build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <project name="jalviewX" default="usage" basedir="."
  21  xmlns:if="ant:if"
  22     xmlns:unless="ant:unless">
  23   <target name="help" depends="usage" />
  24   <target name="usage" depends="init">
  25     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  26     <echo message="Targets include:" />
  27     <echo message="usage - default target, displays this message" />
  28     <echo message="buildindices - generates JavaHelpSearch from the help files" />
  29     <echo message="build - compiles all necessary files for Application" />
  30     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  31     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  32     <echo message="              this needs a keystore and key."/>
  33     <echo message="              Add -Dtimestamp to timestamp signed jars"/>
  34     <echo message="              -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
  35     <echo message="              See docs/building.html for more information." />
  36     <echo message="compileApplet - compiles all necessary files for Applet" />
  37     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  38     <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
  39     <echo message="      you can specify particular test groups as a list via -Dtestng-groups=" />
  40     <echo message="See docs/building.html and the comments in build file for other targets." />
  41     <echo message="note: compile and makeApplet optionally compile/obfuscate applet against a different Java version by specifying -Djava118.home=PathtoJDK/lib which is the lib directory in the JDK install that contains rt.jar " />
  42     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  43   </target>
  44
  45
  46   <!-- utils is a class path to additional utilities needed for
  47     building docs, jars and webstart stuff -->
  48   <!--
  49         Userdefined build property defaults
  50
  51         wsdl.server list (plus namespace mapping info ???)  - also want
  52                 ... to make this a dynamically generatable property
  53         WebStart Location
  54         Build location - provide a temporary root for speed
  55         jarsigner keystore and info
  56         Jakarta and axis classpath ?
  57         Default argument for starting Jalview (if it exists).
  58
  59 -->
  60
  61   <target name="init">
  62     <path id="axis.classpath">
  63       <!-->
  64       <fileset dir="/usr/local/axis/lib">
  65         <include name="**/*.jar" />
  66       </fileset>
  67       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  68         <include name="**/*.jar"/>
  69         <include name="*.jar"/>
  70       </fileset> -->
  71       </path>
  72
  73     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  74     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  75
  76     <property name="INSTALLATION" value="Source" />
  77
  78     <!-- 2.4 (VAMSAS)" -->
  79     <!-- Include debugging information in javac true or false -->
  80     <property name="javac.debug" value="true" />
  81
  82     <!-- JarSigner Key Store for Webstart Distribution -->
  83     <property name="jalview.keystore" value="./keys/.keystore" />
  84     <!-- Keystore Password -->
  85     <property name="jalview.keystore.pass" value="alignmentisfun" />
  86     <!-- Key Name -->
  87     <property name="jalview.key" value="jalview" />
  88     <!-- Key Password -->
  89     <property name="jalview.key.pass" value="alignmentisfun" />
  90     <!-- time stamp server URL -->
  91     <property name="jalview.tsaurl" value="" />
  92     <!-- locally valid proxy for signing with external time server -->
  93     <property name="proxyPort" value="80"/>
  94     <property name="proxyHost" value="sqid"/>
  95     <!-- key sign/digest algorithms -->
  96     <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
  97     <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
  98
  99     <!-- default TestNG groups to run -->
 100     <property name="testng-groups" value="Functional" />
 101     <!-- Java 9 JVM args -->
 102     <condition property="java9">
 103       <equals arg1="${ant.java.version}" arg2="9"/>
 104     </condition>
 105
 106     <!-- Don't change anything below here unless you know what you are doing! -->
 107     <!-- Url path for WebStart in JNLP file -->
 108     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
 109     <!-- Webstart Image - looked for in resources/images -->
 110     <property name="WebStartImage" value="JalviewLogo_big.png" />
 111     <!-- J2SE version needed for webstart launch -->
 112     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
 113     <property name="j2sev" value="1.7+" />
 114     <!-- Java Compilation settings - source and target javac version -->
 115     <property name="javac.source" value="1.8" />
 116     <property name="javac.target" value="1.8" />
 117
 118     <!-- Permissions for running Java applets and applications. -->
 119     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 120     <property name="application.codebase" value="*.jalview.org" />
 121     <!-- and allowing the applet to be deployed from any URL -->
 122     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
 123     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 124     <property name="applet.caller-codebase" value="${applet.codebase}" />
 125
