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="2.3"/>
  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="${libDir}">
  88                                 <include name="*.jar"/>
  89                                 <include name="**/*.jar"/>
  90                         </fileset>
  91                 </path>
  92                 <!-- The Location of the java 1.1.8 jdk -->
  93                 <property name="java118.home" value="C:\Sun\jdk1.1.8" />
  94                 <!-- the classpath for building the 1.1 applet -->
  95                 <path id="jalviewlite.deps">
  96                         <fileset dir="${java118.home}">
  97                                 <include name="lib/classes.zip"/>
  98                         </fileset>
  99                 <pathelement location="lib/${jmolJar}"/>
 100           </path>
 101         </target>
 102
 103
 104         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
 105         <target name="buildPropertiesFile" depends="init">
 106                 <tstamp prefix="build">
 107                         <format property="date" pattern="dd MMMM yyyy"/>
 108                 </tstamp>
 109                 <properties file="${outputDir}/.build_properties">
 110                         <header>
 111           ---Jalview Build Details---
 112         </header>
 113                         <property name="VERSION" value="${JALVIEW_VERSION}"/>
 114                         <property name="BUILD_DATE" value="${build.date}"/>
 115                 </properties>
 116         </target>
 117
 118
 119         <target name="clean" depends="init">
 120                 <!-- not efficient yet. -->
 121                 <delete dir="${outputDir}"/>
 122         </target>
 123
 124         <target name="distclean" depends="init, clean">
 125
 126                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
 127                 <delete>
 128                         <fileset dir=".">
 129                                 <include name="${outputJar}"/>
 130                                 <include name="#*#"/>
 131                                 <include name="#*.*#"/>
 132                                 <include name="**/#*#"/>
 133                                 <include name="**/#*.*#"/>
 134                                 <include name="*~"/>
 135                                 <include name="*.*~"/>
 136                                 <include name="**/*~"/>
 137                                 <include name="**/*.*~"/>
 138                         </fileset>
 139                 </delete>
 140         </target>
 141
 142         <target name="prepare" depends="init">
 143                 <mkdir dir="${outputDir}"/>
 144                 <copy todir="${outputDir}">
 145                         <fileset dir=".">
 146                                 <include name="${docDir}/**/*.*"/>
 147                                 <include name="${helpDir}/**/*.*"/>
 148                                 <include name="${libDir}/*.jar"/>
 149                         </fileset>
 150                         <fileset dir="${resourceDir}">
 151                                 <include name="**/*.*"/>
 152                         </fileset>
 153                 </copy>
 154         </target>
 155
 156         <target name="build" depends="prepare">
 157                 <!-- not efficient yet. -->
 158                 <javac source="1.4" target="1.4"
 159         srcdir ="${sourceDir}"
 160         destdir="${outputDir}"
 161       classpathref="build.classpath">
 162                         <exclude name="jalview/*applet*"/>
 163                         <exclude name="com/stevesoft/**"/>
 164                 </javac>
 165         </target>
 166         <target name="buildindices" depends="init, prepare"
 167     unless="help.uptodate">
 168                 <java
 169       classname="com.sun.java.help.search.Indexer"
 170       classpathref="build.classpath"
 171       fork="true"
 172       dir="${outputDir}/${helpDir}"
 173       >
 174                         <arg line="html"/>
 175                 </java>
 176         </target>
 177
 178         <target name="makefulldist" depends="makedist">
 179                 <!-- the default keystore details might need to be edited here -->
 180                 <signjar
 181       storepass="alignmentisfun"
 182       keypass="alignmentisfun"
 183       keystore="keys/.keystore"
 184       alias="jalview"
 185       lazy="false"
 186       verbose="false"
 187       >
 188
 189                         <fileset dir="${packageDir}">
 190                                 <include name="*.jar"/>
 191                         </fileset>
 192                 </signjar>
 193                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
 194
 195                 <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 196                 <jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp"
 197       codebase="${WebStartLocation}">
 198                         <information>
 199                                 <title>Jalview</title>
 200                                 <vendor>The Barton Group</vendor>
 201                                 <homepage href="http://www.jalview.org"/>
 202                                 <description>Jalview Multiple Alignment Editor</description>
