X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=739423519a5b1fac601264e9640ef041a062959f;hb=refs%2Fheads%2FJalview-BH%2FJAL-3026-JAL-3063-JAXB;hp=1e9964c187284dbcacce03ffa3d249bb338daf7a;hpb=26501f76ef450657c530de489b8404356a98aca3;p=jalview.git

diff --git a/build.xml b/build.xml
index 1e9964c..7394235 100755
--- a/build.xml
+++ b/build.xml
@@ -20,6 +20,9 @@
 <project name="jalviewX" default="usage" basedir="."
  xmlns:if="ant:if"
     xmlns:unless="ant:unless">
+  <taskdef classpath="${clover.jar}" resource="cloverlib.xml" if:set="clover.jar"/>
+  <clover-env if:set="clover.jar"/>
+
   <target name="help" depends="usage" />
   <target name="usage" depends="init">
     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
@@ -40,6 +43,7 @@
     <echo message="See docs/building.html and the comments in build file for other targets." />
     <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 " />
     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
+    <echo message="Useful -D flags: -Dclover.jar to specify path to openclover for testng coverage report" />
   </target>
 
 
@@ -130,7 +134,8 @@
     <property name="docDir" value="doc" />
     <property name="sourceDir" value="src" />
     <property name="schemaDir" value="schemas" />
-    <property name="outputDir" value="classes" />
+    <property name="outputDir" value="classes" unless:set="clover.jar"/>
+    <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
     <property name="packageDir" value="dist" />
     <property name="outputJar" value="jalview.jar" />
     <!-- Jalview Applet JMol Jar Dependency -->
@@ -143,6 +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 -->
@@ -267,6 +273,7 @@
         <include name="**/*.*" />
       </fileset>
     </copy>
+  	<mkdir dir="${cloverOutputDir}" if:set="clover.jar"/>
   </target>
 
   <target name="build" depends="prepare">
@@ -299,6 +306,7 @@
       verbose="2">
       <classpath>
         <pathelement location="${testOutputDir}" />
+        <pathelement location="${clover.jar}" if:set="clover.jar"/>
         <path refid="test.classpath" />
       </classpath>
       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
@@ -352,10 +360,15 @@
     </jar>
 
     <antcall target="writejnlpf">
-      <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
+      <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
       <param name="inih" value="10M" />
       <param name="maxh" value="256M" />
     </antcall>
+    <antcall target="writejnlpf">
+      <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
+      <param name="inih" value="800M" />
+      <param name="maxh" value="1024M" />
+    </antcall>
 
     <antcall target="writejnlpf">
       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
@@ -365,7 +378,7 @@
 
     <antcall target="writejnlpf">
       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
-      <param name="inih" value="256M" />
+      <param name="inih" value="800M" />
       <param name="maxh" value="1024M" />
     </antcall>
 
@@ -392,7 +405,7 @@
         <association mime-type="application-x/ext-file" extensions="jar"/>-->
   </target>
 
-  <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
+  <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
     <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}"
       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
       <fileset dir="${packageDir}">
@@ -400,7 +413,7 @@
       </fileset>
     </signjar>
   </target>
-  <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
+  <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
     <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}">
       <fileset dir="${packageDir}">
         <include name="*.jar" />
@@ -540,6 +553,9 @@
 </target>
 
 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
+  <fail if="clover.jar">
+    Ignoring request to build jalview distribution with clover-instrumented classes
+  </fail>
   <!-- make the package jar if not already existing -->
   <mkdir dir="${packageDir}" />
   <!-- clean dir if it already existed -->
@@ -933,13 +949,13 @@
     <include name="ap_${jsonSimple}" />
   </fileset>
 </target>
-<target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
+<target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
     <fileset refid="signappletjarset" />
   </signjar>
 </target>
 
-<target name="-signapplettsa" if="timestamp" depends="-signapplet">
+<target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
     <fileset refid="signappletjarset" />
   </signjar>
@@ -999,7 +1015,15 @@
     <get url="${java2scriptURL}" dest="eclipse-inst/dropins/net.sf.j2s.core.jar" /> -->
 
 </target>
-<target name="build-site" depends="init,prepare">
+
+<target name="build-site" depends="init,prepare,compile-site,unzip-to-site">
+  <!-- closure compile -->
+  <!-- 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="${eclipse-inst}/eclipse"/>
@@ -1008,7 +1032,12 @@
   <property name="eclipse-work" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace"/>
   <!-- git repository linked to project in workspace -->
   <property name="eclipse-workrepo" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace/jalview-js"/>
-    
+</target>
+  <target name="clean-site" depends="prepare-site">
+    <delete dir="${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="${eclipse-inst}/dropins" overwrite="true" failonerror="true"/>
   <!-- update the git repo linked to the eclipse workspace -->
@@ -1019,15 +1048,21 @@
   </exec>
   <!-- update and checkout the same commit in the workspace project -->
   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
-  <arg value="pull" />
+    <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="${git.commit}" />
+    <arg value="checkout" />
+    <arg value="${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="${eclipse-exec}" failonerror="no">
     <arg value="-nosplash"/>
@@ -1037,43 +1072,52 @@
     <arg value="-data"/>
     <arg value="${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="${git.commit}"/>
+    <arg value="checkout" />
+    <arg value="${git.commit}"/>
     <arg value="--"/>
     <arg value=".classpath" />
-      </exec>
-  
+  </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">
   <property name="swingjs.zip" value="${swingjsdir}/SwingJS-site.zip" />
-  <unzip src="${swingjs.zip}" dest="${site}/" overwrite="true"/>
-  <copy todir="${site}/swingjs/j2s/">
+  <unzip dest="${site}/" overwrite="true">
+    <fileset dir="libjs">
+      <include name="*.zip" />
+    </fileset>
+  </unzip>
+  <copy overwrite="true" todir="${site}/swingjs/j2s/">
     <fileset dir="${resourceDir}">
-    	<include name="**"/>
-	</fileset>
+      <include name="**"/>
+    </fileset>
   </copy>
-  
+
   <!-- copy test files into place in site -->
   <copy todir="${site}/examples">
-  <fileset dir="examples">
-  <include name="*.*"/>
+    <fileset dir="examples">
+      <include name="*.*"/>
     </fileset>
   </copy>
-  <!-- closure compile -->
-  <!-- tarball -->
-  <tar compression="gzip" destfile="site.tar.gz">
-    <tarfileset dir="site"/>
-  </tar>
+  <!-- lastly, update SwingJS -->
+  <unzip dest="${site}/" overwrite="true">
+    <fileset dir="${swingjsdir}">
+      <include name="SwingJS-site.zip"/>
+    </fileset>
+  </unzip>
 </target>
 </project>