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