excluding jsp files. No copying into target directory"/>

    <target name="all" depends="deploy" description="The same as deploy for Tom."/>
    <target name="install" depends="deploy" description="Same as deploy."/>

    <!-- createEnum is no longer needed - use gradle generatePropertiesEnum instead -->
    <target name="createEnum" description="DEPRECATED: Use 'gradle generatePropertiesEnum' instead">
        <echo message="createEnum is deprecated."/>
        <echo message="In the future use 'gradle generatePropertiesEnum' to regenerate ZfinPropertiesEnum.java"/>
        <gradle task="generatePropertiesEnum" />
        <echo message="####"/>
        <echo message="#### TODO: migrate toward using spring @ConfigurationProperties instead of ZfinPropertiesEnum"/>
    </target>

    <!-- rebuildPropertiesFromYaml will invoke the groovy script for creating home/WEB-INF/zfin.properties from all-properties.yml -->
    <target name="rebuildPropertiesFromYaml" description="Rebuilds zfin.properties from all-properties.yml">
        <echo message="Rebuilding ${property.file} from all-properties.yml"/>
        <groovy src="${basedir}/commons/env/PropertiesProcessor.groovy">
            <arg value="-c"/>
            <arg value="${basedir}/commons/env/all-properties.yml"/>
            <arg value="-o"/>
            <arg value="${property.file}"/>
        </groovy>
    </target>

    <target name="rebuildProperties" depends="rebuildPropertiesFromYaml,createEnum"
            description="Rebuilds properties for all instances.">
    </target>

    <path id="extended.classpath">
        <path refid="classpath"/>
        <!-- This class needs to come first to ensure that unit test methods are executed in the order they appear in the source file -->
        <fileset dir="${lib}">
            <include name="junit-orderOfExecution.jar"/>
        </fileset>
        <fileset dir="${lib}">
            <include name="*.jar"/>
            <include name="*.zip"/>
        </fileset>
        <fileset dir="${gwt.lib}">
            <include name="*.jar"/>
        </fileset>
        <fileset dir="${env.GROOVY_HOME}/lib" erroronmissingdir="false">
            <include name="*.jar"/>
        </fileset>
    </path>

    <path id="unittest.classpath">
        <!-- This class needs to come first to ensure that unit test methods are executed in the order they appear in the source file -->
        <fileset dir="${lib}">
            <include name="junit-orderOfExecution.jar"/>
        </fileset>
        <fileset dir="${lib}">
            <include name="*.jar"/>
            <include name="*.zip"/>
        </fileset>
        <fileset dir="${gwt.lib}">
            <include name="*.jar"/>
        </fileset>
        <path refid="classpath"/>
    </path>

    <target name="writeClassPath">
        <pathconvert property="classpathProp1" refid="extended.classpath"/>
        <tempfile property="classpathFile1" suffix=".txt" createfile="true" prefix="extended.classpath." destdir="/tmp"/>
        <echo file="${classpathFile1}">${classpathProp1}</echo>
        <echo>extended.classpath is written to ${classpathFile1}</echo>

        <pathconvert property="classpathProp2" refid="unittest.classpath"/>
        <tempfile property="classpathFile2" suffix=".txt" createfile="true" prefix="unittest.classpath." destdir="/tmp"/>
        <echo file="${classpathFile2}">${classpathProp2}</echo>
        <echo>unittest.classpath is written to ${classpathFile2}</echo>
    </target>

    <target name="instrument" depends="compile">
        <taskdef name="instrument" classname="org.hibernate.tool.instrument.javassist.InstrumentTask">
            <classpath refid="extended.classpath"/>
            <classpath path="${classbin.dir}"/>
        </taskdef>

        <instrument verbose="true">
            <fileset dir="${TARGETROOT}/home/WEB-INF/classes">
                <include name="org/zfin/ontology/GenericTerm.class"/>
                <include name="org/zfin/profile/Person.class"/>
                <include name="org/zfin/expression/Figure.class"/>
                <include name="org/zfin/expression/TextOnlyFigure.class"/>
                <include name="org/zfin/expression/FigureFigure.class"/>
                <include name="org/zfin/ontology/**Term.class"/>
                <include name="org/zfin/publication/CorrespondenceComposedMessage.class"/>
                <include name="org/zfin/publication/CorrespondenceSentMessage.class"/>
                <include name="org/zfin/publication/Publication.class"/>
            </fileset>
            <fileset dir="${SOURCEROOT}/home/WEB-INF/classes">
                <include name="org/zfin/ontology/GenericTerm.class"/>
                <include name="org/zfin/profile/Person.class"/>
                <include name="org/zfin/expression/Figure.class"/>
                <include name="org/zfin/expression/TextOnlyFigure.class"/>
                <include name="org/zfin/expression/FigureFigure.class"/>
                <include name="org/zfin/ontology/**Term.class"/>
                <include name="org/zfin/publication/CorrespondenceComposedMessage.class"/>
                <include name="org/zfin/publication/CorrespondenceSentMessage.class"/>
                <include name="org/zfin/publication/Publication.class"/>
            </fileset>
        </instrument>
    </target>

