build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
   4  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18 -->
  19 <project name="jalviewX" default="usage" basedir=".">
  20         <!-- we use jalopy to format our sources -->
  21         <taskdef name="jalopy"
  22          classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
  23                 <classpath>
  24                         <fileset dir="utils/jalopy/lib">
  25                                 <include name="*.jar" />
  26                         </fileset>
  27                 </classpath>
  28         </taskdef>
  29
  30         <target name="help" depends="usage"/>
  31         <target name="usage">
  32                 <echo message="~~~Jalview Ant build.xml Usage~~~~"/>
  33                 <echo message="Targets include:"/>
  34                 <echo message="usage - default target, displays this message"/>
  35                 <echo message="buildindices - generates JavaHelpSearch from the help files"/>
  36                 <echo message="build - compiles all necessary files for Application"/>
  37                 <echo message="makedist - compiles and places all necessary jar files into directory dist"/>
  38                 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution"/>
  39                 <echo message="              this needs a keystore and key. See docs/building.html for more information."/>
  40                 <echo message="compileApplet - compiles all necessary files for Applet"/>
  41                 <echo message="makeApplet - compiles, then packages and obfuscates the Applet"/>
  42                 <echo message="See docs/building.html and the comments in build file for other targets."/>
  43             <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk."/>
  44             <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation"/>
  45         </target>
  46
  47
  48         <!-- utils is a class path to additional utilities needed for
  49     building docs, jars and webstart stuff -->
  50         <!--
  51         Userdefined build property defaults
  52
  53         wsdl.server list (plus namespace mapping info ???)  - also want
  54                 ... to make this a dynamically generatable property
  55         WebStart Location
  56         Build location - provide a temporary root for speed
  57         jarsigner keystore and info
  58         Jakarta and axis classpath ?
  59         Default argument for starting Jalview (if it exists).
  60
  61 -->
  62
  63         <target name="init">
  64                 <path id="axis.classpath">
  65                         <!-->
  66                         <fileset dir="/usr/local/axis/lib">
  67                                 <include name="**/*.jar" />
  68                         </fileset>
  69                         <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  70                                 <include name="**/*.jar"/>
  71                                 <include name="*.jar"/>
  72                         </fileset> -->
  73       </path>
  74                 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  75     <property name="JALVIEW_VERSION" value="DEVELOPMENT"/> <!-- 2.4 (VAMSAS)" -->
  76                 <!-- Include debugging information in javac true or false -->
  77                 <property name="javac.debug" value="true"/>
  78
  79                 <!-- JarSigner Key Store for Webstart Distribution -->
  80                 <property name="jalview.keystore" value="./keys/.keystore"/>
  81                 <!-- Keystore Password -->
  82                 <property name="jalview.keystore.pass" value="alignmentisfun"/>
  83                 <!-- Key Name -->
  84                 <property name="jalview.key" value="jalview"/>
  85                 <!-- Key Password -->
  86                 <property name="jalview.key.pass" value="alignmentisfun"/>
  87
  88                 <!-- Don't change anything below here unless you know what you are doing! -->
  89                 <!-- Url path for WebStart in JNLP file -->
  90                 <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
  91                 <!-- build directory configuration -->
  92                 <property name="libDir" value="lib"/>
  93                 <property name="resourceDir" value="resources"/>
  94                 <property name="helpDir" value="help"/>
  95                 <property name="docDir" value="doc"/>
  96                 <property name="sourceDir" value="src" />
  97                 <property name="schemaDir" value="schemas" />
  98                 <property name="outputDir" value="classes" />
  99                 <property name="packageDir" value="dist" />
 100                 <property name="outputJar" value="jalview.jar" />
 101           <!-- Jalview Applet JMol Jar Dependency -->
 102     <property name="jmolJar" value="Jmol-11.0.2.jar" />
 103                 <property name="jalviewLiteJar" value="jalviewApplet.jar"/>
 104                 <!-- switch to indicate if we should obfuscate jalviewLite -->
 105                 <!--<property name="donotobfuscate" value="true"/> -->
 106
