X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=dbf1df3753ca330b70fa0e658ab112da373832fb;hb=3412b273e964fb1a9d22564b04a5f0c827ec2461;hp=d4403318135431fa5ff7768353a55ff61282bfe6;hpb=f298945f07518f90f3400bee0451417872321f54;p=jalview.git

diff --git a/build.xml b/build.xml
index d440331..dbf1df3 100755
--- a/build.xml
+++ b/build.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -18,15 +18,6 @@
  * The Jalview Authors are detailed in the 'AUTHORS' file.
 -->
 <project name="jalviewX" default="usage" basedir=".">
-  <!-- we use jalopy to format our sources -->
-  <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
-    <classpath>
-      <fileset dir="utils/jalopy/lib">
-        <include name="*.jar" />
-      </fileset>
-    </classpath>
-  </taskdef>
-
   <target name="help" depends="usage" />
   <target name="usage">
     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
@@ -71,8 +62,12 @@
         <include name="*.jar"/>
       </fileset> -->
       </path>
+  	
     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
+  	
+    <property name="INSTALLATION" value="Source" />
+  	
     <!-- 2.4 (VAMSAS)" -->
     <!-- Include debugging information in javac true or false -->
     <property name="javac.debug" value="true" />
@@ -86,15 +81,14 @@
     <!-- Key Password -->
     <property name="jalview.key.pass" value="alignmentisfun" />
 
-
-
     <!-- Don't change anything below here unless you know what you are doing! -->
     <!-- Url path for WebStart in JNLP file -->
     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
     <!-- Webstart Image - looked for in resources/images -->
     <property name="WebStartImage" value="JalviewLogo_big.png"/>
     <!-- J2SE version needed for webstart launch -->
-    <property name="j2sev" value="1.6+"/>
+    <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
+    <property name="j2sev" value="1.7+"/>
 
     <!-- Permissions for running Java applets and applications. -->
     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
@@ -116,9 +110,18 @@
     <property name="outputJar" value="jalview.jar" />
     <!-- Jalview Applet JMol Jar Dependency -->
     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
+    <property name="varnaJar" value="VARNAv3-91.jar" />
+    <property name="jsoup" value="jsoup-1.8.1.jar" />
+    <property name="jsonSimple" value="json_simple-1.1.jar" />
+    <property name="javaJson" value="java-json.jar" />
     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
+	<property name="reportDir" value="test-reports" />
+	<property name="testDir" value="test" />
+	<property name="testOutputDir" value="tests" />
     <!-- switch to indicate if we should obfuscate jalviewLite -->
-    <!--<property name="donotobfuscate" value="true"/> -->
+    <!-- <property name="donotobfuscate" value="true"/> -->
+    <!-- switch to exclude associations from generated jnlp files -->
+    <!-- <property name="nojnlpfileassocs" value="true"/> -->
 
     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
@@ -145,15 +148,15 @@
         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
 				-->
         <include name="${jmolJar}" />
+        <include name="${varnaJar}" />
       </fileset>
 
     </path>
     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
     <!-- The Location of the java 1.1.8 jdk -->
-    <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
-		-->
+    <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
     <property name="java118.home" value="${java.home}" />
-    <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
+    <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 		-->
     <!-- jre for 1.4 version -->
     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
@@ -167,6 +170,11 @@
         <include name="plugin.jar"/>
       </fileset>
       <pathelement location="appletlib/${jmolJar}" />
+      <pathelement location="lib/${varnaJar}" />
+      <pathelement location="lib/${jsoup}" />
+      <pathelement location="lib/${jsonSimple}" />
+      <pathelement location="lib/${javaJson}" />
+      
     </path>
     <!-- default location for outputting javadoc -->
     <property name="javadocDir" value="${packageDir}/javadoc"/>
@@ -181,8 +189,9 @@
     <properties file="${outputDir}/.build_properties">
       <header>
           ---Jalview Build Details---
-        </header>
+        </header>    	
       <property name="VERSION" value="${JALVIEW_VERSION}" />
+      <property name="INSTALLATION" value="${INSTALLATION}" />
       <property name="BUILD_DATE" value="${build.date}" />
     </properties>
   </target>
@@ -233,6 +242,49 @@
       <exclude name="com/stevesoft/**" />
     </javac>
   </target>
+  
+  
+  <target name="testclean" depends="init">
+    <delete dir="${testOutputDir}" includes="*,**/*"/>
+  </target>
+  
+  <target name="prepareTests" depends="init">
+	<mkdir dir="${testOutputDir}" />
+	<copy todir="${testOutputDir}">
+		<fileset dir=".">
+			<include name="${docDir}/**/*.*" />
+			<include name="${helpDir}/**/*.*" />
+			<include name="${libDir}/*.jar" />
+		</fileset>
+		<fileset dir="${resourceDir}">
+			<include name="**/*.*" />
+		</fileset>
+	</copy>
+  </target>  
+  
+  <target name="buildTests" depends="prepareTests">
+	<javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${testOutputDir}"
+		debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
+		<exclude name="jalview/*applet*" />
+		<exclude name="jalview/appletgui/**" />
+	</javac>
+	<javac source="1.5" target="1.5" srcdir="${testDir}" destdir="${testOutputDir}"
+		debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
+	</javac>
+  </target>
+  
+  <taskdef name="testng" classname="org.testng.TestNGAntTask" >	    
+	<classpath location="utils/testnglibs/testng.jar" />
+  </taskdef>
+  
+  <target name="testng" depends="buildTests">
+	<testng classpathref="build.classpath" outputDir="${reportDir}"
+		haltOnFailure="false">
+		<classpath location="${testOutputDir}" />
+		<xmlfileset dir="utils" includes="jalview_testng.xml" />
+	</testng>
+  </target>
+  
   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
       <arg line="html" />
@@ -328,7 +380,8 @@
     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
       </echo>
   </target>
-  <target name="writejnlpf">
+
+  <target name="-generatejnlpf">
     <presetdef name="jnlpf">
       <jnlp codebase="${WebStartLocation}">
         <information>
@@ -349,9 +402,16 @@
             <include name="*.jar" />
             <include name="*_*.jar" />
             <exclude name="jalview.jar" />
+          	<exclude name="*jnilib.jar"/>
           </fileset>
+      	</resources>
+        <resources os="Mac OS X">
           <property name="jalview.version" value="${JALVIEW_VERSION}" />
+        	<fileset dir="${packageDir}">
+        		<include name="*quaqua*.jnilib.jar"/>
+        	</fileset>
         </resources>
+      	
         <application_desc main_class="jalview.bin.Jalview">
         </application_desc>
         <security>
@@ -361,12 +421,20 @@
     </presetdef>
 
