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