build.xml

   1 <?xml version="1.0"?>
   2   <project name="jalviewX" default="build" basedir=".">
   3 <!-- we use jalopy to format our sources -->
   4 <taskdef name="jalopy"
   5          classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
   6   <classpath>
   7     <fileset dir="utils/jalopy/lib">
   8       <include name="*.jar" />
   9     </fileset>
  10   </classpath>
  11 </taskdef>
  12
  13
  14     <!-- utils is a class path to additional utilities needed for
  15     building docs, jars and webstart stuff -->
  16
  17 <!--
  18         Userdefined build property defaults
  19
  20         wsdl.server list (plus namespace mapping info ???)  - also want
  21                 ... to make this a dynamically generatable property
  22         WebStart Location
  23         Build location - provide a temporary root for speed
  24         jarsigner keystore and info
  25         Jakarta and axis classpath ?
  26         Default argument for starting Jalview (if it exists).
  27
  28 -->
  29
  30     <target name="init">
  31       <path id="axis.classpath">
  32 <!-->        <fileset dir="/usr/local/axis/lib">
  33           <include name="**/*.jar" />
  34         </fileset>
  35         <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  36           <include name="**/*.jar"/>
  37           <include name="*.jar"/>
  38         </fileset> -->
  39       </path>
  40
  41       <property name="JALVIEW_VERSION" value="2.07"/>
  42       <property name="" value=""/>
  43       <property name="libDir" value="lib"/>
  44       <property name="resourceDir" value="resources"/>
  45       <property name="helpDir" value="help"/>
  46       <property name="docDir" value="doc"/>
  47       <property name="sourceDir" value="src" />
  48       <property name="outputDir" value="classes" />
  49       <property name="packageDir" value="dist" />
  50       <property name="outputJar" value="jalview.jar" />
  51       <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
  52       <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
  53       <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
  54       <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
  55       <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
  56         <property name="WSInterf" value="MsaWS" />
  57       <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
  58       <property name="wsdl.Namespace" value="vamsas" />
  59       <property name="wsdl.ClientNS" value="ext.vamsas" />
  60
  61       <path id="build.classpath">
  62         <fileset dir="utils">
  63           <include name="*.jar"/>
  64           <include name="**/*.jar"/>
  65         </fileset>
  66         <fileset dir="${libDir}">
  67           <include name="*.jar"/>
  68           <include name="**/*.jar"/>
  69         </fileset>
  70                 <fileset dir="../VamsasClient/packages">
  71                         <include name="*.jar"/>
  72                         <include name="**/*.jar"/>
  73                 </fileset>
  74 <!--        <fileset dir="old_lib_signed">
  75 <include name="lib_axis.jar"/>
  76
  77         </fileset>-->
  78       </path>
  79       <!-->    <uptodate property="help.uptodate"
  80       targetfile="${helpDir}/helpIndex.xml">
  81       <srcfiles
  82                  dir="${helpDir}"
  83                  includes="**/*.html" />
  84                </uptodate>
  85       -->
  86     </target>
  87
  88
  89     <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
  90     <target name="buildPropertiesFile" depends="init">
  91       <tstamp prefix="build">
  92         <format property="date" pattern="dd MMMM yyyy"/>
  93       </tstamp>
  94       <properties file="${outputDir}/.build_properties">
  95         <header>
  96           ---Jalview Build Details---
  97         </header>
  98         <property name="VERSION" value="${JALVIEW_VERSION}"/>
  99         <property name="BUILD_DATE" value="${build.date}"/>
 100       </properties>
 101     </target>
 102
 103
 104     <target name="clean" depends="init">
 105       <!-- not efficient yet. -->
 106       <delete dir="${outputDir}"/>
 107     </target>
 108
 109     <target name="distclean" depends="init, clean">
 110
 111       <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
 112       <delete>
 113         <fileset dir=".">
 114           <include name="${outputJar}"/>
 115           <include name="#*#"/>
 116           <include name="#*.*#"/>
 117           <include name="**/#*#"/>
 118           <include name="**/#*.*#"/>
 119           <include name="*~"/>
 120           <include name="*.*~"/>
 121           <include name="**/*~"/>
 122           <include name="**/*.*~"/>
 123         </fileset>
 124       </delete>
 125     </target>
 126
 127     <target name="prepare" depends="init">
 128       <mkdir dir="${outputDir}"/>
 129       <copy todir="${outputDir}">
 130         <fileset dir=".">
 131           <include name="${docDir}/**/*.*"/>
