buildEclipse.xml

<?xml version="1.0" encoding="UTF-8"?>
<!-- JFD DON'T DELETE edited by JFD -->
<!-- added memory setting for Java and Junit testing -->


<project name="wattos" default="jar" basedir=".">
    <description>Builds, tests, and runs the project Wattos.</description>
    <echo>Starting Ant with updated build file</echo>
    <property file="wattos.properties" />

    <!-- Added for for functionality. Requires an ant-contrib.jar in classpath. -->
    <!-- Fedora 9: 
    <taskdef classpath="/usr/share/java/ant-contrib.jar" resource="net/sf/antcontrib/antlib.xml" />
    -->
    <!-- macOS: -->
    <taskdef classpath="/Users/jd/workspace/wattos/lib/ant-contrib.jar" resource="net/sf/antcontrib/antlib.xml" />
    <!-- systems where ant-contrib installs properly: -->

    <taskdef resource="net/sf/antcontrib/antlib.xml" />

    <!-- Set the below to development 0 or production 1-->
    <property name="isProduction" value="0" />


    <target name="init" description="init">
        <if>
            <equals arg1="${isProduction}" arg2="1" />
            <then>
                <echo message="Now in environment for production." />
                <property name="servlet.web.machine" value="${servlet.web.machine.prod}" />
                <property name="servlet.web.user" value="${servlet.web.user.prod}" />
                <property name="servlet.web.dir" value="${servlet.web.dir.prod}" />
                <property name="servlet.web.port" value="${servlet.web.port.prod}" />
                <property name="home.web.machine" value="${home.web.machine.prod}" />
                <property name="home.web.machine.looped" value="${home.web.machine.looped.prod}" />
                <property name="home.web.port" value="${home.web.port.prod}" />
                <property name="home.web.dir" value="${home.web.dir.prod}" />
                <property name="home.web.user" value="${home.web.user.prod}" />
            </then>
            <else>
                <echo message="Now in environment for development." />
                <property name="servlet.web.machine" value="${servlet.web.machine.dev}" />
                <property name="servlet.web.user" value="${servlet.web.user.dev}" />
                <property name="servlet.web.dir" value="${servlet.web.dir.dev}" />
                <property name="servlet.web.port" value="${servlet.web.port.dev}" />
                <property name="home.web.machine" value="${home.web.machine.dev}" />
                <property name="home.web.machine.looped" value="${home.web.machine.looped.dev}" />
                <property name="home.web.port" value="${home.web.port.dev}" />
                <property name="home.web.dir" value="${home.web.dir.dev}" />
                <property name="home.web.user" value="${home.web.user.dev}" />
            </else>
        </if>
        <echo message="servlet.web.machine    : ${servlet.web.machine}" />
        <echo message="servlet.web.user       : ${servlet.web.user}" />
        <echo message="servlet.web.dir        : ${servlet.web.dir}" />
        <echo message="servlet.web.port       : ${servlet.web.port}" />

        <echo message="home.web.machine       : ${home.web.machine}" />
        <echo message="home.web.port          : ${home.web.port}" />
        <echo message="home.web.dir           : ${home.web.dir}" />
        <echo message="home.web.user          : ${home.web.user}" />
        <echo message="home.web.machine.looped: ${home.web.machine.looped}" />


        <property name="home.web.url" value="${home.web.machine}/${ant.project.name}" />
        <property name="home.web.usermachine" value="${home.web.user}@${home.web.machine}" />
    </target>

    <!-- Is done automatically by ant build but can be used externally.
    NB the debug settings.
    -->
    <target name="compile" description="compile" depends="init">
        <mkdir dir="${build.dir}" />
        <javac srcdir="${src.dir}" destdir="${build.dir}" debug="on" debuglevel="lines,vars,source">
            <classpath>
                <path path="${javac.classpath}" />
            </classpath>
        </javac>
        <copy todir="${build.dir}">
            <fileset dir="${src.dir}" includes="**/*.H" /> <!--For Wattos/Soup/Data/TOPOLOGY.H-->
            <fileset dir="${src.dir}" includes="**/*.csv" />
            <fileset dir="${src.dir}" includes="**/*.str" />
        </copy>
    </target>

