X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=426e3ca42889eb42dc9a751674feff4eac7dcfa3;hb=6256f785b5baf779b46ac1d9a5d3d9bec7a2b96c;hp=4e9dd871701d43127c7ebe08ea9b374f1f90b79b;hpb=1b7b48c7ec2b6694cd1f06b9838a0b8cfd0b9910;p=jabaws.git

diff --git a/build.xml b/build.xml
index 4e9dd87..426e3ca 100644
--- a/build.xml
+++ b/build.xml
@@ -17,27 +17,27 @@
 	<!-- dependencies on other compbio projects  -->
 	<property name="compbio-annotation" value="compbio-annotations-1.0.jar"/>
 	<property name="compbio-util" value="compbio-util-1.4.jar"/>
+	<property name="compbio-ga" value="compbio-ga-1.0.jar"/>
 	
 	<!-- products -->
 	<property name="jaba_version" value="2.0"/>
 	<property name="datamodel" value="${distdir}/datamodel-${jaba_version}.jar"/>
 	<property name="datamodel-src" value="${distdir}/datamodel-src-${jaba_version}.jar"/>
 	<property name="min-jaba-client" value="${distdir}/min-jaba-client-${jaba_version}.jar"/>
+	<property name="jaba-client-src" value="${distdir}/jaba-client-src-${jaba_version}.jar"/>
+	
 	<property name="aacon-ws-client" value="${distdir}/aacon-ws-client.jar"/>
 	<property name="full-jaba-client" value="${distdir}/full-jaba-client-${jaba_version}.jar"/>
 	<property name="jaba-source-jar" value="${distdir}/jabaws-src-${jaba_version}.jar"/>
 	<property name="full-jaba-client-pack" value="${distdir}/full-jaba-client-pack.zip"/>
-	<property name="jaba-no-jaxws" value="${distdir}/jaba-no-jaxws.war"/>
-	<property name="jaba-no-jaxws-windows" value="${distdir}/jaba-no-jaxws-windows.war"/>
 	<property name="jaba" value="${distdir}/jaba.war"/>
+	<!-- TODO  
 	<property name="jaba-dundee" value="${distdir}/jaba-dundee.war"/>
-	<property name="jaba-no-jaxws-no-binaries" value="${distdir}/jaba-no-jaxws-no-binaries.war"/>
+	 -->
 	<property name="jaba-no-binaries" value="${distdir}/jaba-no-binaries.war"/>
-	<property name="jaba-windows" value="${distdir}/jaba-windows.war"/>
 	<property name="binaries" value="${distdir}/binaries.zip"/>
-	<property name="win-binaries" value="${distdir}/win-binaries.zip"/>
 	<property name="jaba-devel-web" value="${distdir}/jaba-devel-website.zip"/>
-	<property name="jaxws-lib" value="${distdir}/jaxws-lib.zip"/>
+
 	<!--Whole project archive -->
 	<property name="jaba-project" value="${distdir}/jaba-project.zip"/>
 
@@ -184,7 +184,28 @@
 		</jar>
 	</target>
 
-
+	<target name="jaba-client-src-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class" depends="datamodel-source-jar">
+		<echo>Jar file: JABAWS client source</echo>
+		<delete file="${jaba-client-src}">
+		</delete>
+		<jar jarfile="${jaba-client-src}">
+			<zipgroupfileset  excludes="META-INF/*.MF" file="${datamodel-src}"/>
+				<fileset dir="${basedir}/webservices">
+					<!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->
+					<include name="compbio/data/msa/**"/>
+					<exclude name="compbio/ws/client/ServicesUtil**"/>
+					<exclude name="compbio/ws/client/AAConClient**"/>
+					<include name="compbio/ws/client/**"/>
+				</fileset>
+				<manifest>
+					<attribute name="Built-By" value="${author}" />
+					<attribute name="Implementation-Title" value="${product} Client Source Code" />
+					<attribute name="Implementation-Vendor" value="${author}" />
+					<attribute name="Implementation-URL" value="${project.url}" />
+				</manifest>
+			</jar>
+	</target>
+	
 	<target name="minimal-jaba-client-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class" depends="compile, datamodel-jar">
 		<echo>Jar file: Minimal WS client jar</echo>
 		<delete file="${basedir}/${min-jaba-client}">
@@ -309,12 +330,14 @@
 		<echo>Packing binaries, and configuration files</echo>
 		<zip destfile="${full-jaba-client-pack}" >
 			<zipgroupfileset file="${binaries}" />
-			<zipfileset dir="${basedir}/conf" prefix="conf"/>
-			<fileset dir="." includes="${full-jaba-client}" />
+			<zipfileset dir="conf" prefix="conf" >
+				<exclude name="**/temp/**"/>
+			</zipfileset>
+			<fileset file="${full-jaba-client}" />
 		</zip>
 	</target>
 
-
+	
 	<target name="full-jaba-jar" description="Pack datamodel, engine, runners, configuration, binaries and webservices" depends="compile">
 		<echo>Jar file: Full WS client jar</echo>
 		<delete file="${full-jaba-client}">
@@ -347,7 +370,8 @@
 	</target>
 
 	<target name="clearStatDB" description="Remove all records from statistics database">
-		 <java classname="compbio.stat.collector.StatDB" fork="true" failonerror="true" classpath="${classes}">
+		 <echo>Cleaning Statistics database</echo>
+		 <java classname="compbio.stat.collector.StatDB" fork="false" failonerror="true" classpath="${classes}">
 	            <classpath refid="project.classpath" />
 	     </java>
 	</target>
@@ -359,15 +383,7 @@
 		</zip>
 	</target>
 