 132           <include name="${helpDir}/**/*.*"/>
 133           <include name="${libDir}/*.jar"/>
 134         </fileset>
 135         <fileset dir="${resourceDir}">
 136           <include name="**/*.*"/>
 137         </fileset>
 138         <fileset dir="../VamsasClient/packages/">
 139           <include name="**/*.jar"/>
 140         </fileset>
 141       </copy>
 142     </target>
 143
 144     <target name="build" depends="prepare">
 145       <!-- not efficient yet. -->
 146       <javac source="1.4" target="1.4"
 147         srcdir ="${sourceDir}"
 148         destdir="${outputDir}"
 149       classpathref="build.classpath">
 150       <exclude name="jalview/*applet*"/>
 151        <exclude name="com/stevesoft/**"/>
 152       </javac>
 153     </target>
 154     <target name="buildindices" depends="init, prepare"
 155     unless="help.uptodate">
 156     <java
 157       classname="com.sun.java.help.search.Indexer"
 158       classpathref="build.classpath"
 159       fork="true"
 160       dir="${outputDir}/${helpDir}"
 161       >
 162       <arg line="html"/>
 163     </java>
 164     </target>
 165
 166     <target name="makejars" depends="build, buildPropertiesFile, buildindices">
 167       <!-- make the package jar -->
 168       <mkdir dir="${packageDir}"/>
 169
 170       <jar destfile="${packageDir}/${outputJar}">
 171         <manifest>
 172              <attribute name="Main-Class" value="jalview.bin.Jalview"/>
 173         </manifest>
 174         <fileset dir="${outputDir}/">
 175           <exclude name="cache*/**"/>
 176           <exclude name="*.jar" />
 177           <exclude name="*.jar.*" />
 178           <exclude name="**/*.jar" />
 179           <exclude name="**/*.jar.*" />
 180         </fileset>
 181       </jar>
 182
 183       <copy toDir="${packageDir}" flatten="true">
 184         <fileset dir="${outputDir}">
 185           <include name="*.jar"/>
 186           <include name="**/*.jar"/>
 187         </fileset>
 188       </copy>
 189 <!-- the default keystore details might need to be edited here -->
 190       <signjar
 191       storepass="alignmentisfun"
 192       keypass="alignmentisfun"
 193       keystore="keys/.keystore"
 194       alias="jalview"
 195       lazy="false"
 196       verbose="false"
 197       >
 198
 199       <fileset dir="${packageDir}">
 200         <include name="*.jar"/>
 201       </fileset>
 202       </signjar>
 203       <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
 204
 205       <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 206       <jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp"
 207       codebase="${WebStartLocation}">
 208       <information>
 209         <title>Jalview</title>
 210         <vendor>The Barton Group</vendor>
 211         <homepage href="http://www.jalview.org"/>
 212         <description>Jalview Multiple Alignment Editor</description>
 213         <description kind="short">Jalview</description>
 214         <icon href="logo_big.gif"/>
 215         <offline_allowed/>
 216         <!--
 217         <association mime-type="application-x/ext-file" extensions="fa"/>
 218         <association mime-type="application-x/ext-file" extensions="fasta"/>
 219         <association mime-type="application-x/ext-file" extensions="fastq"/>
 220         <association mime-type="application-x/ext-file" extensions="blc"/>
 221         <association mime-type="application-x/ext-file" extensions="msf"/>
 222         <association mime-type="application-x/ext-file" extensions="pfam"/>
 223         <association mime-type="application-x/ext-file" extensions="aln"/>
 224         <association mime-type="application-x/ext-file" extensions="pir"/>
 225         -->
 226        </information>
 227         <resources>
 228           <j2se version="1.4+"/>
 229           <fileset dir="${packageDir}">
 230             <include name="jalview.jar"/>
 231           </fileset>
 232           <fileset dir="${packageDir}">
 233             <include name="*.jar"/>
 234             <exclude name="jalview.jar"/>
 235           </fileset>
 236           <property name="jalview.version" value="${JALVIEW_VERSION}"/>
 237         </resources>
 238         <application_desc main_class="jalview.bin.Jalview">
 239           </application_desc>
 240         <security>
 241           <all_permissions/>
 242         </security>
 243       </jnlp>
 244     </target>
 245     <target name="runenv" depends="init">
 246       <path id="run.classpath">
 247         <pathelement location="${outputDir}"/>
 248         <fileset dir="${outputDir}">
 249           <include name="${libDir}/*.jar"/>
 250         </fileset>
 251       </path>
 252       <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
 253
 254       <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 255       </echo>
 256     </target>
 257
 258     <target name="buildextclients" depends="init">
 259 <!-- Currently, this doesn't happen automatically.