    <target name="clean" description="clean class files" depends="init">
        <delete dir="${build.dir}" />
    </target>

    <target name="-init-macrodef-junit">
        <macrodef name="junit" uri="http://www.netbeans.org/ns/web-project/2">
            <attribute name="includes" default="**/*Test.java" />
            <sequential>
                <junit showoutput="true" fork="true" maxmemory="256m" dir="tmp_dir" failureproperty="tests.failed" errorproperty="tests.failed" jvm="${platform.java}">
                    <batchtest todir="${build.dir}">
                        <fileset dir="${test.test.dir}" includes="@{includes}" />
                    </batchtest>
                    <classpath>
                        <path path="${run.test.classpath}" />
                    </classpath>
                    <syspropertyset>
                        <propertyref prefix="test-sys-prop." />
                        <mapper type="glob" from="test-sys-prop.*" to="*" />
                    </syspropertyset>
                    <formatter type="brief" usefile="false" />
                    <formatter type="xml" />
                </junit>
            </sequential>
        </macrodef>
    </target>


    <target name="-init-macrodef-java">
        <macrodef name="java" uri="http://www.netbeans.org/ns/web-project/1">
            <attribute name="classname" default="${main.class}" />
            <attribute name="args" default="${application.args}" />
            <element name="customize" optional="true" />
            <sequential>
                <java fork="true" maxmemory="256m" dir="tmp_dir" classname="@{classname}" jvm="${platform.java}">
                    <jvmarg line="${runmain.jvmargs}" />
                    <classpath>
                        <path path="${build.dir}:${javac.classpath}:${j2ee.platform.classpath}" />
                    </classpath>
                    <syspropertyset>
                        <propertyref prefix="run-sys-prop." />
                        <mapper type="glob" from="run-sys-prop.*" to="*" />
                    </syspropertyset>
                    <customize />
                    <arg line="@{args}" />
                </java>
            </sequential>
        </macrodef>
    </target>

    <!--
    ====================
    JAR BUILDING SECTION
    ====================
    Use:
        for resigning all jars. They need to be the same for WebApps such as Sjors.
    -->
    <target name="jar" depends="init,compile" description="Build JAR.">
        <jar destfile="${jar.name}" basedir="${build.dir}" />
        <!--
        <signjar
                    alias="business"
                    storepass="secret"
                    keypass="test123"
                    keystore="${keystore}">
            <fileset dir="lib"
                    includes="Wattos.jar" />
        </signjar>
        -->
    </target>

    <target name="jarsign" depends="init" description="Resign all jars">
        <signjar alias="business" storepass="secret" keypass="test123" keystore="${keystore}">
            <fileset dir="lib" includes="**.jar" excludes="JFlex.jar ant-contrib.jar" />
        </signjar>
    </target>


    <!--
    ====================
    MACRO FILE EXECUTION.
    ====================
        <for list="FilterSTAR.wcf" param="fn">
        <for list="ReadEntryMmCIF.wcf" param="fn">
        <for list="CheckSurplus.wcf" param="fn">
        <for list="WriteSQLDump.wcf" param="fn">
        <for list="AddMissingAtoms.wcf" param="fn">
        <for list="WriteEntryPDB.wcf" param="fn">
        <for list="CheckAssignment.wcf" param="fn">
        <for list="CheckAtomNomenclature.wcf" param="fn">
        <for list="CalcDistConstrViolation.wcf" param="fn">
        <for list="CalcDihConstrViolation.wcf" param="fn">
        <for list="ReadEntryMmCIF.wcf" param="fn">
        <for list="WriteEntryXplor.wcf" param="fn">