 126     <!-- build directory configuration -->
 127     <property name="libDir" value="lib" />
 128     <property name="resourceDir" value="resources" />
 129     <property name="helpDir" value="help" />
 130     <property name="docDir" value="doc" />
 131     <property name="sourceDir" value="src" />
 132     <property name="schemaDir" value="schemas" />
 133     <property name="outputDir" value="classes" />
 134     <property name="packageDir" value="dist" />
 135     <property name="outputJar" value="jalview.jar" />
 136     <!-- Jalview Applet JMol Jar Dependency -->
 137     <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
 138     <property name="varnaJar" value="VARNAv3-93.jar" />
 139     <property name="jsoup" value="jsoup-1.8.1.jar" />
 140     <property name="jsonSimple" value="json_simple-1.1.jar" />
 141     <property name="javaJson" value="java-json.jar" />
 142     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 143     <property name="reportDir" value="test-reports" />
 144     <property name="testDir" value="test" />
 145     <property name="testOutputDir" value="tests" />
 146     <!-- switch to indicate if we should obfuscate jalviewLite -->
 147     <!-- <property name="donotobfuscate" value="true"/> -->
 148     <!-- switch to exclude associations from generated jnlp files -->
 149     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 150
 151     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 152     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 153     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 154     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 155     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 156     <property name="WSInterf" value="MsaWS" />
 157     <property name="wsdl.Namespace" value="vamsas" />
 158     <property name="wsdl.ClientNS" value="ext.vamsas" />
 159     <!-- the class path for building the application -->
 160     <path id="build.classpath">
 161       <fileset dir="utils">
 162         <include name="*.jar" />
 163         <include name="**/*.jar" />
 164       </fileset>
 165       <fileset dir="${libDir}">
 166         <include name="*.jar" />
 167         <include name="**/*.jar" />
 168       </fileset>
 169       <fileset dir="${java.home}/lib">
 170         <include name="plugin.jar" />
 171       </fileset>
 172       <fileset dir="appletlib">
 173         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 174                                 -->
 175         <include name="${jmolJar}" />
 176         <include name="${varnaJar}" />
 177       </fileset>
 178     </path>
 179     <path id="test.classpath">
 180       <pathelement path="${outputDir}" />
 181       <path refid="build.classpath" />
 182     </path>
 183     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 184     <!-- The Location of the java 1.1.8 jdk -->
 185     <property name="java118.home" value="${java.home}" />
 186     <!-- jre for 1.4 version -->
 187     <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
 188
 189     <!-- the classpath for building the 1.1 applet -->
 190     <path id="jalviewlite.deps">
 191       <fileset dir="${java118.home}">
 192         <include name="lib/rt.jar" />
 193       </fileset>
 194       <fileset dir="${java.home}/lib">
 195         <include name="plugin.jar" />
 196       </fileset>
 197       <pathelement location="appletlib/${jmolJar}" />
 198       <pathelement location="lib/${varnaJar}" />
 199       <pathelement location="appletlib/${jsoup}" />
 200       <pathelement location="appletlib/${jsonSimple}" />
 201       <pathelement location="appletlib/${javaJson}" />
 202
 203     </path>
 204     <!-- default location for outputting javadoc -->
 205     <property name="javadocDir" value="${packageDir}/javadoc" />
 206   </target>
 207
 208
 209   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 210   <target name="buildPropertiesFile" depends="init">
 211     <tstamp prefix="build">
 212       <format property="date" pattern="dd MMMM yyyy" />
 213     </tstamp>
 214     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 215       <arg value="rev-parse" />
 216       <arg value="--short" />
 217       <arg value="HEAD" />
 218     </exec>
 219     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 220       <arg value="rev-parse" />
 221       <arg value="--abbrev-ref" />
 222       <arg value="HEAD" />
 223     </exec>
 224     <properties file="${outputDir}/.build_properties">
 225       <header>
 226           ---Jalview Build Details---
 227         </header>
 228       <property name="VERSION" value="${JALVIEW_VERSION}" />
 229       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 230       <property name="BUILD_DATE" value="${build.date}" />
 231     </properties>
 232   </target>
 233
 234
 235   <target name="clean" depends="init">
 236     <!-- not efficient yet. -->
 237     <delete dir="${outputDir}" includes="*,**/*" />
 238   </target>
 239
 240   <target name="distclean" depends="init, clean">
 241
 242     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 243     <delete>
 244       <fileset dir=".">
 245         <include name="${outputJar}" />
 246         <include name="#*#" />
 247         <include name="#*.*#" />
 248         <include name="**/#*#" />
 249         <include name="**/#*.*#" />
 250         <include name="*~" />
 251         <include name="*.*~" />
 252         <include name="**/*~" />
 253         <include name="**/*.*~" />
