X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=8d2cd7d9f798929ee86815298475df27aebfe16c;hb=refs%2Fheads%2Ftask%2FJAL-3210_ben_testing_jalviewJS_building;hp=ce56b69f4f06a342958de8590298bf14b1da1937;hpb=77946fe2c6e1faa3f1ca2d1eae6e0e96b5d4f902;p=jalview.git

diff --git a/build.xml b/build.xml
index ce56b69..8d2cd7d 100755
--- a/build.xml
+++ b/build.xml
@@ -106,15 +106,6 @@
     <condition property="java9">
       <equals arg1="${ant.java.version}" arg2="9"/>
     </condition>
-    <!-- Java 10 JVM args -->
-    <condition property="java10">
-      <equals arg1="${ant.java.version}" arg2="10"/>
-    </condition>
-    <!-- Java 11 JVM args -->
-    <condition property="java11">
-      <equals arg1="${ant.java.version}" arg2="11"/>
-    </condition>
-    <echo message="ant.java.version is ${ant.java.version}"/>
 
     <!-- Don't change anything below here unless you know what you are doing! -->
     <!-- Url path for WebStart in JNLP file -->
@@ -125,12 +116,8 @@
     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
     <property name="j2sev" value="1.7+" />
     <!-- Java Compilation settings - source and target javac version -->
-    <property name="javac.source" value="11" if:set="java11" />
-    <property name="javac.target" value="11" if:set="java11" />
-    <property name="javac.source" value="1.8" unless:set="java11" />
-    <property name="javac.target" value="1.8" unless:set="java11" />
-    <echo message="javac.source is ${javac.source}"/>
-    <echo message="javac.target is ${javac.target}"/>
+    <property name="javac.source" value="1.8" />
+    <property name="javac.target" value="1.8" />
 
     <!-- Permissions for running Java applets and applications. -->
     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
@@ -141,8 +128,7 @@
     <property name="applet.caller-codebase" value="${applet.codebase}" />
 
     <!-- build directory configuration -->
-    <property name="libDir" value="lib" />
-    <property name="j11libDir" value="j11lib" />
+    <property name="libDir" value="j11lib" />
     <property name="resourceDir" value="resources" />
     <property name="helpDir" value="help" />
     <property name="docDir" value="doc" />
@@ -162,6 +148,7 @@
     <property name="reportDir" value="test-reports" />
     <property name="testDir" value="test" />
     <property name="testOutputDir" value="tests" />
+  	<property name="cloverOutputDir" value="clover" if:set="clover.jar" />
     <!-- switch to indicate if we should obfuscate jalviewLite -->
     <!-- <property name="donotobfuscate" value="true"/> -->
     <!-- switch to exclude associations from generated jnlp files -->
@@ -181,10 +168,6 @@
         <include name="*.jar" />
         <include name="**/*.jar" />
       </fileset>
-      <fileset dir="${j11libDir}">
-        <include name="*.jar" />
-        <include name="**/*.jar" />
-      </fileset>
       <fileset dir="${libDir}">
         <include name="*.jar" />
         <include name="**/*.jar" />
@@ -198,7 +181,6 @@
         <include name="${jmolJar}" />
         <include name="${varnaJar}" />
       </fileset>
-      <pathelement location="${clover.jar}" if:set="clover.jar"/>
     </path>
     <path id="test.classpath">
       <pathelement path="${outputDir}" />
@@ -291,16 +273,12 @@
         <include name="**/*.*" />
       </fileset>
     </copy>
+  	<mkdir dir="${cloverOutputDir}" if:set="clover.jar"/>
   </target>
 
   <target name="build" depends="prepare">
     <!-- not efficient yet. -->
-    <!-- Echo the build.classpath
-    <pathconvert property="echoClasspath" refid="build.classpath" />
-    <echo message="build.classpath is '${echoClasspath}'" />
-    -->
-    <echo message="javac.target is '${javac.target}'" />
-    <javac includeantruntime="false" source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
+    <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
       <exclude name="jalview/*applet*" />
       <exclude name="jalview/appletgui/**" />
       <exclude name="com/stevesoft/**" />
@@ -331,7 +309,6 @@
         <pathelement location="${clover.jar}" if:set="clover.jar"/>
         <path refid="test.classpath" />
       </classpath>
-      <jvmarg value="--module-path=${j11libDir}" if:set="java11"/>
       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
       <jvmarg value="--illegal-access=warn" if:set="java9"/>
       <classfileset dir="${testOutputDir}" includes="**/*.class" />
@@ -340,7 +317,9 @@
 