        <for list="CalcDistConstrViolation.wcf,CalcDistance.wcf,CheckAssignment.wcf,CheckCompleteness.wcf,CheckSurplus.wcf,FilterSTAR.wcf,GetCoplanarBases.wcf,GetHydrogenBonds.wcf,ReadEntryPDB.wcf,QuitBeforeBegun.wcf,SetAtomNomenclatureToIUPAC.wcf,ShowClassification.wcf,Sleep.wcf,WriteEntryXplor.wcf" param="fn">
            <replace file="${tmp.local.dir}/@{fn}.log" token="ERROR" value="ERROR" summary="true"/>
    -->
    <target name="macro_tests" depends="init" description="">
        <echo message="Running in: ${test_data.local.dir}" />
        <echo message="Output to : ${tmp.local.dir}" />
        <!-- <echo message="classpath: ${build.dir}:${javac.classpath}:${j2ee.platform.classpath}"/>
    -->

        <for list="CheckCompleteness.wcf" param="fn">
            <sequential>
                <echo message="Executing macro: ${macros.local.dir}/@{fn}" />
                <java jvm="${platform.java}" fork="true" failonerror="false" resultproperty="result" maxmemory="512m" classname="Wattos.CloneWars.UserInterface" dir="${test_data.local.dir}" input="${macros.local.dir}/@{fn}" output="${tmp.local.dir}/@{fn}.log" timeout="240000">
                    <!-- FAILS IN IDE <jvmarg line="-DWATTOSSCRIPT=${wattos.root}/${macros.local.dir}/@{fn}"/> -->
                    <arg line="-at -verbosity 9" />
                    <classpath>
                        <path path="${build.dir}:${javac.classpath}:${j2ee.platform.classpath}" />
                    </classpath>
                </java>
                <loadfile property="error_list" srcFile="${tmp.local.dir}/@{fn}.log">
                    <filterchain>
                        <linecontainsregexp>
                            <regexp pattern="(^ERROR)|(^Exception in thread)|(^\tat )" />
                        </linecontainsregexp>
                    </filterchain>
                </loadfile>
                <antcall target="report_errors" />
                <echo />
                <echo />
                <echo message="Log file:" />
                <!--
             <loadfile property="contentLogFile"
                    srcFile="${tmp.local.dir}/@{fn}.log"/>
             <echo message="${contentLogFile}"/>
               -->
            </sequential>
        </for>
    </target>

    <target name="report_errors" if="error_list">
        <echo message="${error_list}" />
    </target>
    <!--
    ======================
    JAVADOC SECTION
    ======================
    Can't use "linksource" as there's a bug http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4511110
    trying with javadoc 1.5 as set in wattos.properties: platform.javadoc
    -->
    <target name="javadoc" depends="init,javadoc-build,javadoc-copy" description="Build Javadoc and copy some extra files from the src to doc dir" />
    <target name="javadoc-build">
        <mkdir dir="${dist.javadoc.dir}" />
        <javadoc additionalparam="" access="private" author="true" breakiterator="true" destdir="${dist.javadoc.dir}" doctitle="Wattos" nodeprecated="false" nodeprecatedlist="false" noindex="false" nonavbar="false" notree="false" overview="${src.dir}/${ant.project.name}/overview.html" source="1.5" sourcepath="src" splitindex="true" use="true" useexternalfile="false" version="false" Windowtitle="${ant.project.name}">
            <classpath>
                <path path="${javac.classpath}" />
            </classpath>
            <packageset dir="${src.dir}" includes="*/**" />
        </javadoc>
    </target>

    <!-- A couple of items should be moved along with the newly generated html -->
    <target name="javadoc-copy" depends="init">
        <copy todir="${dist.javadoc.dir}">
            <fileset dir="${src.dir}" includes="**/*.gif **/*.str **/*.xls **/*.html **/*.csv" excludes="**/package.html" />
        </copy>
    </target>
    <!-- Installation of production site jars including Wattos -->
    <target name="install-jars" depends="jar">
        <echo message="Installing Wattos jar(s) to production site: ${install.dir}" />
        <scp todir="${servlet.web.user}@${servlet.web.machine}:${install.dir}" keyfile="${servlet.web.keyfile}" knownhosts="${servlet.web.knownhosts}" passphrase="${servlet.web.passphrase}" verbose="true">
            <fileset dir="${lib.local.dir}" includes="Wattos.jar" />
        </scp>
    </target>
    <!-- Installation of production site scripts -->
    <target name="install-scripts">
        <copy todir="${install.dir}/scripts" verbose="true">
            <fileset dir="scripts" includes="*" />
        </copy>
    </target>
    <!-- Installation of production site python code -->
    <target name="install-python">
        <copy todir="${install.dir}/python" verbose="true">
            <fileset dir="python" includes="**" />
        </copy>
    </target>