 254       </fileset>
 255     </delete>
 256   </target>
 257
 258   <target name="prepare" depends="init">
 259     <mkdir dir="${outputDir}" />
 260     <copy todir="${outputDir}">
 261       <fileset dir=".">
 262         <include name="${docDir}/**/*.*" />
 263         <include name="${helpDir}/**/*.*" />
 264         <include name="${libDir}/*.jar" />
 265       </fileset>
 266       <fileset dir="${resourceDir}">
 267         <include name="**/*.*" />
 268       </fileset>
 269     </copy>
 270   </target>
 271
 272   <target name="build" depends="prepare">
 273     <!-- not efficient yet. -->
 274     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 275       <exclude name="jalview/*applet*" />
 276       <exclude name="jalview/appletgui/**" />
 277       <exclude name="com/stevesoft/**" />
 278     </javac>
 279   </target>
 280
 281
 282   <target name="testclean" depends="init">
 283     <delete dir="${testOutputDir}" includes="*,**/*" />
 284   </target>
 285
 286   <target name="prepareTests" depends="init,testclean">
 287     <mkdir dir="${testOutputDir}" />
 288   </target>
 289
 290   <target name="buildTests" depends="build,buildindices,prepareTests">
 291     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 292     </javac>
 293   </target>
 294
 295   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 296
 297   <target name="testng" depends="buildTests">
 298     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
 299       verbose="2">
 300       <classpath>
 301         <pathelement location="${testOutputDir}" />
 302         <path refid="test.classpath" />
 303       </classpath>
 304       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
 305       <jvmarg value="--illegal-access=warn" if:set="java9"/>
 306       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 307     </testng>
 308   </target>
 309
 310   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 311     <replace value="${JALVIEW_VERSION}">
 312       <replacetoken>
 313         <![CDATA[$$Version-Rel$$]]>
 314       </replacetoken>
 315       <fileset dir="${outputDir}/${helpDir}">
 316         <include name="help.jhm" />
 317       </fileset>
 318     </replace>
 319
 320     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 321       <arg line="html" />
 322     </java>
 323   </target>
 324
 325   <target name="preparejnlp" depends="makedist">
 326     <copy todir="${packageDir}">
 327       <fileset dir="${resourceDir}/images">
 328         <include name="${WebStartImage}" />
 329       </fileset>
 330     </copy>
 331
 332     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 333
 334     <!-- create a dummy jar which will eventually contain the jnlp template -->
 335     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 336       <fileset dir="${packageDir}">
 337         <include name="jalview.jar" />
 338       </fileset>
 339     </jar>
 340
 341     <mkdir dir="${packageDir}/JNLP-INF" />
 342     <antcall target="writejnlpf">
 343       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 344       <param name="inih" value="*" />
 345       <param name="maxh" value="*" />
 346     </antcall>
 347
 348     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 349       <fileset dir="${packageDir}">
 350         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 351       </fileset>
 352     </jar>
 353
 354     <antcall target="writejnlpf">
 355       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 356       <param name="inih" value="10M" />
 357       <param name="maxh" value="256M" />
 358     </antcall>
 359
 360     <antcall target="writejnlpf">
 361       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 362       <param name="inih" value="128M" />
 363       <param name="maxh" value="512M" />
 364     </antcall>
 365
 366     <antcall target="writejnlpf">
 367       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 368       <param name="inih" value="256M" />
 369       <param name="maxh" value="1024M" />
 370     </antcall>
 371
 372     <!-- finally, need to postprocess to add in associations at end of 'information' element
 373
 374                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 375
 376                 </xslt>
 377
 378
 379                         -->
 380     <!--
 381                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 382         <association mime-type="application-x/ext-file" extensions="fasta"/>
 383         <association mime-type="application-x/ext-file" extensions="mfa"/>
 384         <association mime-type="application-x/ext-file" extensions="fastq"/>
 385         <association mime-type="application-x/ext-file" extensions="blc"/>
 386         <association mime-type="application-x/ext-file" extensions="msf"/>
 387         <association mime-type="application-x/ext-file" extensions="pfam"/>
 388         <association mime-type="application-x/ext-file" extensions="aln"/>
 389         <association mime-type="application-x/ext-file" extensions="pir"/>
 390         <association mime-type="application-x/ext-file" extensions="amsa"/>
 391         <association mime-type="application-x/ext-file" extensions="stk"/>
 392         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 393   </target>
 394
 395   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
 396     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
 397       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 398       <fileset dir="${packageDir}">