 107                 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 108                 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 109                 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 110                 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 111                 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 112                 <property name="WSInterf" value="MsaWS" />
 113                 <property name="wsdl.Namespace" value="vamsas" />
 114                 <property name="wsdl.ClientNS" value="ext.vamsas" />
 115                 <!-- the class path for building the application -->
 116                 <path id="build.classpath">
 117                         <fileset dir="utils">
 118                                 <include name="*.jar"/>
 119                                 <include name="**/*.jar"/>
 120                         </fileset>
 121                         <fileset dir="${libDir}">
 122                                 <include name="*.jar"/>
 123                                 <include name="**/*.jar"/>
 124                         </fileset>
 125
 126                 </path>
 127                 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz"/>
 128                 <!-- The Location of the java 1.1.8 jdk -->
 129                 <property name="java118.home" value="C:\Sun\jdk1.1.8" />
 130                 <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip"/>
 131                 <!-- jre for 1.4 version
 132                 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 133                 -->
 134                 <!-- the classpath for building the 1.1 applet -->
 135                 <path id="jalviewlite.deps">
 136                         <fileset dir="${java118.home}">
 137                                 <include name="lib/classes.zip"/>
 138                         </fileset>
 139                 <pathelement location="lib/${jmolJar}"/>
 140           </path>
 141         </target>
 142
 143
 144         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
 145         <target name="buildPropertiesFile" depends="init">
 146                 <tstamp prefix="build">
 147                         <format property="date" pattern="dd MMMM yyyy"/>
 148                 </tstamp>
 149                 <properties file="${outputDir}/.build_properties">
 150                         <header>
 151           ---Jalview Build Details---
 152         </header>
 153                         <property name="VERSION" value="${JALVIEW_VERSION}"/>
 154                         <property name="BUILD_DATE" value="${build.date}"/>
 155                 </properties>
 156         </target>
 157
 158
 159         <target name="clean" depends="init">
 160                 <!-- not efficient yet. -->
 161                 <delete dir="${outputDir}"/>
 162         </target>
 163
 164         <target name="distclean" depends="init, clean">
 165
 166                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
 167                 <delete>
 168                         <fileset dir=".">
 169                                 <include name="${outputJar}"/>
 170                                 <include name="#*#"/>
 171                                 <include name="#*.*#"/>
 172                                 <include name="**/#*#"/>
 173                                 <include name="**/#*.*#"/>
 174                                 <include name="*~"/>
 175                                 <include name="*.*~"/>
 176                                 <include name="**/*~"/>
 177                                 <include name="**/*.*~"/>
 178                         </fileset>
 179                 </delete>
 180         </target>
 181
 182         <target name="prepare" depends="init">
 183                 <mkdir dir="${outputDir}"/>
 184                 <copy todir="${outputDir}">
 185                         <fileset dir=".">
 186                                 <include name="${docDir}/**/*.*"/>
 187                                 <include name="${helpDir}/**/*.*"/>
 188                                 <include name="${libDir}/*.jar"/>
 189                         </fileset>
 190                         <fileset dir="${resourceDir}">
 191                                 <include name="**/*.*"/>
 192                         </fileset>
 193                 </copy>
 194         </target>
 195
 196         <target name="build" depends="prepare">
 197                 <!-- not efficient yet. -->
 198                 <javac source="1.4" target="1.4"
 199         srcdir ="${sourceDir}"
 200         destdir="${outputDir}"
 201                                 debug="${javac.debug}"
 202       classpathref="build.classpath">
 203                         <exclude name="jalview/*applet*"/>
 204                         <exclude name="com/stevesoft/**"/>
 205                 </javac>
 206         </target>
 207         <target name="buildindices" depends="init, prepare"
 208     unless="help.uptodate">
 209                 <java
 210       classname="com.sun.java.help.search.Indexer"
 211       classpathref="build.classpath"
 212       fork="true"
 213       dir="${outputDir}/${helpDir}"
 214       >
 215                         <arg line="html"/>