 260      1. Run WSDL2Java as below, which generates an ext.vamsas +
 261      vamsas.<datapackages> fileset.
 262      2. refactor ext.vamsas.SpecificserviceWS* to
 263      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 264      3. Update the jalview.ws.*WServices classes to reflect the
 265      interface type, and all locations of this wsdl type that Jalview
 266      might be using.
 267
 268 -->
 269       <path id="axisbuild">
 270         <!--        <path refid="axis.classpath"/> -->
 271         <path refid="build.classpath"/>
 272       </path>
 273       <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
 274       <move todir="./bak">
 275         <fileset dir="${sourceDir}" id="client">
 276           <include name="${wsdl.ClientNS}/*.*"/>
 277         </fileset>
 278       </move>
 279
 280       <axis-wsdl2java
 281       output="${sourceDir}"
 282       verbose="true"
 283       url="${wsdl.MsaWS2}"
 284       serverside="false"
 285       deployscope="Request"
 286       debug="false"
 287       helpergen="true"
 288       all="true"
 289       >
 290       <mappingSet>
 291         <mapping
 292         namespace="${wsdl.Namespace}"
 293         package="${wsdl.ClientNS}"
 294         />
 295         <mapping namespace="http://dataTypes.vamsas"
 296         package="${wsdl.ClientNS}"/>
 297         </mappingSet>
 298     </axis-wsdl2java>
 299
 300   </target>
 301   <target name="package" depends="init, build">
 302
 303   </target>
 304   <!-- jalopy code reformatter -->
 305   <target name="sourcescrub" depends="init,build">
 306     <jalopy destdir="jsrc" classpathref="run.classpath"
 307       convention="jalview-jalopy.xml">
 308       <fileset dir="${sourceDir}">
 309         <include name="*.java"/>
 310         <include name="**/*.java"/>
 311         <include name="**/**/*.java"/>
 312       </fileset>
 313       </jalopy>
 314   </target>
 315
 316
 317
 318   <!-- Compile, package and obfuscate Jalview Applet -->
 319   <target name="makeApplet" depends="obfuscate"/>
 320
 321   <target name="compileApplet" depends="init,clean">
 322     <mkdir dir="${outputDir}"/>
 323     <javac source="1.2" target="1.1" srcdir="${sourceDir}" destdir="${outputDir}"
 324        includes="jalview/analysis/**,jalview/appletgui/**,jalview/datamodel/**jalview/jbappletgui/**,jalview/math/**,jalview/schemes/**"
 325        excludes="ext/**,MCview/**,org/**,vamsas/**"/>
 326   </target>
 327
 328   <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 329   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
 330        <jar destfile="in.jar">
 331         <manifest>
 332             <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
 333         </manifest>
 334         <fileset dir="${outputDir}">
 335           <include name="com/**"/>
 336           <include name="MCview/**"/>
 337           <include name="jalview/**"/>
 338           <include name=".build_properties"/>
 339           <include name="images/idwidth.gif"/>
 340         </fileset>
 341       </jar>
 342   </target>
 343
 344   <target name="obfuscate" depends="packageApplet">
 345     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 346     <proguard>
 347       -libraryjars "${java.home}/lib/rt.jar"
 348       -injars      in.jar
 349       -outjars     jalviewApplet.jar
 350       -keep public class jalview.bin.JalviewLite
 351        { public * ; }
 352     </proguard>
 353     <delete file="in.jar"/>
 354   </target>
 355
 356
 357 </project>