 399         <include name="*.jar" />
 400       </fileset>
 401     </signjar>
 402   </target>
 403   <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
 404     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
 405       <fileset dir="${packageDir}">
 406         <include name="*.jar" />
 407       </fileset>
 408     </signjar>
 409   </target>
 410
 411   <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
 412     <!-- and sign the jars -->
 413     <!-- the default keystore details might need to be edited here -->
 414   </target>
 415
 416   <target name="runenv" depends="init">
 417     <path id="run.classpath">
 418       <pathelement location="${outputDir}" />
 419       <fileset dir="${outputDir}">
 420         <include name="${libDir}/*.jar" />
 421       </fileset>
 422     </path>
 423     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 424
 425     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 426       </echo>
 427   </target>
 428
 429   <target name="-generatejnlpf">
 430     <presetdef name="jnlpf">
 431       <jnlp codebase="${WebStartLocation}">
 432         <information>
 433           <title>Jalview</title>
 434           <vendor>The Barton Group</vendor>
 435           <homepage href="http://www.jalview.org" />
 436           <description>Jalview Multiple Alignment Editor</description>
 437           <description kind="short">Jalview</description>
 438           <icon href="${WebStartImage}" />
 439           <offline_allowed />
 440         </information>
 441         <resources>
 442           <j2se version="1.8+" />
 443           <jar main="true" href="jalview.jar"/>
 444           <fileset dir="${packageDir}">
 445             <exclude name="jalview.jar" />
 446             <include name="*.jar" />
 447             <include name="*_*.jar" />
 448             <exclude name="*quaqua*.jar" />
 449           </fileset>
 450           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 451         </resources>
 452         <resources os="Mac OS X">
 453           <fileset dir="${packageDir}">
 454             <include name="quaqua-filechooser-only-8.0.jar"/>
 455             <include name="*quaqua64*.jnilib.jar" />
 456           </fileset>
 457         </resources>
 458
 459         <application_desc main_class="jalview.bin.Jalview">
 460         </application_desc>
 461         <security>
 462           <all_permissions />
 463         </security>
 464       </jnlp>
 465     </presetdef>
 466
 467     <jnlpf toFile="${jnlpFile}" />
 468     <!-- add the add-modules j2se attribute for java 9 -->
 469     <replace file="${jnlpFile}" value="j2se version=&quot;1.8+&quot; initial-heap-size=&quot;${inih}&quot; max-heap-size=&quot;${maxh}&quot; java-vm-args=&quot;--add-modules=java.se.ee --illegal-access=warn&quot;">
 470       <replacetoken>j2se version="1.8+"</replacetoken>
 471     </replace>
 472   </target>
 473
 474   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 475     <echo message="Not adding JNLP File Associations" />
 476   </target>
 477
 478   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 479     <replace file="${jnlpFile}">
 480       <replacetoken>
 481         <![CDATA[</information>]]></replacetoken>
 482       <replacevalue>
 483         <![CDATA[
 484           <association mime-type="application-x/ext-file" extensions="fa" />
 485         <association mime-type="application-x/ext-file" extensions="fasta" />
 486         <association mime-type="application-x/ext-file" extensions="mfa" />
 487         <association mime-type="application-x/ext-file" extensions="fastq" />
 488         <association mime-type="application-x/ext-file" extensions="blc" />
 489         <association mime-type="application-x/ext-file" extensions="msf" />
 490         <association mime-type="application-x/ext-file" extensions="pfam" />
 491         <association mime-type="application-x/ext-file" extensions="aln"/>
 492         <association mime-type="application-x/ext-file" extensions="pir"/>
 493         <association mime-type="application-x/ext-file" extensions="amsa"/>
 494         <association mime-type="application-x/ext-file" extensions="stk"/>
 495         <association mime-type="application-x/ext-file" extensions="jvp"/>
 496       </information>]]></replacevalue>
 497   </replace>
 498   <echo message="Added file associations to JNLP file" />
 499 </target>
 500 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 501 </target>
 502
 503 <target name="buildextclients" depends="init">
 504   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 505   <condition property="dontextbuild">
 506     <equals arg1="n" arg2="${doextbuild.response}" />
 507   </condition>
 508   <condition property="dontextbuild">
 509     <equals arg1="N" arg2="${doextbuild.response}" />
 510   </condition>
 511   <fail if="dontextbuild">
 512         Build External Client Code process aborted by user. Jalview source is unchanged.
 513       </fail>
 514   <!-- Currently, this doesn't happen automatically.
 515      1. Run WSDL2Java as below, which generates an ext.vamsas +
 516      vamsas.<datapackages> fileset.
 517      2. refactor ext.vamsas.SpecificserviceWS* to
 518      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 519      3. Update the jalview.ws.*WServices classes to reflect the
 520      interface type, and all locations of this wsdl type that Jalview
 521      might be using.