   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
     <replace value="${JALVIEW_VERSION}">
-      <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
+      <replacetoken>
+        <![CDATA[$$Version-Rel$$]]>
+      </replacetoken>
       <fileset dir="${outputDir}/${helpDir}">
         <include name="help.jhm" />
       </fileset>
@@ -485,7 +464,7 @@
         </resources>
         <resources os="Mac OS X">
           <fileset dir="${packageDir}">
-          	 <include name="quaqua-filechooser-only-8.0.jar"/>
+            <include name="quaqua-filechooser-only-8.0.jar"/>
             <include name="*quaqua64*.jnilib.jar" />
           </fileset>
         </resources>
@@ -501,7 +480,7 @@
     <jnlpf toFile="${jnlpFile}" />
     <!-- add the add-modules j2se attribute for java 9 -->
     <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;">
-          <replacetoken>j2se version="1.8+"</replacetoken>
+      <replacetoken>j2se version="1.8+"</replacetoken>
     </replace>
   </target>
 
@@ -724,6 +703,50 @@
   <delete file="in.jar" />
 </target>
 
+<target name="jaxb-bindings" depends="init" description="Generates JAXB bindings for supported Jalview XML models (needs xjc on the path)">
+  <delete>
+    <fileset dir="${sourceDir}/jalview/xml/binding/jalview">
+      <include name="*.java" />
+    </fileset>
+  </delete>
+  <exec executable="xjc">
+    <arg value="${schemaDir}/jalview.xsd"/>
+    <arg value="-d"/>
+    <arg value="${sourceDir}"/>
+    <arg value="-p"/>
+    <arg value="jalview.xml.binding.jalview"/>
+  </exec>
+  <delete>
+    <fileset dir="${sourceDir}/jalview/xml/binding/embl">
+      <include name="*.java" />
+    </fileset>
+  </delete>
+
+  <exec executable="xjc">
+    <arg value="${schemaDir}/embl.xsd"/>
+    <arg value="-d"/>
+    <arg value="${sourceDir}"/>
+    <arg value="-b"/>
+    <arg value="${schemaDir}/embl_bindings.xml"/>
+    <arg value="-p"/>
+    <arg value="jalview.xml.binding.embl"/>
+  </exec>
+
+  <delete>
+    <fileset dir="${sourceDir}/jalview/xml/binding/uniprot">
+      <include name="*.java" />
+    </fileset>
+  </delete>
+
+  <exec executable="xjc">
+    <arg value="${schemaDir}/uniprot.xsd"/>
+    <arg value="-d"/>
+    <arg value="${sourceDir}"/>
+    <arg value="-p"/>
+    <arg value="jalview.xml.binding.uniprot"/>
+  </exec>
+</target>
+
 <target name="sourcedist" description="create jalview source distribution" depends="init">
   <delete file="${source.dist.name}" />
   <!-- temporary copy of source to update timestamps -->
@@ -774,13 +797,17 @@
   <!-- each replacetoken CDATA body must be on one line - 
        otherwise the pattern doesn't match -->
   <replace value="${JALVIEW_VERSION}">
-    <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
+    <replacetoken>
+      <![CDATA[$$Version-Rel$$]]>
+    </replacetoken>
     <fileset dir="_sourcedist">
       <include name="**/*" />
     </fileset>
   </replace>
   <replace dir="_sourcedist" value="${build.year}">
-    <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
+    <replacetoken>
+      <![CDATA[$$Year-Rel$$]]>
+    </replacetoken>
     <fileset dir="_sourcedist">
       <include name="**/*" />
     </fileset>
@@ -955,8 +982,9 @@
 </target>
 
 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
+<target name="pubapplet" description="Dummy target to keep legacy Jalview build system happy. We don't actually publish the applet anymore."/>
 
