build.xml

   1 <?xml version="1.0"?>
   2   <project name="jalviewX" default="usage" 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    <target name="help" depends="usage"/>
  14    <target name="usage">
  15      <echo message="~~~Jalview Ant build.xml Usage~~~~"/>
  16      <echo message="Targets include:"/>
  17      <echo message="usage - default target, displays this message"/>
  18      <echo message="buildindices - generates JavaHelpSearch from the help files"/>
  19      <echo message="build - compiles all necessary files for Application"/>
  20      <echo message="makedist - compiles and places all necessary jar files into directory dist"/>
  21      <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution"/>
  22      <echo message="              this needs a keystore and key. See docs/building.html for more information."/>
  23      <echo message="compileApplet - compiles all necessary files for Applet"/>
  24      <echo message="makeApplet - compiles, then packages and obfuscates the Applet"/>
  25      <echo message="See docs/building.html and the comments in build file for other targets."/>
  26    </target>
  27
  28
  29     <!-- utils is a class path to additional utilities needed for
  30     building docs, jars and webstart stuff -->
  31
  32 <!--
  33         Userdefined build property defaults
  34
  35         wsdl.server list (plus namespace mapping info ???)  - also want
  36                 ... to make this a dynamically generatable property
  37         WebStart Location
  38         Build location - provide a temporary root for speed
  39         jarsigner keystore and info
  40         Jakarta and axis classpath ?
  41         Default argument for starting Jalview (if it exists).
  42
  43 -->
  44
  45     <target name="init">
  46       <path id="axis.classpath">
  47 <!-->        <fileset dir="/usr/local/axis/lib">
  48           <include name="**/*.jar" />
  49         </fileset>
  50         <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  51           <include name="**/*.jar"/>
  52           <include name="*.jar"/>
  53         </fileset> -->
  54       </path>
  55       <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  56       <property name="JALVIEW_VERSION" value="ANNOTATION_TEST"/>
  57       <!-- Don't change anything below here unless you know what you are doing! -->
  58       <!-- Url path for WebStart in JNLP file -->
  59       <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
  60       <!-- build directory configuration -->
  61       <property name="libDir" value="lib"/>
  62       <property name="resourceDir" value="resources"/>
  63       <property name="helpDir" value="help"/>
  64       <property name="docDir" value="doc"/>
  65       <property name="sourceDir" value="src" />
  66       <property name="outputDir" value="classes" />
  67       <property name="packageDir" value="dist" />
  68       <property name="outputJar" value="jalview.jar" />
  69       <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
  70       <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
  71       <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
  72       <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
  73       <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
  74       <property name="WSInterf" value="MsaWS" />
  75       <property name="wsdl.Namespace" value="vamsas" />
  76       <property name="wsdl.ClientNS" value="ext.vamsas" />
  77       <!-- the class path for building the application -->
  78       <path id="build.classpath">
  79         <fileset dir="utils">
  80           <include name="*.jar"/>
  81           <include name="**/*.jar"/>
  82         </fileset>
  83         <fileset dir="${libDir}">
  84           <include name="*.jar"/>
  85           <include name="**/*.jar"/>
  86         </fileset>
  87       </path>
  88     </target>
  89
  90
  91     <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
  92     <target name="buildPropertiesFile" depends="init">
  93       <tstamp prefix="build">
  94         <format property="date" pattern="dd MMMM yyyy"/>
  95       </tstamp>
  96       <properties file="${outputDir}/.build_properties">
  97         <header>
  98           ---Jalview Build Details---
  99         </header>
 100         <property name="VERSION" value="${JALVIEW_VERSION}"/>
 101         <property name="BUILD_DATE" value="${build.date}"/>
 102       </properties>
 103     </target>
 104
 105
 106     <target name="clean" depends="init">
 107       <!-- not efficient yet. -->
 108       <delete dir="${outputDir}"/>
 109     </target>
 110
 111     <target name="distclean" depends="init, clean">
 112
 113       <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
 114       <delete>
 115         <fileset dir=".">
 116           <include name="${outputJar}"/>
 117           <include name="#*#"/>
 118           <include name="#*.*#"/>
 119           <include name="**/#*#"/>
 120           <include name="**/#*.*#"/>