 522
 523 -->
 524   <path id="axisbuild">
 525     <path refid="build.classpath" />
 526   </path>
 527   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 528   <move todir="./bak">
 529     <fileset dir="${sourceDir}" id="client">
 530       <include name="${wsdl.ClientNS}/*.*" />
 531     </fileset>
 532   </move>
 533
 534   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 535     <mappingSet>
 536       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 537       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 538     </mappingSet>
 539   </axis-wsdl2java>
 540 </target>
 541
 542 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
 543   <!-- make the package jar if not already existing -->
 544   <mkdir dir="${packageDir}" />
 545   <!-- clean dir if it already existed -->
 546   <delete>
 547     <fileset dir="${packageDir}">
 548       <include name="*.jar" />
 549     </fileset>
 550   </delete>
 551   <jar destfile="${packageDir}/${outputJar}" index="true">
 552     <manifest>
 553       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 554       <attribute name="Permissions" value="all-permissions" />
 555       <attribute name="Application-Name" value="Jalview Desktop" />
 556       <attribute name="Codebase" value="${application.codebase}" />
 557     </manifest>
 558     <fileset dir="${outputDir}/">
 559       <exclude name="cache*/**" />
 560       <exclude name="*.jar" />
 561       <exclude name="*.jar.*" />
 562       <exclude name="**/*.jar" />
 563       <exclude name="**/*.jar.*" />
 564     </fileset>
 565   </jar>
 566
 567   <copy toDir="${packageDir}" flatten="true">
 568     <fileset dir="${outputDir}">
 569       <include name="*.jar" />
 570       <include name="**/*.jar" />
 571     </fileset>
 572   </copy>
 573 </target>
 574
 575
 576 <!-- jalopy code reformatter -->
 577 <target name="sourcescrub" depends="init,build">
 578   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 579     <fileset dir="${sourceDir}">
 580       <include name="*.java" />
 581       <include name="**/*.java" />
 582       <include name="**/**/*.java" />
 583     </fileset>
 584   </jalopy>
 585 </target>
 586
 587
 588
 589 <!-- Compile, package and obfuscate Jalview Applet -->
 590 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 591
 592 <target name="compileApplet" depends="init,clean">
 593   <mkdir dir="${outputDir}" />
 594   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 595 </target>
 596
 597 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 598   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 599   <copy todir="${outputDir}/lang">
 600     <fileset dir="${resourceDir}/lang">
 601       <include name="**.*" />
 602     </fileset>
 603   </copy>
 604   <jar destfile="in.jar" index="true">
 605     <manifest>
 606       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 607       <attribute name="Application-Name" value="JalviewLite" />
 608       <attribute name="Codebase" value="${applet.codebase}" />
 609     </manifest>
 610     <fileset dir="${outputDir}">
 611       <include name="com/**" />
 612       <include name="MCview/**" />
 613       <include name="jalview/**" />
 614       <include name=".build_properties" />
 615       <include name="images/link.gif" />
 616       <include name="lang/**" />
 617     </fileset>
 618   </jar>
 619 </target>
 620 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 621 </target>
 622 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 623   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 624   <delete file="in.jar" />
 625 </target>
 626 <target name="-obfuscatereally" unless="donotobfuscate">
 627
 628   <path id="obfuscateDeps.path">
 629     <pathelement location="${applet.jre.tools}" />
 630     <pathelement location="appletlib/${jmolJar}" />
 631     <pathelement location="lib/${varnaJar}" />
 632     <pathelement location="appletlib/${jsoup}" />
 633     <pathelement location="appletlib/${jsonSimple}" />
 634     <pathelement location="appletlib/${javaJson}" />
 635     <fileset dir="${java.home}/lib">
 636       <include name="plugin.jar" />
 637     </fileset>
 638   </path>
 639   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
 640
 641   <proguard verbose="true" >
 642     <injar file="in.jar" />
 643     <outjar file="${jalviewLiteJar}" />
 644     <libraryjar refid="obfuscateDeps.path" />
 645     <dontwarn />
 646     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 647       <field access="public" />
 648       <method access="public" />
 649       <constructor access="public" />
 650     </keep>
 651     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 652       <field access="public" />
 653       <method access="public" />
 654       <constructor access="public" />
 655     </keep>
 656
 657     <keep name="jalview.json.binding**">
 658       <constructor/>
 659       <method name="*"/>
 660     </keep>
 661
 662     <keep access="public" type="class" name="MCview.PDBfile">
 663       <field access="public" />
 664       <method access="public" />
 665       <constructor access="public" />
 666     </keep>
 667
 668     <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
 669       <field access="public" />
 670       <method access="public" />
 671       <constructor access="public" />
 672     </keep>
 673
 674     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
 675       <field access="public" />
 676       <method access="public" />
 677       <constructor access="public" />
 678     </keep>
 679
 680
 681     <!--      -libraryjars "${obfuscateDeps}"
 682       -injars      in.jar
 683       -outjars     jalviewApplet.jar
 684       -keep public class jalview.bin.JalviewLite
 685        { public * ; } -->
 686   </proguard>
 687   <delete file="in.jar" />
 688 </target>
 689