    <!--
    ======================
    HOME SECTION
    ======================
    -->
    <target name="home" depends="init,jar,home-cp,home-doc-cp" description="Creates the Wattos home page with javadoc files." />
    <target name="home-clean" depends="init" description="Fails to create new dirs so disabled until debugged.">
        <input message="Sure you want to delete the Wattos webserver directory: ${home.web.dir}" validargs="y,n" addproperty="do.delete" />
        <condition property="do.abort">
            <equals arg1="n" arg2="${do.delete}" />
        </condition>
        <fail if="do.abort">Build aborted by user.</fail>
        <sshexec host="${home.web.machine.looped}" username="${home.web.user}" keyfile="${home.web.keyfile}" knownhosts="${home.web.knownhosts}" passphrase="${home.web.passphrase}" command="\rm -rf ${home.web.dir}/*;mkdir ${home.web.dir}/doc;mkdir ${home.web.dir}/scripts;mkdir ${home.web.dir}/lib;mkdir ${home.web.dir}/macros">
        </sshexec>
    </target>
    <target name="home-cp" depends="init">
        <scp todir="${home.web.user}@${home.web.machine.looped}:${home.web.dir}" port="${home.web.port}" keyfile="${home.web.keyfile}" knownhosts="${home.web.knownhosts}" passphrase="${home.web.passphrase}" verbose="true">
            <fileset dir="${home.local.dir}" />
        </scp>
    </target>
    <target name="home-doc-cp" depends="init" description="takes a long time (3:29) to send these many files.">
        <scp todir="${home.web.user}@${home.web.machine.looped}:${home.web.dir}/${doc.web.dir}" port="${home.web.port}" keyfile="${home.web.keyfile}" knownhosts="${home.web.knownhosts}" passphrase="${home.web.passphrase}">
            <fileset dir="${doc.local.dir}" />
        </scp>
    </target>

    <!--
    ======================
    SERVLET SECTION
    ======================
    -->

    <target name="servlet-wattos-new-install" depends="init">
        <echo message="Ensure that the tomcat and apache are already setup. As well as the production staging area." />

        <copy todir="${wattos.production.local.dir}/WEB-INF/classes">
            <fileset dir="build" />
        </copy>
        <!-- The Wattos code changes every now and then so it needs to be included live. Every now and then.
        ISN'T THIS EXACTLY THE SAME AS THE ABOVE?
        <copy todir="${wattos.production.local.dir}/WEB-INF/classes">
            <fileset dir="${WS}/wattos/build"/>
        </copy>
        -->

        <zip destfile="${wattos.war.file}">
            <fileset dir="${wattos.production.local.dir}" />
        </zip>
        <echo message="toDir: ${servlet.web.user}@${servlet.web.machine}:${servlet.web.dir}"/>
        <echo message="with port = ${servlet.web.port} and knownhosts=${servlet.web.knownhosts} passphrase=${servlet.web.passphrase} keyfile=${servlet.web.keyfile} "/>

        <scp todir="${servlet.web.user}@${servlet.web.machine}:${servlet.web.dir}" keyfile="${servlet.web.keyfile}"
            knownhosts="${servlet.web.knownhosts}" passphrase="${servlet.web.passphrase}" verbose="true" >
            <fileset file="${wattos.war.file}" />
        </scp>
    </target>

    <target name="servlet-install" depends="init,jar,servlet-jar-cp,servlet-resources-cp" description="Publishes the Wattos jar. Manual restart of server still needed.">
        <echo message="Make sure the following two remote directories are open for writing:" />
        <echo message="${servlet.web.usermachine}:${servlet.web.dir}/${servlet.lib.dir}" />
        <echo message="${servlet.web.usermachine}:${servlet.web.dir}/${servlet.resource.remote.dir}" />
    </target>

