X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=build.xml;h=327cc334c774faa18262bfa1256a3ccfbced337a;hb=77fe5f2b4f597d9b872c44938af8ee6b003041d2;hp=4ff78e0738534dcc9b46d74b4e9628b29f621cc1;hpb=98a4aef73b7b3056bb37a4ef2d527010484b01d8;p=jalview.git

diff --git a/build.xml b/build.xml
index 4ff78e0..327cc33 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"/>
@@ -307,7 +315,7 @@
     </testng>
   </target>
 
-  <target name="buildindices" depends="init, prepare" unless="help.uptodate">
+  <target name="buildindices" depends="init, prepare, buildPropertiesFile" unless="help.uptodate">
     <replace value="${JALVIEW_VERSION}">
       <replacetoken>
         <![CDATA[$$Version-Rel$$]]>
@@ -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 -->
@@ -687,30 +703,50 @@
   <delete file="in.jar" />
 </target>
 
-<target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
-  <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
+<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/schemabinding/version2">
+    <fileset dir="${sourceDir}/jalview/xml/binding/embl">
       <include name="*.java" />
-      <include name="descriptors/*.java" />
     </fileset>
   </delete>
-  <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-  <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-  <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-  <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-  <!-- 
-		now build the jalview.binding package with the old schema set
-		-->
+
+  <exec executable="xjc">
+    <arg value="${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="${sourceDir}/jalview/binding/">
-      <include name="**" />
+    <fileset dir="${sourceDir}/jalview/xml/binding/uniprot">
+      <include name="*.java" />
     </fileset>
   </delete>
-  <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
-  <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
-  <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+
+  <exec executable="xjc">
+    <arg value="${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 -->
@@ -933,21 +969,22 @@
     <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>
 </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" />
@@ -1000,14 +1037,13 @@
 
 </target>
 
-<target name="build-site" depends="init,prepare,compile-site,unzip-to-site">
-  <!-- closure compile -->
+<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">
+<target name="prepare-site" depends="init,prepare,buildPropertiesFile">
   <property name="swingjsdir" value="swingjs"/>
   <property name="eclipse-inst" value="/home/bamboo/buildtools/eclipse/eclipse-js"/>
   <property name="eclipse-exec" value="${eclipse-inst}/eclipse"/>
@@ -1017,7 +1053,11 @@
   <!-- git repository linked to project in workspace -->
   <property name="eclipse-workrepo" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace/jalview-js"/>
 </target>
-<target name="compile-site" depends="prepare-site">
+  <target name="clean-site" depends="prepare-site">
+    <delete dir="${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="${eclipse-inst}/dropins" overwrite="true" failonerror="true"/>
   <!-- update the git repo linked to the eclipse workspace -->
@@ -1028,7 +1068,11 @@
   </exec>
   <!-- update and checkout the same commit in the workspace project -->
   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${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" />
@@ -1036,7 +1080,9 @@
   </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="${eclipse-exec}" failonerror="no">
     <arg value="-nosplash"/>
@@ -1046,7 +1092,10 @@
     <arg value="-data"/>
     <arg value="${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}/${site}" /> -->
@@ -1063,31 +1112,13 @@
   <!-- finally copy artefacts from eclipse project checkout to the build site -->
   <copy todir="${site}">
     <fileset dir="${eclipse-workrepo}/site"/>
-  </copy>
+  </copy>  
 </target>
 <target name="unzip-to-site" depends="prepare-site">
-  <property name="swingjs.zip" value="${swingjsdir}/SwingJS-site.zip" />
-  <unzip dest="${site}/" overwrite="true">
-    <fileset dir="${swingjsdir}">
-      <include name="SwingJS-site.zip"/>
-    </fileset>
-  </unzip>
-  <unzip dest="${site}/" overwrite="true">
-    <fileset dir="libjs">
-      <include name="*.zip" />
-    </fileset>
-  </unzip>
-  <copy overwrite="true" todir="${site}/swingjs/j2s/">
-    <fileset dir="${resourceDir}">
-      <include name="**"/>
-    </fileset>
-  </copy>
-
-  <!-- copy test files into place in site -->
-  <copy todir="${site}/examples">
-    <fileset dir="examples">
-      <include name="*.*"/>
-    </fileset>
-  </copy>
+  <ant antfile="build-site.xml"/>
 </target>
+
+  <target name="make-j2s-cores" depends="">
+    <ant antfile="buildcore.xml" target="build-all-cores"/>
+  </target>
 </project>