 690 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 691   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 692   <delete>
 693     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 694       <include name="*.java" />
 695       <include name="descriptors/*.java" />
 696     </fileset>
 697   </delete>
 698   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 699   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 700   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 701   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 702   <!--
 703                 now build the jalview.binding package with the old schema set
 704                 -->
 705   <delete>
 706     <fileset dir="${sourceDir}/jalview/binding/">
 707       <include name="**" />
 708     </fileset>
 709   </delete>
 710   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 711   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 712   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 713 </target>
 714 <target name="sourcedist" description="create jalview source distribution" depends="init">
 715   <delete file="${source.dist.name}" />
 716   <!-- temporary copy of source to update timestamps -->
 717   <copy todir="_sourcedist">
 718     <fileset dir=".">
 719       <exclude name=".*" />
 720       <exclude name="**/.*" />
 721       <exclude name="*.class" />
 722       <exclude name="**/*.class" />
 723       <include name="LICENSE" />
 724       <include name="README" />
 725       <include name="build.xml" />
 726       <include name="jalview-jalopy.xml" />
 727       <include name="JalviewApplet.jpx" />
 728       <include name="JalviewX.jpx" />
 729       <include name="nbbuild.xml" />
 730       <include name="nbproject/genfiles.properties" />
 731       <include name="nbproject/project.properties" />
 732       <include name="nbproject/project.xml" />
 733       <include name="${sourceDir}/*.java" />
 734       <include name="${sourceDir}/**/*.java" />
 735       <include name="${sourceDir}/**/*.cdr" />
 736       <include name="${libDir}/**/*" />
 737       <include name="${resourceDir}/**/*" />
 738       <include name="${helpDir}/**/*" />
 739       <include name="appletlib/${jmolJar}" />
 740       <include name="appletlib/${jsonSimple}" />
 741       <include name="appletlib/${javaJson}" />
 742       <exclude name="**/*locales" />
 743       <exclude name="*locales/**" />
 744       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 745       <exclude name="utils/InstallAnywhere/**Build*/**" />
 746       <exclude name="utils/InstallAnywhere/**Build*/**" />
 747       <exclude name="utils/InstallAnywhere/.build*.*/**" />
 748       <exclude name="utils/InstallAnywhere/**locale*" />
 749       <exclude name="utils/InstallAnywhere/**locale*/**" />
 750       <exclude name="utils/InstallAnywhere/**locale*/**" />
 751       <include name="${schemaDir}/**/*" />
 752       <include name="utils/**/*" />
 753       <include name="${docDir}/**/*" />
 754       <include name="examples/**/*" />
 755     </fileset>
 756   </copy>
 757
 758   <tstamp prefix="build">
 759     <format property="year" pattern="yyyy" />
 760   </tstamp>
 761   <!-- each replacetoken CDATA body must be on one line -
 762        otherwise the pattern doesn't match -->
 763   <replace value="${JALVIEW_VERSION}">
 764     <replacetoken>
 765       <![CDATA[$$Version-Rel$$]]>
 766     </replacetoken>
 767     <fileset dir="_sourcedist">
 768       <include name="**/*" />
 769     </fileset>
 770   </replace>
 771   <replace dir="_sourcedist" value="${build.year}">
 772     <replacetoken>
 773       <![CDATA[$$Year-Rel$$]]>
 774     </replacetoken>
 775     <fileset dir="_sourcedist">
 776       <include name="**/*" />
 777     </fileset>
 778   </replace>
 779
 780   <tar destfile="${source.dist.name}" compression="gzip">
 781     <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
 782     </tarfileset>
 783   </tar>
 784
 785   <delete dir="_sourcedist" />
 786 </target>
 787 <target name="prepubapplet_1" depends="makeApplet">
 788   <copy todir="${packageDir}/examples">
 789     <fileset dir="examples">
 790       <include name="**/*" />
 791       <include name="javascript/*" />
 792       <include name="jmol/*" />
 793     </fileset>
 794     <fileset dir=".">
 795       <include name="${jalviewLiteJar}" />
 796     </fileset>
 797     <fileset dir="appletlib">
 798       <include name="**/*" />
 799     </fileset>
 800   </copy>
 801   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 802   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 803   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 804   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 805     <manifest>
 806       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 807       <!--          <attribute name="Permissions" value="sandbox" /> -->
 808       <!--<attribute name="Trusted-Lib" value="true" /> -->
 809       <attribute name="Codebase" value="${applet.codebase}" />
 810       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 811     </manifest>
 812   </jar>
 813
 814   <presetdef name="ap_applet.jar">
 815     <!-- build a signed applet with 'all-permissions' -
 816                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 817                           JalviewLite+JmolApplet linked sequence/structure fails
 818                           Mixed code warnings are raised
 819                           -->
 820     <jar update="true" index="true">
 821       <manifest>
 822         <attribute name="Application-Name" value="JalviewLite" />
 823         <attribute name="Permissions" value="all-permissions" />
 824         <attribute name="Codebase" value="${applet.codebase}" />
 825         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 826         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 827       </manifest>
 828     </jar>