 216                 </java>
 217         </target>
 218
 219         <target name="makefulldist" depends="makedist">
 220                 <!-- the default keystore details might need to be edited here -->
 221                 <signjar
 222       storepass="${jalview.keystore.pass}"
 223       keypass="${jalview.key.pass}"
 224       keystore="${jalview.keystore}"
 225       alias="${jalview.key}"
 226       lazy="false"
 227       verbose="false"
 228       >
 229
 230                         <fileset dir="${packageDir}">
 231                                 <include name="*.jar"/>
 232                         </fileset>
 233                 </signjar>
 234                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
 235
 236                 <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 237                 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
 238                 <jnlp toFile="${packageDir}/jalview.jnlp"
 239       codebase="${WebStartLocation}">
 240                         <information>
 241                                 <title>Jalview</title>
 242                                 <vendor>The Barton Group</vendor>
 243                                 <homepage href="http://www.jalview.org"/>
 244                                 <description>Jalview Multiple Alignment Editor</description>
 245                                 <description kind="short">Jalview</description>
 246                                 <icon href="logo_big.gif"/>
 247                                 <offline_allowed/>
 248                                 <!--
 249         <association mime-type="application-x/ext-file" extensions="fa"/>
 250         <association mime-type="application-x/ext-file" extensions="fasta"/>
 251         <association mime-type="application-x/ext-file" extensions="fastq"/>
 252         <association mime-type="application-x/ext-file" extensions="blc"/>
 253         <association mime-type="application-x/ext-file" extensions="msf"/>
 254         <association mime-type="application-x/ext-file" extensions="pfam"/>
 255         <association mime-type="application-x/ext-file" extensions="aln"/>
 256         <association mime-type="application-x/ext-file" extensions="pir"/>
 257         <association mime-type="application-x/ext-file" extensions="amsa"/>
 258         -->
 259                         </information>
 260                         <resources>
 261                                 <j2se version="1.4+"/>
 262                                 <fileset dir="${packageDir}">
 263                                         <include name="jalview.jar"/>
 264                                 </fileset>
 265                                 <fileset dir="${packageDir}">
 266                                         <include name="*.jar"/>
 267                                         <include name="*_*.jar"/>
 268                                         <exclude name="jalview.jar"/>
 269                                 </fileset>
 270                                 <property name="jalview.version" value="${JALVIEW_VERSION}"/>
 271                         </resources>
 272                         <application_desc main_class="jalview.bin.Jalview">
 273                         </application_desc>
 274                         <security>
 275                                 <all_permissions/>
 276                         </security>
 277                 </jnlp>
 278         </target>
 279         <target name="runenv" depends="init">
 280                 <path id="run.classpath">
 281                         <pathelement location="${outputDir}"/>
 282                         <fileset dir="${outputDir}">
 283                                 <include name="${libDir}/*.jar"/>
 284                         </fileset>
 285                 </path>
 286                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
 287
 288                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 289       </echo>
 290         </target>
 291
 292         <target name="buildextclients" depends="init">
 293                 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
 294       validargs="Y,y,n,N" defaultvalue="N"
 295       addproperty="doextbuild.response"/>
 296                 <condition property="dontextbuild">
 297                         <equals arg1="n" arg2="${doextbuild.response}"/>
 298                 </condition>
 299                 <condition property="dontextbuild">
 300                         <equals arg1="N" arg2="${doextbuild.response}"/>
 301                 </condition>
 302                 <fail if="dontextbuild">
 303         Build External Client Code process aborted by user. Jalview source is unchanged.
 304       </fail>
 305                 <!-- Currently, this doesn't happen automatically.
 306      1. Run WSDL2Java as below, which generates an ext.vamsas +
 307      vamsas.<datapackages> fileset.
 308      2. refactor ext.vamsas.SpecificserviceWS* to
 309      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 310      3. Update the jalview.ws.*WServices classes to reflect the
 311      interface type, and all locations of this wsdl type that Jalview
 312      might be using.