     <jnlpf toFile="${jnlpFile}"/>
+
+  </target>
+
+  <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
+    <echo message="Not adding JNLP File Associations"/>
+  </target>
+
+  <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
     <replace file="${jnlpFile}">
       <replacetoken>
         <![CDATA[</information>]]></replacetoken>
       <replacevalue>
         <![CDATA[
-        <association mime-type="application-x/ext-file" extensions="fa" />
+          <association mime-type="application-x/ext-file" extensions="fa" />
         <association mime-type="application-x/ext-file" extensions="fasta" />
         <association mime-type="application-x/ext-file" extensions="mfa" />
         <association mime-type="application-x/ext-file" extensions="fastq" />
@@ -380,7 +448,11 @@
         <association mime-type="application-x/ext-file" extensions="jvp"/>
       </information>]]></replacevalue>
   </replace>
+  <echo message="Added file associations to JNLP file"/>
+</target>
+<target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 </target>
+
 <target name="buildextclients" depends="init">
   <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" />
   <condition property="dontextbuild">
@@ -474,7 +546,7 @@
   <mkdir dir="${outputDir}" />
   <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
 			classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
-			excludes="ext/**,MCview/**,org/**,vamsas/**" />
+			excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
 </target>
 
 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
@@ -513,6 +585,8 @@
   <path id="obfuscateDeps.path">
     <pathelement location="${applet.jre.tools}" />
     <pathelement location="appletlib/${jmolJar}" />
+    <pathelement location="appletlib/${jsonSimple}" />
+    <pathelement location="appletlib/${javaJson}" />
   </path>
   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 
@@ -614,6 +688,8 @@
     </fileset>
   </copy>
   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}"/>
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}"/>
   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
     <manifest>
       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
@@ -694,21 +770,37 @@
   <!-- create differently privileged artefacts -->
   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true"/>
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true"/>
   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}"/>
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}"/>
   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
+  <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
+  <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
+  <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
+  <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
+  <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
+  <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
   <!-- finally, create manifest for original jars -->
   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
+  <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
+  <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 
   <!-- todo - write examples/downloads for alternate versions of the applet -->
   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
@@ -717,16 +809,38 @@
       <exclude name="u_*.jar"/>
       <include name="${jalviewLiteJar}" />
       <include name="${jmolJar}" />
+      <include name="${javaJson}" />
+      <include name="${jsonSimple}" />
       <include name="to_${jalviewLiteJar}" />
       <include name="to_${jmolJar}" />
+      <include name="to_${javaJson}" />
+      <include name="to_${jsonSimple}" />
       <include name="tl_${jalviewLiteJar}" />
       <include name="tl_${jmolJar}" />
+      <include name="tl_${javaJson}" />
+      <include name="tl_${jsonSimple}" />
       <include name="ap_${jalviewLiteJar}" />
       <include name="ap_${jmolJar}" />
+      <include name="ap_${javaJson}" />
+      <include name="ap_${jsonSimple}" />
     </fileset>
   </signjar>
   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+	<!-- finally, replace any launchApp servlet tags with a version specification -->
+	<replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
+		<replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
+		<fileset dir="${packageDir}/examples">
+			<include name="**/*.html"/>
+		</fileset>
+	</replace>
+	<replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
+		<replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
+		<fileset dir="${packageDir}/examples">
+			<include name="**/*.html"/>
+		</fileset>
+	</replace>
+
 </target>
 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
   <javadoc destdir="${javadocDir}">