 829   </presetdef>
 830   <presetdef name="applet.jar">
 831     <!-- build signed applet with sandbox permissions -
 832                           Needs 'param name="permissions' value="sandbox"' in applet tag
 833                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 834                         -->
 835
 836     <jar update="true" index="true">
 837       <manifest>
 838         <attribute name="Application-Name" value="JalviewLite" />
 839         <attribute name="Permissions" value="sandbox" />
 840         <attribute name="Codebase" value="${applet.codebase}" />
 841         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 842         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 843       </manifest>
 844     </jar>
 845   </presetdef>
 846   <presetdef name="tl_applet.jar">
 847     <!-- build signed applet with trusted library/trusted permissions -
 848                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 849                                j1.7_45:
 850                                No mixed code warnings raised
 851                                Jmol/JalviewLite sequence/structure example doesn't link structures
 852                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 853
 854                               -->
 855
 856     <jar update="true" index="true">
 857       <manifest>
 858         <attribute name="Application-Name" value="JalviewLite" />
 859         <attribute name="Permissions" value="all-permissions" />
 860         <attribute name="Codebase" value="${applet.codebase}" />
 861         <attribute name="Trusted-Only" value="true" />
 862         <attribute name="Trusted-Library" value="true" />
 863       </manifest>
 864     </jar>
 865   </presetdef>
 866   <presetdef name="to_applet.jar">
 867     <!-- not fully test variant (yet) -->
 868     <jar update="true" index="true">
 869       <manifest>
 870         <attribute name="Application-Name" value="JalviewLite" />
 871         <attribute name="Permissions" value="all-permissions" />
 872         <attribute name="Codebase" value="${applet.codebase}" />
 873         <attribute name="Trusted-Only" value="true" />
 874       </manifest>
 875     </jar>
 876   </presetdef>
 877   <!-- create differently privileged artefacts -->
 878   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 879   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 880   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 881   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 882   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 883   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 884   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 885   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 886   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 887   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 888   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 889   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 890   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 891   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 892   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 893   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 894   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 895   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 896   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 897   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 898   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 899   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 900   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 901   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 902   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 903   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 904   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 905   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 906   <!-- finally, create manifest for original jars -->
 907   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 908   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 909   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 910   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 911
 912   <!-- todo - write examples/downloads for alternate versions of the applet
 913     probably don't need to do this now since we don't have alternate versions anymore !-->
 914 </target>
 915 <target name="-signapplet" depends="prepubapplet_1">
 916   <fileset id="signappletjarset" dir="${packageDir}/examples">
 917     <exclude name="u_*.jar" />
 918     <include name="${jalviewLiteJar}" />
 919     <include name="${jmolJar}" />
 920     <include name="${javaJson}" />
 921     <include name="${jsonSimple}" />
 922     <include name="to_${jalviewLiteJar}" />
 923     <include name="to_${jmolJar}" />
 924     <include name="to_${javaJson}" />
 925     <include name="to_${jsonSimple}" />
 926     <include name="tl_${jalviewLiteJar}" />
 927     <include name="tl_${jmolJar}" />
 928     <include name="tl_${javaJson}" />
 929     <include name="tl_${jsonSimple}" />
 930     <include name="ap_${jalviewLiteJar}" />
 931     <include name="ap_${jmolJar}" />
 932     <include name="ap_${javaJson}" />
 933     <include name="ap_${jsonSimple}" />
 934   </fileset>
 935 </target>
 936 <target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
 937   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 938     <fileset refid="signappletjarset" />
 939   </signjar>
 940 </target>
 941
 942 <target name="-signapplettsa" if="timestamp" depends="-signapplet">
 943   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 944     <fileset refid="signappletjarset" />
 945   </signjar>
 946 </target>
 947
 948 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
 949