 313
 314 -->
 315                 <path id="axisbuild">
 316                         <path refid="build.classpath"/>
 317                 </path>
 318                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
 319                 <move todir="./bak">
 320                         <fileset dir="${sourceDir}" id="client">
 321                                 <include name="${wsdl.ClientNS}/*.*"/>
 322                         </fileset>
 323                 </move>
 324
 325                 <axis-wsdl2java
 326       output="${sourceDir}"
 327       verbose="true"
 328       url="${wsdl.MsaWS2}"
 329       serverside="false"
 330       deployscope="Request"
 331       debug="false"
 332       helpergen="true"
 333       all="true"
 334       >
 335                         <mappingSet>
 336                                 <mapping
 337         namespace="${wsdl.Namespace}"
 338         package="${wsdl.ClientNS}"
 339         />
 340                                 <mapping namespace="http://dataTypes.vamsas"
 341         package="${wsdl.ClientNS}"/>
 342                         </mappingSet>
 343                 </axis-wsdl2java>
 344         </target>
 345
 346         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 347                 <!-- make the package jar -->
 348                 <mkdir dir="${packageDir}"/>
 349
 350                 <jar destfile="${packageDir}/${outputJar}">
 351                         <manifest>
 352                                 <attribute name="Main-Class" value="jalview.bin.Jalview"/>
 353                         </manifest>
 354                         <fileset dir="${outputDir}/">
 355                                 <exclude name="cache*/**"/>
 356                                 <exclude name="*.jar" />
 357                                 <exclude name="*.jar.*" />
 358                                 <exclude name="**/*.jar" />
 359                                 <exclude name="**/*.jar.*" />
 360                         </fileset>
 361                 </jar>
 362
 363                 <copy toDir="${packageDir}" flatten="true">
 364                         <fileset dir="${outputDir}">
 365                                 <include name="*.jar"/>
 366                                 <include name="**/*.jar"/>
 367                         </fileset>
 368                 </copy>
 369         </target>
 370
 371
 372         <!-- jalopy code reformatter -->
 373         <target name="sourcescrub" depends="init,build">
 374                 <jalopy destdir="jsrc" classpathref="run.classpath"
 375       convention="jalview-jalopy.xml">
 376                         <fileset dir="${sourceDir}">
 377                                 <include name="*.java"/>
 378                                 <include name="**/*.java"/>
 379                                 <include name="**/**/*.java"/>
 380                         </fileset>
 381                 </jalopy>
 382         </target>
 383
 384
 385
 386   <!-- Compile, package and obfuscate Jalview Applet -->
 387   <target name="makeApplet" depends="obfuscate"/>
 388
 389   <target name="compileApplet" depends="init,clean">
 390     <mkdir dir="${outputDir}"/>
 391     <javac source="1.2"
 392     target="1.1"
 393     srcdir="${sourceDir}"
 394     destdir="${outputDir}"
 395         debug="${javac.debug}"
 396     classpath="lib/${jmolJar}"
 397        includes="jalview/appletgui/**"
 398        excludes="ext/**,MCview/**,org/**,vamsas/**"
 399        />
 400   </target>
 401
 402   <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 403   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
 404   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
 405        <jar destfile="in.jar">
 406         <manifest>
 407             <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
 408         </manifest>
 409         <fileset dir="${outputDir}">
 410           <include name="com/**"/>
 411           <include name="MCview/**"/>
 412           <include name="jalview/**"/>
 413           <include name=".build_properties"/>
 414           <include name="images/idwidth.gif"/>
 415           <include name="images/link.gif"/>
 416         </fileset>
 417       </jar>
 418   </target>
 419   <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
 420   </target>
 421         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 422         <copy file="in.jar" tofile="${jalviewLiteJar}" />
 423     <delete file="in.jar"/>
 424   </target>
 425         <target name="-obfuscatereally" unless="donotobfuscate">
 426
 427         <path id="obfuscateDeps.path">
 428     <pathelement location="${applet.jre.tools}"/>
 429     <pathelement location="lib/${jmolJar}"/>
 430     </path>
 431     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 432
 433     <proguard>
 434       <injar file="in.jar"/>
 435       <outjar file="${jalviewLiteJar}"/>
 436       <libraryjar refid="obfuscateDeps.path"/>
 437       <keep access="public" type="class"
 438       name="jalview.bin.JalviewLite">
 439         <field access="public"/>
 440         <method access="public"/>
 441         <constructor access="public"/>
 442       </keep>
 443 <!--      -libraryjars "${obfuscateDeps}"
 444       -injars      in.jar
 445       -outjars     jalviewApplet.jar
 446       -keep public class jalview.bin.JalviewLite
 447        { public * ; } -->
 448       </proguard>
 449     <delete file="in.jar"/>
 450   </target>
 451
 452         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 453                 <taskdef name="castor-srcgen"
 454                           classname="org.castor.anttask.CastorCodeGenTask"
 455                       classpathref="build.classpath" />