-<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
+<target name="_pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 
   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
@@ -991,7 +1019,110 @@
   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
   <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
     <arg file="${helpDir}"/>
-    <arg value="-nointernet"/>
+    <arg value="-nointernet" />
   </java>
 </target>
+
+<target name="eclipse-install" depends="init,prepare">
+<!--
+  <property name="eclipseTempFile" value="eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
+  <property name="eclipseInstallURL" value="http://mirror.csclub.uwaterloo.ca/eclipse/technology/epp/downloads/release/oxygen/R/eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
+  <property name="java2scriptURL" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.core/dist/dropins/net.sf.j2s.core.jar?raw=true"/>
+-->
+  <property name="eclipseTempFile" value="eclipse-jee-2019-06-R-linux-gtk-x86_64.tar.gz"/>
+  <property name="eclipseInstallURL" value="http://ftp.fau.de/eclipse/technology/epp/downloads/release/2019-06/R/eclipse-jee-2019-06-R-linux-gtk-x86_64.tar.gz"/>
+  <property name="java2scriptURL" value="https://github.com/BobHanson/java2script/raw/master/sources/net.sf.j2s.core/dist/swingjs/net.sf.j2s.core.jar"/>
+
+  <get src="${eclipseInstallURL}" dest="${eclipseTempFile}"/>
+  <untar compression="gzip" src="${eclipseTempFile}" dest="${eclipse-inst}"/>
+
+  <!-- not needed since we ship transpiler with source
+    <get url="${java2scriptURL}" dest="eclipse-inst/dropins/net.sf.j2s.core.jar" /> -->
+
+</target>
+
+<target name="build-site" depends="init,prepare,compile-site,unzip-to-site,make-j2s-cores">
+  <!-- tarball -->
+  <tar compression="gzip" destfile="site.tar.gz">
+    <tarfileset dir="site" />
+  </tar>
+</target>
+<target name="prepare-site" depends="init,prepare">
+  <property name="swingjsdir" value="swingjs"/>
+  <property name="eclipse-inst" value="/home/bamboo/buildtools/eclipse/eclipse-js"/>
+  <property name="eclipse-exec" value="${eclipse-inst}/eclipse"/>
+  <property name="site" value="site"/>
+  <!-- where the eclipse js workspace has been initialised -->
+  <property name="eclipse-work" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace"/>
+  <!-- git repository linked to project in workspace -->
+  <property name="eclipse-workrepo" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace/jalview-js"/>
+</target>
+  <target name="clean-site" depends="prepare-site">
+    <delete dir="${eclipse-workrepo}/${site}"/>
+    <mkdir dir="${eclipse-workrepo}/${site}"/>
+  </target>
+<target name="compile-site" depends="prepare-site,clean-site">
+  <!-- update transpiler -->
+  <copy file="${swingjsdir}/net.sf.j2s.core.jar" todir="${eclipse-inst}/dropins" overwrite="true" failonerror="true"/>
+  <!-- update the git repo linked to the eclipse workspace -->
+  <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="true">
+    <arg value="rev-parse" />
+    <arg value="--short" />
+    <arg value="HEAD" />
+  </exec>
+  <!-- update and checkout the same commit in the workspace project -->
+  <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
+    <arg value="reset" />
+    <arg value="--hard" />
+  </exec>
+  <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
+      <arg value="pull" />
+  </exec>
+  <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
+    <arg value="checkout" />
+    <arg value="${git.commit}" />
+  </exec>
+  <!-- custom classpath for .js builds -->
+  <copy file=".classpath.js" tofile="${eclipse-workrepo}/.classpath" overwrite="true"/>
+  <!-- clean eclipse log -->
+  <delete file="${eclipse-work}/.metadata/.log"/>
+    
+  <!-- execute the eclipse build - the build may fail but valid javascript may still be produced, so we ignore return codes -->
+  <exec executable="${eclipse-exec}" failonerror="no">
+    <arg value="-nosplash"/>
+    <arg value="--launcher.suppressErrors"/>
+    <arg value="-application"/>
+    <arg value="org.eclipse.jdt.apt.core.aptBuild"/>
+    <arg value="-data"/>
+    <arg value="${eclipse-work}"/>
+  </exec>
+  <!-- report log -->
+  <exec executable="/bin/cat">
+    <arg value="${eclipse-work}/.metadata/.log"/>
+  </exec>
+  <!-- TODO: run jslint and something else here to check we have a complete set of .js files for java -->
+  <!-- possibly compare timestamps between .js files and their mate in source - any newer or not present triggers a new build -->
+  <!-- <mkdir dir="${packageDir}/${site}" /> -->
+  <!--   <property name="swingjs.zipurl" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.java.core/dist/SwingJS-site.zip?raw=true" /> -->
+
+  <!-- and reset the .classpath -->
+  <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
+    <arg value="checkout" />
+    <arg value="${git.commit}"/>
+    <arg value="--"/>
+    <arg value=".classpath" />
+  </exec>
+
+  <!-- finally copy artefacts from eclipse project checkout to the build site -->
+  <copy todir="${site}">
+    <fileset dir="${eclipse-workrepo}/site"/>
+  </copy>
+</target>
+<target name="unzip-to-site" depends="prepare-site">
+  <ant antfile="build-site.xml"/>
+</target>
+
+  <target name="make-j2s-cores" depends="">
+    <ant antfile="buildcore.xml" target="build-all-cores"/>
+  </target>
 </project>