 950 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 951
 952   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 953   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 954   <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 955   <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 956   <!-- finally, replace any launchApp servlet tags with a version specification -->
 957   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 958     <replacetoken>
 959       <![CDATA[http://www.jalview.org/services/launchApp"]]>
 960     </replacetoken>
 961     <fileset dir="${packageDir}/examples">
 962       <include name="**/*.html" />
 963     </fileset>
 964   </replace>
 965   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 966     <replacetoken>
 967       <![CDATA[http://www.jalview.org/services/launchApp']]>
 968     </replacetoken>
 969     <fileset dir="${packageDir}/examples">
 970       <include name="**/*.html" />
 971     </fileset>
 972   </replace>
 973
 974 </target>
 975 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 976   <javadoc destdir="${javadocDir}">
 977     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 978     </packageset>
 979   </javadoc>
 980 </target>
 981 <target name="linkcheck" depends="init,prepare">
 982   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
 983   <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
 984     <arg file="${helpDir}"/>
 985     <arg value="-nointernet" />
 986   </java>
 987 </target>
 988
 989 <target name="eclipse-install" depends="init,prepare">
 990
 991   <property name="eclipseTempFile" value="eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
 992   <property name="eclipseInstallURL" value="http://mirror.csclub.uwaterloo.ca/eclipse/technology/epp/downloads/release/oxygen/R/eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
 993   <property name="java2scriptURL" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.core/dist/dropins/net.sf.j2s.core.jar?raw=true"/>
 994
 995   <get url="${eclipseInstallURL}" dest="${eclipseTempFile}"/>
 996   <untar compression="gzip" src="${eclipseTempFile}" dest="${eclipse-inst}"/>
 997
 998   <!-- not needed since we ship transpiler with source
 999     <get url="${java2scriptURL}" dest="eclipse-inst/dropins/net.sf.j2s.core.jar" /> -->
1000
1001 </target>
1002 <target name="build-site" depends="init,prepare">
1003   <property name="swingjsdir" value="swingjs"/>
1004   <property name="eclipse-inst" value="/home/bamboo/buildtools/eclipse/eclipse-js"/>
1005   <property name="eclipse-exec" value="${eclipse-inst}/eclipse"/>
1006   <property name="site" value="site"/>
1007   <!-- where the eclipse js workspace has been initialised -->
1008   <property name="eclipse-work" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace"/>
1009   <!-- git repository linked to project in workspace -->
1010   <property name="eclipse-workrepo" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace/jalview-js"/>
1011
1012   <!-- update transpiler -->
1013   <copy file="${swingjsdir}/net.sf.j2s.core.jar" todir="${eclipse-inst}/dropins" overwrite="true" failonerror="true"/>
1014   <!-- update the git repo linked to the eclipse workspace -->
1015   <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="true">
1016     <arg value="rev-parse" />
1017     <arg value="--short" />
1018     <arg value="HEAD" />
1019   </exec>
1020   <!-- update and checkout the same commit in the workspace project -->
1021   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1022   <arg value="pull" />
1023   </exec>
1024   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1025   <arg value="checkout" />
1026   <arg value="${git.commit}" />
1027   </exec>
1028   <!-- custom classpath for .js builds -->
1029   <copy file=".classpath.js" tofile="${eclipse-workrepo}/.classpath" overwrite="true"/>
1030
1031   <!-- execute the eclipse build - the build may fail but valid javascript may still be produced, so we ignore return codes -->
1032   <exec executable="${eclipse-exec}" failonerror="no">
1033     <arg value="-nosplash"/>
1034     <arg value="--launcher.suppressErrors"/>
1035     <arg value="-application"/>
1036     <arg value="org.eclipse.jdt.apt.core.aptBuild"/>
1037     <arg value="-data"/>
1038     <arg value="${eclipse-work}"/>
1039   </exec>
1040
1041   <!-- TODO: run jslint and something else here to check we have a complete set of .js files for java -->
1042   <!-- possibly compare timestamps between .js files and their mate in source - any newer or not present triggers a new build -->
1043   <!-- <mkdir dir="${packageDir}/${site}" /> -->
1044   <!--   <property name="swingjs.zipurl" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.java.core/dist/SwingJS-site.zip?raw=true" /> -->
1045
1046   <!-- and reset the .classpath -->
1047   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1048       <arg value="checkout" />
1049       <arg value="${git.commit}"/>
1050     <arg value="--"/>
1051     <arg value=".classpath" />
1052       </exec>
1053
1054   <!-- finally copy artefacts from eclipse project checkout to the build site -->
1055   <copy todir="${site}">
1056     <fileset dir="${eclipse-workrepo}/site"/>
1057   </copy>
1058
1059   <property name="swingjs.zip" value="${swingjsdir}/SwingJS-site.zip" />
1060   <unzip src="${swingjs.zip}" dest="${site}/" overwrite="true"/>
1061   <copy todir="${site}/swingjs/j2s/">
1062     <fileset dir="${resourceDir}">
1063         <include name="**"/>
1064         </fileset>
1065   </copy>
1066
1067   <!-- copy test files into place in site -->
1068   <copy todir="${site}/examples">
1069   <fileset dir="examples">
1070   <include name="*.*"/>
1071     </fileset>
1072   </copy>
1073   <!-- closure compile -->
1074   <!-- tarball -->
1075   <tar compression="gzip" destfile="site.tar.gz">
1076     <tarfileset dir="site"/>
1077   </tar>
1078 </target>
1079 </project>