 456                 <delete>
 457                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 458                                 <include name="*.java"/>
 459                                 <include name="descriptors/*.java"/>
 460                         </fileset>
 461                 </delete>
 462                 <castor-srcgen file="${schemaDir}/vamsas.xsd"
 463                               todir="${sourceDir}"
 464                               package="jalview.schemabinding.version2"
 465                               warnings="false"
 466                                         nodesc="false"
 467                                                 verbose="true"
 468                                                 properties="${schemaDir}/jalview.properties"
 469                 />
 470                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
 471                               todir="${sourceDir}"
 472                               package="jalview.schemabinding.version2"
 473                               warnings="false"
 474                                         nodesc="false"
 475                                                 verbose="true"
 476                                                 properties="${schemaDir}/jalview.properties"
 477                 />
 478                 <castor-srcgen file="${schemaDir}/jalview.xsd"
 479                               todir="${sourceDir}"
 480                               package="jalview.schemabinding.version2"
 481                               warnings="false"
 482                                           nodesc="false"
 483                                                 verbose="true"
 484                                                 properties="${schemaDir}/jalview.properties"
 485
 486                 />
 487                 <!--
 488                 now build the jalview.binding package with the old schema set
 489                 -->
 490                 <delete>
 491                         <fileset dir="${sourceDir}/jalview/binding/">
 492                                 <include name="**"/>
 493                         </fileset>
 494                 </delete>
 495                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd"
 496                               todir="${sourceDir}"
 497                               package="jalview.binding"
 498                               warnings="false"
 499                                         nodesc="true"
 500                                                 verbose="true"
 501                                                 properties="${schemaDir}/jalview.nodesc.properties"
 502                 />
 503                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
 504                               todir="${sourceDir}"
 505                               package="jalview.binding"
 506                               warnings="false"
 507                                         nodesc="true"
 508                                                 verbose="true"
 509                                                 properties="${schemaDir}/jalview.nodesc.properties"
 510                 />
 511                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd"
 512                               todir="${sourceDir}"
 513                               package="jalview.binding"
 514                               warnings="false"
 515                                           nodesc="true"
 516                                                 verbose="true"
 517                                                 properties="${schemaDir}/jalview.nodesc.properties"
 518         />
 519         </target>
 520         <target name="sourcedist" description="create jalview source distribution" depends="init">
 521                 <delete file="${source.dist.name}"/>
 522                 <tar destfile="${source.dist.name}" compression="gzip">
 523                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 524                                 <include name="LICENSE"/>
 525                                 <include name="README"/>
 526                                 <include name="build.xml"/>
 527                                 <include name="jalview-jalopy.xml"/>
 528                                 <include name="JalviewApplet.jpx"/>
 529                                 <include name="JalviewX.jpx"/>
 530                                 <include name="${sourceDir}/*.java"/>
 531                                 <include name="${sourceDir}/**/*.java"/>
 532                                 <include name="${sourceDir}/**/*.cdr"/>
 533                                 <include name="${libDir}/**/*"/>
 534                                 <include name="${resourceDir}/**/*"/>
 535                                 <include name="${helpDir}/**/*"/>
 536                                 <exclude name="**/*locales"/>
 537                                 <exclude name="*locales/**"/>
 538                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml"/>
 539                                 <exclude name="utils/InstallAnywhere/**Build*/**"/>
 540                                 <exclude name="utils/InstallAnywhere/**Build*/**"/>
 541                                 <exclude name="utils/InstallAnywhere/**locale*"/>
 542                                 <exclude name="utils/InstallAnywhere/**locale*/**"/>
 543                                 <include name="${schemaDir}/**/*"/>
 544                                 <include name="utils/**/*"/>
 545                                 <include name="${docDir}/**/*"/>
 546                         </tarfileset>
 547                 </tar>
 548         </target>
 549 </project>