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