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