 121           <include name="*~"/>
 122           <include name="*.*~"/>
 123           <include name="**/*~"/>
 124           <include name="**/*.*~"/>
 125         </fileset>
 126       </delete>
 127     </target>
 128
 129     <target name="prepare" depends="init">
 130       <mkdir dir="${outputDir}"/>
 131       <copy todir="${outputDir}">
 132         <fileset dir=".">
 133           <include name="${docDir}/**/*.*"/>
 134           <include name="${helpDir}/**/*.*"/>
 135           <include name="${libDir}/*.jar"/>
 136         </fileset>
 137         <fileset dir="${resourceDir}">
 138           <include name="**/*.*"/>
 139         </fileset>
 140       </copy>
 141     </target>
 142
 143     <target name="build" depends="prepare">
 144       <!-- not efficient yet. -->
 145       <javac source="1.4" target="1.4"
 146         srcdir ="${sourceDir}"
 147         destdir="${outputDir}"
 148       classpathref="build.classpath">
 149       <exclude name="jalview/*applet*"/>
 150        <exclude name="com/stevesoft/**"/>
 151       </javac>
 152     </target>
 153     <target name="buildindices" depends="init, prepare"
 154     unless="help.uptodate">
 155     <java
 156       classname="com.sun.java.help.search.Indexer"
 157       classpathref="build.classpath"
 158       fork="true"
 159       dir="${outputDir}/${helpDir}"
 160       >
 161       <arg line="html"/>
 162     </java>
 163     </target>
 164
 165     <target name="makefulldist" depends="makedist">
 166  <!-- the default keystore details might need to be edited here -->
 167       <signjar
 168       storepass="alignmentisfun"
 169       keypass="alignmentisfun"
 170       keystore="keys/.keystore"
 171       alias="jalview"
 172       lazy="false"
 173       verbose="false"
 174       >
 175
 176       <fileset dir="${packageDir}">
 177         <include name="*.jar"/>
 178       </fileset>
 179       </signjar>
 180       <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
 181
 182       <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 183       <jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp"
 184       codebase="${WebStartLocation}">
 185       <information>
 186         <title>Jalview</title>
 187         <vendor>The Barton Group</vendor>
 188         <homepage href="http://www.jalview.org"/>
 189         <description>Jalview Multiple Alignment Editor</description>
 190         <description kind="short">Jalview</description>
 191         <icon href="logo_big.gif"/>
 192         <offline_allowed/>
 193         <!--
 194         <association mime-type="application-x/ext-file" extensions="fa"/>
 195         <association mime-type="application-x/ext-file" extensions="fasta"/>
 196         <association mime-type="application-x/ext-file" extensions="fastq"/>
 197         <association mime-type="application-x/ext-file" extensions="blc"/>
 198         <association mime-type="application-x/ext-file" extensions="msf"/>
 199         <association mime-type="application-x/ext-file" extensions="pfam"/>
 200         <association mime-type="application-x/ext-file" extensions="aln"/>
 201         <association mime-type="application-x/ext-file" extensions="pir"/>
 202         -->
 203        </information>
 204         <resources>
 205           <j2se version="1.4+"/>
 206           <fileset dir="${packageDir}">
 207             <include name="jalview.jar"/>
 208           </fileset>
 209           <fileset dir="${packageDir}">
 210             <include name="*.jar"/>
 211             <exclude name="jalview.jar"/>
 212           </fileset>
 213           <property name="jalview.version" value="${JALVIEW_VERSION}"/>
 214         </resources>
 215         <application_desc main_class="jalview.bin.Jalview">
 216           </application_desc>
 217         <security>
 218           <all_permissions/>
 219         </security>
 220       </jnlp>
 221     </target>
 222     <target name="runenv" depends="init">
 223       <path id="run.classpath">
 224         <pathelement location="${outputDir}"/>
 225         <fileset dir="${outputDir}">
 226           <include name="${libDir}/*.jar"/>
 227         </fileset>
 228       </path>
 229       <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
 230
 231       <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 232       </echo>
 233     </target>
 234
 235     <target name="buildextclients" depends="init">
 236       <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
 237       validargs="Y,y,n,N" defaultvalue="N"
 238       addproperty="doextbuild.response"/>
 239       <condition property="dontextbuild">
 240         <equals arg1="n" arg2="${doextbuild.response}"/>
 241       </condition>
 242       <condition property="dontextbuild">
 243         <equals arg1="N" arg2="${doextbuild.response}"/>
 244       </condition>
 245       <fail if="dontextbuild">
 246         Build External Client Code process aborted by user. Jalview source is unchanged.
 247       </fail>
 248 <!-- Currently, this doesn't happen automatically.
