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             <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk."/>
  27         </target>
  28
  29
  30         <!-- utils is a class path to additional utilities needed for
  31     building docs, jars and webstart stuff -->
  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                         <!-->
  48                         <fileset dir="/usr/local/axis/lib">
  49                                 <include name="**/*.jar" />
  50                         </fileset>
  51                         <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  52                                 <include name="**/*.jar"/>
  53                                 <include name="*.jar"/>
  54                         </fileset> -->
  55       </path>
  56                 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  57     <property name="JALVIEW_VERSION" value="DEVELOPMENT"/> <!-- 2.4 (VAMSAS)" -->
  58                 <!-- Include debugging information in javac true or false -->
  59                 <property name="javac.debug" value="true"/>
  60                 <!-- Don't change anything below here unless you know what you are doing! -->
  61                 <!-- Url path for WebStart in JNLP file -->
  62                 <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
  63                 <!-- build directory configuration -->
  64                 <property name="libDir" value="lib"/>
  65                 <property name="resourceDir" value="resources"/>
  66                 <property name="helpDir" value="help"/>
  67                 <property name="docDir" value="doc"/>
  68                 <property name="sourceDir" value="src" />
  69                 <property name="schemaDir" value="schemas" />
  70                 <property name="outputDir" value="classes" />
  71                 <property name="packageDir" value="dist" />
  72                 <property name="outputJar" value="jalview.jar" />
  73                 <!-- Jalview Applet JMol Jar Dependency -->
  74                 <property name="jmolJar" value="Jmol-11.0.2.jar" />
  75                 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
  76                 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
  77                 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
  78                 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
  79                 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
  80                 <property name="WSInterf" value="MsaWS" />
  81                 <property name="wsdl.Namespace" value="vamsas" />
  82                 <property name="wsdl.ClientNS" value="ext.vamsas" />
  83                 <!-- the class path for building the application -->
  84                 <path id="build.classpath">
  85                         <fileset dir="utils">
  86                                 <include name="*.jar"/>
  87                                 <include name="**/*.jar"/>
  88                         </fileset>
  89                         <fileset dir="${libDir}">
  90                                 <include name="*.jar"/>
  91                                 <include name="**/*.jar"/>
  92                         </fileset>
  93
  94                 </path>
  95                 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz"/>
  96                 <!-- The Location of the java 1.1.8 jdk -->
  97                 <property name="java118.home" value="C:\Sun\jdk1.1.8" />
  98                 <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip"/>
  99                 <!-- jre for 1.4 version
 100                 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 101                 -->
 102                 <!-- the classpath for building the 1.1 applet -->
 103                 <path id="jalviewlite.deps">
 104                         <fileset dir="${java118.home}">
 105                                 <include name="lib/classes.zip"/>
 106                         </fileset>
 107                 <pathelement location="lib/${jmolJar}"/>
 108           </path>
 109         </target>
 110
 111
 112         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
 113         <target name="buildPropertiesFile" depends="init">
 114                 <tstamp prefix="build">
 115                         <format property="date" pattern="dd MMMM yyyy"/>
 116                 </tstamp>
 117                 <properties file="${outputDir}/.build_properties">
 118                         <header>
 119           ---Jalview Build Details---
 120         </header>
 121                         <property name="VERSION" value="${JALVIEW_VERSION}"/>
 122                         <property name="BUILD_DATE" value="${build.date}"/>
 123                 </properties>
 124         </target>
 125
 126
 127         <target name="clean" depends="init">
 128                 <!-- not efficient yet. -->
 129                 <delete dir="${outputDir}"/>
 130         </target>
 131
 132         <target name="distclean" depends="init, clean">
 133
 134                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
 135                 <delete>
 136                         <fileset dir=".">
 137                                 <include name="${outputJar}"/>
 138                                 <include name="#*#"/>
 139                                 <include name="#*.*#"/>
 140                                 <include name="**/#*#"/>
 141                                 <include name="**/#*.*#"/>
 142                                 <include name="*~"/>
 143                                 <include name="*.*~"/>
 144                                 <include name="**/*~"/>
 145                                 <include name="**/*.*~"/>
 146                         </fileset>
 147                 </delete>
 148         </target>
 149
 150         <target name="prepare" depends="init">
 151                 <mkdir dir="${outputDir}"/>