 203                                 <description kind="short">Jalview</description>
 204                                 <icon href="logo_big.gif"/>
 205                                 <offline_allowed/>
 206                                 <!--
 207         <association mime-type="application-x/ext-file" extensions="fa"/>
 208         <association mime-type="application-x/ext-file" extensions="fasta"/>
 209         <association mime-type="application-x/ext-file" extensions="fastq"/>
 210         <association mime-type="application-x/ext-file" extensions="blc"/>
 211         <association mime-type="application-x/ext-file" extensions="msf"/>
 212         <association mime-type="application-x/ext-file" extensions="pfam"/>
 213         <association mime-type="application-x/ext-file" extensions="aln"/>
 214         <association mime-type="application-x/ext-file" extensions="pir"/>
 215         -->
 216                         </information>
 217                         <resources>
 218                                 <j2se version="1.4+"/>
 219                                 <fileset dir="${packageDir}">
 220                                         <include name="jalview.jar"/>
 221                                 </fileset>
 222                                 <fileset dir="${packageDir}">
 223                                         <include name="*.jar"/>
 224                                         <exclude name="jalview.jar"/>
 225                                 </fileset>
 226                                 <property name="jalview.version" value="${JALVIEW_VERSION}"/>
 227                         </resources>
 228                         <application_desc main_class="jalview.bin.Jalview">
 229                         </application_desc>
 230                         <security>
 231                                 <all_permissions/>
 232                         </security>
 233                 </jnlp>
 234         </target>
 235         <target name="runenv" depends="init">
 236                 <path id="run.classpath">
 237                         <pathelement location="${outputDir}"/>
 238                         <fileset dir="${outputDir}">
 239                                 <include name="${libDir}/*.jar"/>
 240                         </fileset>
 241                 </path>
 242                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
 243
 244                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 245       </echo>
 246         </target>
 247
 248         <target name="buildextclients" depends="init">
 249                 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
 250       validargs="Y,y,n,N" defaultvalue="N"
 251       addproperty="doextbuild.response"/>
 252                 <condition property="dontextbuild">
 253                         <equals arg1="n" arg2="${doextbuild.response}"/>
 254                 </condition>
 255                 <condition property="dontextbuild">
 256                         <equals arg1="N" arg2="${doextbuild.response}"/>
 257                 </condition>
 258                 <fail if="dontextbuild">
 259         Build External Client Code process aborted by user. Jalview source is unchanged.
 260       </fail>
 261                 <!-- Currently, this doesn't happen automatically.
 262      1. Run WSDL2Java as below, which generates an ext.vamsas +
 263      vamsas.<datapackages> fileset.
 264      2. refactor ext.vamsas.SpecificserviceWS* to
 265      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 266      3. Update the jalview.ws.*WServices classes to reflect the
 267      interface type, and all locations of this wsdl type that Jalview
 268      might be using.
 269
 270 -->
 271                 <path id="axisbuild">
 272                         <path refid="build.classpath"/>
 273                 </path>
 274                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
 275                 <move todir="./bak">
 276                         <fileset dir="${sourceDir}" id="client">
 277                                 <include name="${wsdl.ClientNS}/*.*"/>
 278                         </fileset>
 279                 </move>
 280
 281                 <axis-wsdl2java
 282       output="${sourceDir}"
 283       verbose="true"
 284       url="${wsdl.MsaWS2}"
 285       serverside="false"
 286       deployscope="Request"
 287       debug="false"
 288       helpergen="true"
 289       all="true"
 290       >
 291                         <mappingSet>
 292                                 <mapping
 293         namespace="${wsdl.Namespace}"
 294         package="${wsdl.ClientNS}"
 295         />
 296                                 <mapping namespace="http://dataTypes.vamsas"
 297         package="${wsdl.ClientNS}"/>
 298                         </mappingSet>
 299                 </axis-wsdl2java>
 300         </target>
 301
 302         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 303                 <!-- make the package jar -->
 304                 <mkdir dir="${packageDir}"/>
 305
 306                 <jar destfile="${packageDir}/${outputJar}">
 307                         <manifest>
 308                                 <attribute name="Main-Class" value="jalview.bin.Jalview"/>
 309                         </manifest>
 310                         <fileset dir="${outputDir}/">
