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