    <target name="compile" depends="prepare"
            description="Target to compile all classes, excluding test files, and moving anything from the source
            folder to the class folder.">
        <!-- Delegate to Gradle for compilation (handles Lombok, annotation processing, etc.) -->
        <exec executable="./gradlew" failonerror="true">
            <arg value="antCompile"/>
        </exec>
    </target>

    <target name="cleanClasses" description="Remove java classes directory contents. ">
        <delete includeemptydirs="true" quiet="true">
            <fileset dir="${classbin.dir}" includes="**/*"/>
            <fileset dir="${lib.dir}" includes="**/*"/>
        </delete>
        <!--<delete includeemptydirs="true" quiet="true">-->
        <!--<fileset dir="${domain-work}" includes="**/*"/>-->
        <!--</delete>-->
    </target>

    <target name="cleanTarget" description="Remove target values. ">
        <removeWebAppLocation location="${home.target}"/>
    </target>

    <target name="clobber" depends="cleanTarget" description="Remove target values. "/>

    <target name="clean-javadoc" description="Cleans javadoc">
        <delete dir="${java-doc.dir}"/>
    </target>

    <target name="javadocs" depends="clean-javadoc" description="Generate Javadocs into ${java-doc.dir}">
        <mkdir dir="${java-doc.dir}"/>
        <javadoc packagenames="org.zfin.*"
                 sourcepath="${source.dir}"
                 excludepackagenames="org.zfin.properties.*"
                 classpathref="combined.classpath"
                 destdir="${java-doc.dir}/zfin"
                 author="true"
                 version="true"
                 maxmemory="300m"
                 use="true"
                 private="yes"
                 windowtitle="ZFIN API"
                 doctitle="ZFIN"
                 bottom="Copyright &#169; 2008 ZFIN"
                 locale="en"
        />
    </target>


    <target name="deploy-javadoc" depends="javadocs" description="Deploy the Javadoc into webroot/util/javadoc/zfin">
        <mkdir dir="${TARGETROOT}/${zfin-javadoc}"/>
        <copy verbose="true" todir="${TARGETROOT}/${zfin-javadoc}">
            <fileset dir="${java-doc.dir}/zfin">
                <include name="**/"/>
            </fileset>
        </copy>
    </target>

    <!-- ====================================================================== -->
    <!-- CONFIGURATION TASKS                                                    -->
    <!-- ====================================================================== -->

    <target name="hibernate-available" description="Verifies that hibernate is available">
        <available file="${conf.dir}/hibernate.properties" property="${hibernate.exists}"/>
    </target>


    <!-- ====================================================================== -->
    <!-- Generate WAR.                                                          -->
    <!-- ====================================================================== -->

    <target name="schemaVersion" description="Prints schema version">
        <java fork="yes" classname="org.zfin.database.SchemaManager" taskname="junit" failonerror="true">
            <arg value="-checkSchema"/>
            <classpath refid="extended.classpath"/>
        </java>
    </target>

    <target name="prepare-properties" description="Copy jaxb properties into class hierarchy">
        <copy todir="${classbin.dir}/">
            <fileset dir="${source.dir}">
                <include name="**/jaxb.properties"/>
                <include name="**/bgm.ser"/>
            </fileset>
        </copy>
    </target>


    <target name="remove-archives" description="Removes archived builds (older than post-builds)">
        <delete verbose="true" includeemptydirs="true">
            <fileset dir="${TARGETROOT}/home" includes="archive*/**"/>
        </delete>
    </target>

    <macrodef name="emailMessage">
        <attribute name="message"/>
        <attribute name="email"/>
        <sequential>
            <java classname="org.zfin.framework.mail.IntegratedJavaMailSender"
                  fork="yes"
                  classpathref="combined.classpath">
                <!-- subject -->
                <arg value="@{message}"/>
                <!-- message -->
                <arg value="@{message}"/>
                <!-- email -->
                <arg value="@{email}"/>
            </java>
        </sequential>
    </macrodef>


    <target name="deploy" depends="deploy-without-tests,test,productionSmokeTests"
            description="Performs the full build, test, move to production, and tomcat restart appropriate for the current environment"/>

    <target name="deploy-without-tests"
            depends="cleanClasses,pre-deploy,build-properties,unittests-quiet,restart,deploy-solr"/>

    <target name="deploy-without-tests-and-tomcat-restart"
            depends="cleanClasses,pre-deploy,build-properties,unittests-quiet,deploy-solr"/>

    <target name="pre-deploy" depends="do,gwt,npmInstall,npmBuild,deployGitInfoFile,gradle-tomcat-deploy"
            description="Target to compile all classes (excluding jsp files) and then deploy the necessary files to user's web environment.">
        <!--        <jsp-compile/> -->
    </target>

    <target name="dirtydeploy">
        <gradle task="dirtydeploy"/>
    </target>

    <target name="watch">
        <exec executable="./gradlew" dir="." failonerror="true">
            <arg value="watch" />
            <arg value="--continuous" />
        </exec>
    </target>