 152                 <copy todir="${outputDir}">
 153                         <fileset dir=".">
 154                                 <include name="${docDir}/**/*.*"/>
 155                                 <include name="${helpDir}/**/*.*"/>
 156                                 <include name="${libDir}/*.jar"/>
 157                         </fileset>
 158                         <fileset dir="${resourceDir}">
 159                                 <include name="**/*.*"/>
 160                         </fileset>
 161                 </copy>
 162         </target>
 163
 164         <target name="build" depends="prepare">
 165                 <!-- not efficient yet. -->
 166                 <javac source="1.4" target="1.4"
 167         srcdir ="${sourceDir}"
 168         destdir="${outputDir}"
 169                                 debug="${javac.debug}"
 170       classpathref="build.classpath">
 171                         <exclude name="jalview/*applet*"/>
 172                         <exclude name="com/stevesoft/**"/>
 173                 </javac>
 174         </target>
 175         <target name="buildindices" depends="init, prepare"
 176     unless="help.uptodate">
 177                 <java
 178       classname="com.sun.java.help.search.Indexer"
 179       classpathref="build.classpath"
 180       fork="true"
 181       dir="${outputDir}/${helpDir}"
 182       >
 183                         <arg line="html"/>
 184                 </java>
 185         </target>
 186
 187         <target name="makefulldist" depends="makedist">
 188                 <!-- the default keystore details might need to be edited here -->
 189                 <signjar
 190       storepass="alignmentisfun"
 191       keypass="alignmentisfun"
 192       keystore="keys/.keystore"
 193       alias="jalview"
 194       lazy="false"
 195       verbose="false"
 196       >
 197
 198                         <fileset dir="${packageDir}">
 199                                 <include name="*.jar"/>
 200                         </fileset>
 201                 </signjar>
 202                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
 203
 204                 <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 205                 <jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp"
 206       codebase="${WebStartLocation}">
 207                         <information>
 208                                 <title>Jalview</title>
 209                                 <vendor>The Barton Group</vendor>
 210                                 <homepage href="http://www.jalview.org"/>
 211                                 <description>Jalview Multiple Alignment Editor</description>
 212                                 <description kind="short">Jalview</description>
 213                                 <icon href="logo_big.gif"/>
 214                                 <offline_allowed/>
 215                                 <!--
 216         <association mime-type="application-x/ext-file" extensions="fa"/>
 217         <association mime-type="application-x/ext-file" extensions="fasta"/>
 218         <association mime-type="application-x/ext-file" extensions="fastq"/>
 219         <association mime-type="application-x/ext-file" extensions="blc"/>
 220         <association mime-type="application-x/ext-file" extensions="msf"/>
 221         <association mime-type="application-x/ext-file" extensions="pfam"/>
 222         <association mime-type="application-x/ext-file" extensions="aln"/>
 223         <association mime-type="application-x/ext-file" extensions="pir"/>
 224         -->
 225                         </information>
 226                         <resources>
 227                                 <j2se version="1.4+"/>
 228                                 <fileset dir="${packageDir}">
 229                                         <include name="jalview.jar"/>
 230                                 </fileset>
 231                                 <fileset dir="${packageDir}">
 232                                         <include name="*.jar"/>
 233                                         <exclude name="jalview.jar"/>
 234                                 </fileset>
 235                                 <property name="jalview.version" value="${JALVIEW_VERSION}"/>
 236                         </resources>
 237                         <application_desc main_class="jalview.bin.Jalview">
 238                         </application_desc>
 239                         <security>
 240                                 <all_permissions/>
 241                         </security>
 242                 </jnlp>
 243         </target>
 244         <target name="runenv" depends="init">
 245                 <path id="run.classpath">
 246                         <pathelement location="${outputDir}"/>
 247                         <fileset dir="${outputDir}">
 248                                 <include name="${libDir}/*.jar"/>
 249                         </fileset>
 250                 </path>
 251                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
 252
 253                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 254       </echo>
 255         </target>
 256
 257         <target name="buildextclients" depends="init">
 258                 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
 259       validargs="Y,y,n,N" defaultvalue="N"
 260       addproperty="doextbuild.response"/>
 261                 <condition property="dontextbuild">
 262                         <equals arg1="n" arg2="${doextbuild.response}"/>
 263                 </condition>
 264                 <condition property="dontextbuild">
 265                         <equals arg1="N" arg2="${doextbuild.response}"/>
 266                 </condition>
 267                 <fail if="dontextbuild">
 268         Build External Client Code process aborted by user. Jalview source is unchanged.
 269       </fail>
 270                 <!-- Currently, this doesn't happen automatically.