 311                                 <exclude name="cache*/**"/>
 312                                 <exclude name="*.jar" />
 313                                 <exclude name="*.jar.*" />
 314                                 <exclude name="**/*.jar" />
 315                                 <exclude name="**/*.jar.*" />
 316                         </fileset>
 317                 </jar>
 318
 319                 <copy toDir="${packageDir}" flatten="true">
 320                         <fileset dir="${outputDir}">
 321                                 <include name="*.jar"/>
 322                                 <include name="**/*.jar"/>
 323                         </fileset>
 324                 </copy>
 325         </target>
 326
 327
 328         <!-- jalopy code reformatter -->
 329         <target name="sourcescrub" depends="init,build">
 330                 <jalopy destdir="jsrc" classpathref="run.classpath"
 331       convention="jalview-jalopy.xml">
 332                         <fileset dir="${sourceDir}">
 333                                 <include name="*.java"/>
 334                                 <include name="**/*.java"/>
 335                                 <include name="**/**/*.java"/>
 336                         </fileset>
 337                 </jalopy>
 338         </target>
 339
 340
 341
 342   <!-- Compile, package and obfuscate Jalview Applet -->
 343   <target name="makeApplet" depends="obfuscate"/>
 344
 345   <target name="compileApplet" depends="init,clean">
 346     <mkdir dir="${outputDir}"/>
 347     <javac source="1.2"
 348     target="1.1"
 349     srcdir="${sourceDir}"
 350     destdir="${outputDir}"
 351     classpath="lib/${jmolJar}"
 352        includes="jalview/appletgui/**"
 353        excludes="ext/**,MCview/**,org/**,vamsas/**"
 354        />
 355   </target>
 356
 357   <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 358   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
 359   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
 360        <jar destfile="in.jar">
 361         <manifest>
 362             <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
 363         </manifest>
 364         <fileset dir="${outputDir}">
 365           <include name="com/**"/>
 366           <include name="MCview/**"/>
 367           <include name="jalview/**"/>
 368           <include name=".build_properties"/>
 369           <include name="images/idwidth.gif"/>
 370           <include name="images/link.gif"/>
 371         </fileset>
 372       </jar>
 373   </target>
 374
 375   <target name="obfuscate" depends="packageApplet">
 376     <path id="obfuscateDeps.path">
 377     <pathelement location="${java.home}/lib/rt.jar"/>
 378     <pathelement location="lib/${jmolJar}"/>
 379     </path>
 380     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 381     <proguard>
 382       <injar file="in.jar"/>
 383       <outjar file="jalviewApplet.jar"/>
 384       <libraryjar refid="obfuscateDeps.path"/>
 385       <keep access="public" type="class"
 386       name="jalview.bin.JalviewLite">
 387         <field access="public"/>
 388         <method access="public"/>
 389         <constructor access="public"/>
 390       </keep>
 391 <!--      -libraryjars "${obfuscateDeps}"
 392       -injars      in.jar
 393       -outjars     jalviewApplet.jar
 394       -keep public class jalview.bin.JalviewLite
 395        { public * ; }
 396        -->
 397     </proguard>
 398     <delete file="in.jar"/>
 399   </target>
 400
 401         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 402                 <taskdef name="castor-srcgen"
 403                                   classname="org.exolab.castor.tools.ant.taskdefs.CastorSourceGenTask"
 404                               classpathref="build.classpath" />
 405                 <delete>
 406                         <fileset dir="${sourceDir}/jalview/schemabinding/version2/">
 407                                 <filename name="*"/>
 408                         </fileset>
 409                 </delete>
 410                 <castor-srcgen file="${schemaDir}/vamsas.xsd"
 411                               todir="${sourceDir}"
 412                               package="jalview.schemabinding.version2"
 413                               warnings="true"
 414                                         nodesc="false"
 415                                                 properties="${schemaDir}/jalview.properties"
 416                 />
 417                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
 418                               todir="${sourceDir}"
 419                               package="jalview.schemabinding.version2"
 420                               warnings="true"
 421                                         nodesc="false"
 422                                                 properties="${schemaDir}/jalview.properties"
 423                 />
 424                 <castor-srcgen file="${schemaDir}/jalview.xsd"
 425                               todir="${sourceDir}"
 426                               package="jalview.schemabinding.version2"
 427                               warnings="true"
 428                                           nodesc="false"
 429                                                 properties="${schemaDir}/jalview.properties"
 430
 431         />
 432         </target>
 433 </project>