    <target name="servlet-jar-cp" depends="init">
        <echo message="Installing Wattos jar(s) to servlet engine: ${servlet.web.usermachine}:${servlet.web.dir}/${servlet.lib.dir}" />
        <scp todir="${servlet.web.usermachine}:${servlet.web.dir}/${servlet.lib.dir}" port="${servlet.web.port}" keyfile="${servlet.web.keyfile}" knownhosts="${servlet.web.knownhosts}" passphrase="${servlet.web.passphrase}" verbose="true">
            <fileset dir="${lib.local.dir}" includes="Wattos.jar" />
        </scp>
    </target>

    <target name="servlet-resources-cp" depends="init">
        <echo message="Installing giffies and html to servlet engine: ${servlet.web.usermachine}:${servlet.web.dir}/${servlet.resource.remote.dir}" />
        <scp todir="${servlet.web.usermachine}:${servlet.web.dir}/${servlet.resource.remote.dir}" port="${servlet.web.port}" keyfile="${servlet.web.keyfile}" knownhosts="${servlet.web.knownhosts}" passphrase="${servlet.web.passphrase}" verbose="true">
            <fileset dir="${servlet.resource.local.dir}" excludes=".svn" />
        </scp>
    </target>


    <!--
    ====================
    PROFILE EXECUTION.
    ====================
    Failed to work with redirecting the output.
                output="${tmp.local.dir}/${fn}.log"
    -->
    <target name="profile-wattos" depends="init" description="">
        <property name="fn" value="FilterSTAR.wcf" />
        <echo message="Executing macro: ${macros.local.dir}/${fn}" />
        <java jvm="${platform.java}" fork="true" failonerror="false" resultproperty="result" maxmemory="512m" classname="Wattos.CloneWars.UserInterface" dir="${test_data.local.dir}" input="${macros.local.dir}/${fn}" timeout="960000">
            <arg line="-at" />
            <jvmarg line="${profile.jvmarg}" />
            <classpath>
                <path path="${build.dir}:${javac.classpath}:${j2ee.platform.classpath}" />
            </classpath>
        </java>
    </target>

    <!--
        Found that after checkout to Windows there were extra eols but fixed with the below.
Default is based on the platform on which you are running this task.
For Unix platforms, the default is "lf".
For DOS based systems (including Windows), the default is "crlf".
For Mac OS, the default is "cr".
    -->
    <target name="fixcrlf" description="Change the end-of-line string to single cr like under Linux" depends="init">
        <property name="dir_todo" value="scripts" />
        <echo message="Starting to fixcrlf on dir: ${dir_todo}" />
        <fixcrlf srcDir="${dir_todo}" eol="lf" />
    </target>

    <!--Dimitri's STAR parser now with line by line processing instead of character at
        a time for semi colon delimited values-->
    <taskdef name="jflex" classname="JFlex.anttask.JFlexTask" classpath="${lib.local.dir}/JFlex.jar" />
    <target name="star_scanner" description="generate scanner class" depends="init">
        <jflex file="${src.dir}/Wattos/Star/star.flex" verbose="on" />
    </target>

    <!--
    rm -f ParseException.java SimpleCharStream.java Token.java TokenMgrError.java
    rm -f AmberParser.java AmberParserConstants.java AmberParserTokenManager.java
    -->

    <target name="parserAmber" depends="init" description="JavaCC compiler compiler Amber">
        <echo message="JavaCC compiler compiler Amber" />
        <delete verbose="true">
            <fileset dir="${src.dir}/Wattos/Converters/Amber" includes="ParseException.java SimpleCharStream.java Token.java TokenMgrError.java AmberParser.java AmberParserConstants.java AmberParserTokenManager.java" />
        </delete>
        <java jvm="${platform.java}" fork="true" failonerror="true" classname="javacc" dir="${src.dir}/Wattos/Converters/Amber" timeout="9600">
            <arg line="AmberParserAll.jj" />
            <jvmarg line="-classpath C:\Docume~1\JURGEN~1.000\workspace\wattos\lib\javacc.jar" />
        </java>
    </target>
</project>