 271      1. Run WSDL2Java as below, which generates an ext.vamsas +
 272      vamsas.<datapackages> fileset.
 273      2. refactor ext.vamsas.SpecificserviceWS* to
 274      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 275      3. Update the jalview.ws.*WServices classes to reflect the
 276      interface type, and all locations of this wsdl type that Jalview
 277      might be using.
 278
 279 -->
 280                 <path id="axisbuild">
 281                         <path refid="build.classpath"/>
 282                 </path>
 283                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
 284                 <move todir="./bak">
 285                         <fileset dir="${sourceDir}" id="client">
 286                                 <include name="${wsdl.ClientNS}/*.*"/>
 287                         </fileset>
 288                 </move>
 289
 290                 <axis-wsdl2java
 291       output="${sourceDir}"
 292       verbose="true"
 293       url="${wsdl.MsaWS2}"
 294       serverside="false"
 295       deployscope="Request"
 296       debug="false"
 297       helpergen="true"
 298       all="true"
 299       >
 300                         <mappingSet>
 301                                 <mapping
 302         namespace="${wsdl.Namespace}"
 303         package="${wsdl.ClientNS}"
 304         />
 305                                 <mapping namespace="http://dataTypes.vamsas"
 306         package="${wsdl.ClientNS}"/>
 307                         </mappingSet>
 308                 </axis-wsdl2java>
 309         </target>
 310
 311         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 312                 <!-- make the package jar -->
 313                 <mkdir dir="${packageDir}"/>
 314
 315                 <jar destfile="${packageDir}/${outputJar}">
 316                         <manifest>
 317                                 <attribute name="Main-Class" value="jalview.bin.Jalview"/>
 318                         </manifest>
 319                         <fileset dir="${outputDir}/">
 320                                 <exclude name="cache*/**"/>
 321                                 <exclude name="*.jar" />
 322                                 <exclude name="*.jar.*" />
 323                                 <exclude name="**/*.jar" />
 324                                 <exclude name="**/*.jar.*" />
 325                         </fileset>
 326                 </jar>
 327
 328                 <copy toDir="${packageDir}" flatten="true">
 329                         <fileset dir="${outputDir}">
 330                                 <include name="*.jar"/>
 331                                 <include name="**/*.jar"/>
 332                         </fileset>
 333                 </copy>
 334         </target>
 335
 336
 337         <!-- jalopy code reformatter -->
 338         <target name="sourcescrub" depends="init,build">
 339                 <jalopy destdir="jsrc" classpathref="run.classpath"
 340       convention="jalview-jalopy.xml">
 341                         <fileset dir="${sourceDir}">
 342                                 <include name="*.java"/>
 343                                 <include name="**/*.java"/>
 344                                 <include name="**/**/*.java"/>
 345                         </fileset>
 346                 </jalopy>
 347         </target>
 348
 349
 350
 351   <!-- Compile, package and obfuscate Jalview Applet -->
 352   <target name="makeApplet" depends="obfuscate"/>
 353
 354   <target name="compileApplet" depends="init,clean">
 355     <mkdir dir="${outputDir}"/>
 356     <javac source="1.2"
 357     target="1.1"
 358     srcdir="${sourceDir}"
 359     destdir="${outputDir}"
 360     classpath="lib/${jmolJar}"
 361        includes="jalview/appletgui/**"
 362        excludes="ext/**,MCview/**,org/**,vamsas/**"
 363        />
 364   </target>
 365
 366   <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 367   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
 368   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
 369        <jar destfile="in.jar">
 370         <manifest>
 371             <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
 372         </manifest>
 373         <fileset dir="${outputDir}">
 374           <include name="com/**"/>
 375           <include name="MCview/**"/>
 376           <include name="jalview/**"/>
 377           <include name=".build_properties"/>
 378           <include name="images/idwidth.gif"/>
 379           <include name="images/link.gif"/>
 380         </fileset>
 381       </jar>
 382   </target>
 383
 384   <target name="obfuscate" depends="packageApplet">
 385     <path id="obfuscateDeps.path">
 386     <pathelement location="${applet.jre.tools}"/>
 387     <pathelement location="lib/${jmolJar}"/>
 388     </path>
 389     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 390     <proguard>
 391       <injar file="in.jar"/>
 392       <outjar file="jalviewApplet.jar"/>
 393       <libraryjar refid="obfuscateDeps.path"/>
 394       <keep access="public" type="class"
 395       name="jalview.bin.JalviewLite">
 396         <field access="public"/>
 397         <method access="public"/>
 398         <constructor access="public"/>
 399       </keep>
 400 <!--      -libraryjars "${obfuscateDeps}"
 401       -injars      in.jar
 402       -outjars     jalviewApplet.jar
 403       -keep public class jalview.bin.JalviewLite
 404        { public * ; }
 405        -->
 406     </proguard>