    <macrodef name="removeWebAppLocation">
        <attribute name="location"/>
        <sequential>
            <delete dir="@{location}/dist"/>
            <delete dir="@{location}/fonts"/>
            <delete dir="@{location}/images"/>
            <delete dir="@{location}/templates"/>
            <delete dir="@{location}/WEB-INF"/>
        </sequential>
    </macrodef>

    <macrodef name="replaceProperties">
        <attribute name="to"/>
        <sequential>
            <!--I don't think doing the full-scale delete is necessary.  -->
            <!--<echo message="@{to}"/>-->
            <!--<delete dir="@{to}" verbose="true"/>-->
            <copy todir="@{to}" verbose="false">
                <fileset dir="${commons.dir}">
                    <include name="*.properties"/>
                </fileset>
            </copy>
        </sequential>
    </macrodef>

    <target name="build-properties" description="Describes build properties for environment">
        <echo>If properties are defined as true, they will show up that way, otherwise will just produce string
            version.
        </echo>
        <echo message="Is informix: ${isinformix}"/>
        <echo message="Is mutant: ${ismutant}"/>
        <echo message="Not production: ${notproduction}"/>
    </target>

    <!--
    Grand: Ant build visualization tool (JAR provided via Gradle/JitPack)
    ============================================
    task.properties is in the grand jar: https://github.com/Ant-Grand/Grand/blob/157df7cb1505804be453c3e5ffb157267c360529/src/main/resources/task.properties
     and it contains the single line:
        grand=net.ggtools.grand.tasks.GrandTask

     If you want to use grand, add the dependency to build.gradle:
            implementation "com.github.Ant-Grand:Grand:1.9.7"  // Ant build visualization tool (via JitPack)

     Then uncomment the following:
    <taskdef resource="task.properties" classpathref="combined.classpath"/>
    <target name="graph" description="Creates graph of build process">
        <grand output="build.dot" buildfile="build.xml"/>
        <exec executable="dot">
            <arg line="-Tps -Gsize=11.69,8.27 -Grotate=90 -o build.ps build.dot"/>
        </exec>
    </target>
     -->
    <target name="graph" description="Creates graph of build process">
        <echo message="To use the 'graph' target, please add the Grand dependency to build.gradle and uncomment the relevant code in build.xml"/>
        <echo message="See comments in build.xml for details."/>
    </target>

    <macrodef name="regenerateSSHKey">
        <attribute name="ssh-command"/>
        <sequential>
            <delete file="@{ssh-command}"/>
            <delete file="@{ssh-command}.pub"/>
            <exec command="ssh-keygen">
                <arg value="-f"/>
                <arg value="@{ssh-command}"/>
                <arg value="-t"/>
                <arg value="dsa"/>
                <arg value="-N"/>
                <arg value=""/>
            </exec>

            <exec command="./buildfiles/fixKey.sh">
                <arg value="@{ssh-command}"/>
            </exec>
        </sequential>
    </macrodef>


    <target name="generateSSHKeys">
        <regenerateSSHKey ssh-command="cp"/>
        <regenerateSSHKey ssh-command="xdget"/>
        <regenerateSSHKey ssh-command="xdformat"/>
        <regenerateSSHKey ssh-command="blastn"/>
        <regenerateSSHKey ssh-command="blastp"/>
        <regenerateSSHKey ssh-command="blastx"/>
        <regenerateSSHKey ssh-command="tblastn"/>
        <regenerateSSHKey ssh-command="tblastx"/>
    </target>


    <target name="validateDatabases" depends="compile,build-tests">
        <java classname="org.zfin.sequence.blast.ValidateBlastDatabases" fork="yes"
              classpathref="combined.classpath"
        >
        </java>
    </target>

    <target name="generateWebServiceClasses">
        <exec executable="xjc">
            <arg value="home/WEB-INF/conf/zfin.xsd"/>
            <arg value="-p"/>
            <arg value="org.zfin.webservice.schema"/>
            <arg value="-d"/>
            <arg value="source"/>
            <arg value="-mark-generated"/>
        </exec>
    </target>

    <target name="npmInstall">
        <exec executable="npm" failonerror="true">
            <arg value="ci"/>
        </exec>
    </target>

    <target name="npmBuild">
        <exec executable="npm" failonerror="true">
            <arg value="run"/>
            <arg value="build"/>
        </exec>
    </target>

    <target name="npmLint">
        <exec executable="npm" failonerror="true">
            <arg value="run"/>
            <arg value="lint"/>
        </exec>
    </target>

    <taskdef name="groovy"
             classname="org.codehaus.groovy.ant.Groovy"
             classpathref="combined.classpath.with.groovy"/>

    <target name="deployGitInfoFile">
        <gradle task="deployGitInfoFile" />
    </target>

    <macrodef name="gradle">
        <attribute name="task" />
        <sequential>
            <exec executable="./gradlew" dir="." failonerror="true">
                <arg value="@{task}" />
            </exec>
        </sequential>
    </macrodef>
</project>