 249      1. Run WSDL2Java as below, which generates an ext.vamsas +
 250      vamsas.<datapackages> fileset.
 251      2. refactor ext.vamsas.SpecificserviceWS* to
 252      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 253      3. Update the jalview.ws.*WServices classes to reflect the
 254      interface type, and all locations of this wsdl type that Jalview
 255      might be using.
 256
 257 -->
 258       <path id="axisbuild">
 259         <path refid="build.classpath"/>
 260       </path>
 261       <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
 262       <move todir="./bak">
 263         <fileset dir="${sourceDir}" id="client">
 264           <include name="${wsdl.ClientNS}/*.*"/>
 265         </fileset>
 266       </move>
 267
 268       <axis-wsdl2java
 269       output="${sourceDir}"
 270       verbose="true"
 271       url="${wsdl.MsaWS2}"
 272       serverside="false"
 273       deployscope="Request"
 274       debug="false"
 275       helpergen="true"
 276       all="true"
 277       >
 278       <mappingSet>
 279         <mapping
 280         namespace="${wsdl.Namespace}"
 281         package="${wsdl.ClientNS}"
 282         />
 283         <mapping namespace="http://dataTypes.vamsas"
 284         package="${wsdl.ClientNS}"/>
 285         </mappingSet>
 286     </axis-wsdl2java>
 287     </target>
 288
 289     <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 290       <!-- make the package jar -->
 291       <mkdir dir="${packageDir}"/>
 292
 293       <jar destfile="${packageDir}/${outputJar}">
 294         <manifest>
 295              <attribute name="Main-Class" value="jalview.bin.Jalview"/>
 296         </manifest>
 297         <fileset dir="${outputDir}/">
 298           <exclude name="cache*/**"/>
 299           <exclude name="*.jar" />
 300           <exclude name="*.jar.*" />
 301           <exclude name="**/*.jar" />
 302           <exclude name="**/*.jar.*" />
 303         </fileset>
 304       </jar>
 305
 306       <copy toDir="${packageDir}" flatten="true">
 307         <fileset dir="${outputDir}">
 308           <include name="*.jar"/>
 309           <include name="**/*.jar"/>
 310         </fileset>
 311       </copy>
 312   </target>
 313
 314
 315   <!-- jalopy code reformatter -->
 316   <target name="sourcescrub" depends="init,build">
 317     <jalopy destdir="jsrc" classpathref="run.classpath"
 318       convention="jalview-jalopy.xml">
 319       <fileset dir="${sourceDir}">
 320         <include name="*.java"/>
 321         <include name="**/*.java"/>
 322         <include name="**/**/*.java"/>
 323       </fileset>
 324       </jalopy>
 325   </target>
 326
 327
 328
 329   <!-- Compile, package and obfuscate Jalview Applet -->
 330   <target name="makeApplet" depends="obfuscate"/>
 331
 332   <target name="compileApplet" depends="init,clean">
 333     <mkdir dir="${outputDir}"/>
 334     <javac source="1.2" target="1.1" srcdir="${sourceDir}" destdir="${outputDir}"
 335        includes="jalview/analysis/**,jalview/appletgui/**,jalview/datamodel/**jalview/jbappletgui/**,jalview/math/**,jalview/schemes/**"
 336        excludes="ext/**,MCview/**,org/**,vamsas/**"/>
 337   </target>
 338
 339   <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 340   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
 341   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
 342        <jar destfile="in.jar">
 343         <manifest>
 344             <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
 345         </manifest>
 346         <fileset dir="${outputDir}">
 347           <include name="com/**"/>
 348           <include name="MCview/**"/>
 349           <include name="jalview/**"/>
 350           <include name=".build_properties"/>
 351           <include name="images/idwidth.gif"/>
 352           <include name="images/link.gif"/>
 353         </fileset>
 354       </jar>
 355   </target>
 356
 357   <target name="obfuscate" depends="packageApplet">
 358     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 359     <proguard>
 360       -libraryjars "${java.home}/lib/rt.jar"
 361       -injars      in.jar
 362       -outjars     jalviewApplet.jar
 363       -keep public class jalview.bin.JalviewLite
 364        { public * ; }
 365     </proguard>
 366     <delete file="in.jar"/>
 367   </target>
 368
 369
 370 </project>