 407     <delete file="in.jar"/>
 408   </target>
 409
 410         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 411                 <taskdef name="castor-srcgen"
 412                           classname="org.castor.anttask.CastorCodeGenTask"
 413                       classpathref="build.classpath" />
 414                 <delete>
 415                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 416                                 <include name="*.java"/>
 417                                 <include name="descriptors/*.java"/>
 418                         </fileset>
 419                 </delete>
 420                 <castor-srcgen file="${schemaDir}/vamsas.xsd"
 421                               todir="${sourceDir}"
 422                               package="jalview.schemabinding.version2"
 423                               warnings="false"
 424                                         nodesc="false"
 425                                                 verbose="true"
 426                                                 properties="${schemaDir}/jalview.properties"
 427                 />
 428                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
 429                               todir="${sourceDir}"
 430                               package="jalview.schemabinding.version2"
 431                               warnings="false"
 432                                         nodesc="false"
 433                                                 verbose="true"
 434                                                 properties="${schemaDir}/jalview.properties"
 435                 />
 436                 <castor-srcgen file="${schemaDir}/jalview.xsd"
 437                               todir="${sourceDir}"
 438                               package="jalview.schemabinding.version2"
 439                               warnings="false"
 440                                           nodesc="false"
 441                                                 verbose="true"
 442                                                 properties="${schemaDir}/jalview.properties"
 443
 444                 />
 445                 <!--
 446                 now build the jalview.binding package with the old schema set
 447                 -->
 448                 <delete>
 449                         <fileset dir="${sourceDir}/jalview/binding/">
 450                                 <include name="**"/>
 451                         </fileset>
 452                 </delete>
 453                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd"
 454                               todir="${sourceDir}"
 455                               package="jalview.binding"
 456                               warnings="false"
 457                                         nodesc="true"
 458                                                 verbose="true"
 459                                                 properties="${schemaDir}/jalview.nodesc.properties"
 460                 />
 461                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
 462                               todir="${sourceDir}"
 463                               package="jalview.binding"
 464                               warnings="false"
 465                                         nodesc="true"
 466                                                 verbose="true"
 467                                                 properties="${schemaDir}/jalview.nodesc.properties"
 468                 />
 469                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd"
 470                               todir="${sourceDir}"
 471                               package="jalview.binding"
 472                               warnings="false"
 473                                           nodesc="true"
 474                                                 verbose="true"
 475                                                 properties="${schemaDir}/jalview.nodesc.properties"
 476         />
 477         </target>
 478         <target name="sourcedist" description="create jalview source distribution" depends="init">
 479                 <delete file="${source.dist.name}"/>
 480                 <tar destfile="${source.dist.name}" compression="gzip">
 481                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 482                                 <include name="LICENSE"/>
 483                                 <include name="README"/>
 484                                 <include name="build.xml"/>
 485                                 <include name="jalview-jalopy.xml"/>
 486                                 <include name="JalviewApplet.jpx"/>
 487                                 <include name="JalviewX.jpx"/>
 488                                 <include name="${sourceDir}/*.java"/>
 489                                 <include name="${sourceDir}/**/*.java"/>
 490                                 <include name="${sourceDir}/**/*.cdr"/>
 491                                 <include name="${libDir}/**/*"/>
 492                                 <include name="${resourceDir}/**/*"/>
 493                                 <include name="${helpDir}/**/*"/>
 494                                 <include name="utils/**/*"/>
 495                                 <include name="${schemaDir}/**/*"/>
 496                                 <include name="${docDir}/**/*"/>
 497                         </tarfileset>
 498                 </tar>
 499         </target>
 500 </project>