-	<target name="pack-jaxws" description="Zip all JAXWS libraries">
-		<delete file="${jaxws-lib}" failonerror="false"/>
-		<zip destfile="${jaxws-lib}" update="false" >
-			<zipfileset dir="${web.lib.path}" includes="webservices-tools.jar"  prefix="WEB-INF/lib"  />
-			<zipfileset dir="${web.lib.path}" includes="webservices-rt.jar"   prefix="WEB-INF/lib" />
-			<zipfileset dir="${web.lib.path}" includes="webservices-api.jar"  prefix="WEB-INF/lib" />
-		</zip>
-	</target>
-
+<!-- DEPRICATED 
 	<target name="pack-windows-binaries" description="Zip only windows binary files">
 		<delete file="${win-binaries}" failonerror="false" />
 		<zip destfile="${win-binaries}">
@@ -377,30 +393,37 @@
 			</zipfileset>
 		</zip>
 	</target>
+-->
 
-	<target name="jaba-no-jaxws-no-binaries" description="Prepare JWS2 war file without runtime dependency - JAXWS jars and native binaries" depends="full-jaba-jar">
-		<echo>Preparing war file without JAXWS and binaries</echo>
-		<delete file="${jaba}">
-		</delete>
-		<delete file="${jaba-no-jaxws-no-binaries}">
+	<target name="jaba-no-binaries" description="Prepare JABAWS war file without native binaries" depends="full-jaba-jar,  clearStatDB">
+		<echo>Preparing a war file without binaries</echo>
+		<delete file="${jaba-no-binaries}">
 		</delete>
-		<zip destfile="${jaba-no-jaxws-no-binaries}" whenempty="create">
+		<zip destfile="${jaba-no-binaries}" whenempty="create">
 			<zipfileset dir="${basedir}/WEB-INF" prefix="WEB-INF">
+				<exclude name="classes"/>
+				<!-- These are included into JABA client so exclude the jars -->
+				<exclude name="lib/drmaa.jar"/>
+				<exclude name="lib/log4j-1.2.15.jar"/>
+				<exclude name="lib/${compbio-annotation}"/>
+				<exclude name="lib/${compbio-util}"/>
+				
 				<include name="web.xml"/>
 				<include name="sun-jaxws.xml"/>
-				<exclude name="classes"/>
-				<exclude name="lib"/>
+				<include name="lib/*"/>
 			</zipfileset>
 			<zipfileset dir="${basedir}/ExecutionStatistic" prefix="ExecutionStatistic" />
+			<zipfileset dir="${basedir}/statpages" prefix="statpages" />
 			<zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="**/*"/>
-			<zipfileset dir="${basedir}/conf" prefix="conf" excludes="**/log4j.properties*"/>
+			<zipfileset dir="conf" prefix="conf" >
+				<exclude name="**/temp/**"/>
+				<exclude name="**/log4j.properties*"/>
+			</zipfileset>
 			<!-- Add JABAWS web site apart from the binary archive -->
-			<zipfileset dir="${basedir}/website" excludes="archive/**, full_javadoc/**, devel*.html, tests/**, template.html"/>
+			<zipfileset dir="${basedir}/website" excludes="archive/**, devel*.html, tests/**, template.html"/>
 			<zipfileset dir="." includes="${full-jaba-client}" fullpath="WEB-INF/lib/jaba-client.jar"/>
 			<!-- Put a copy of log4j configuration file where it can be used  -->
 			<zipfileset dir="conf" includes="log4j.properties" prefix="WEB-INF/classes"/>
-			<!-- This is runtime dependency must be supplied by the container -->
-			<!-- zipfileset dir="${web.lib.path}" includes="servlet-api.jar" prefix="WEB-INF/lib" / -->
 		</zip>
 	</target>
 
@@ -414,71 +437,30 @@
 		</zip>
 	</target>
 
-	<target name="jaba-without-jaxws" description="Prepare JWS2 war file without runtime dependency - JAXWS jars" depends="jaba-no-jaxws-no-binaries, pack-binaries">
-		<echo>Preparing war file without JAXWS</echo>
-		<delete file="${jaba-no-jaxws}">
-		</delete>
-		<copy tofile="${jaba-no-jaxws}" file="${jaba-no-jaxws-no-binaries}"/>
-		<zip destfile="${jaba-no-jaxws}" update="true" >
-			<zipgroupfileset file="${binaries}" />
-		</zip>
-	</target>
-
-	<target name="jaba-without-jaxws-windows" description="Prepare JWS2 war file without runtime dependency - JAXWS jars" 
-		depends="full-jaba-jar, pack-windows-binaries, clearStatDB">
-		<echo>Preparing war file without JAXWS</echo>
-		<delete file="${jaba-windows}">
-		</delete>
-		<delete dir="${basedir}/jobsout/*"/>
-		<delete file="${jaba-no-jaxws-windows}">
-		</delete>
-		<zip destfile="${jaba-no-jaxws-windows}" >
-			<zipfileset dir="${basedir}/WEB-INF" prefix="WEB-INF">
-				<include name="web.xml"/>
-				<include name="sun-jaxws.xml"/>
-				<exclude name="classes"/>
-				<exclude name="lib"/>
-			</zipfileset>
-			<zipgroupfileset file="${win-binaries}" />
-			<zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="**/*"/>
-			<zipfileset dir="${basedir}/conf" prefix="conf" excludes="**/log4j.properties*"/>
-			<zipfileset dir="." includes="${full-jaba-client}" fullpath="WEB-INF/lib/jaba-client.jar"/>
-			<zipfileset dir="conf" includes="log4j.properties" prefix="WEB-INF/classes"/>
-			<!-- Add JABAWS web site apart from the binary archive -->
-			<zipfileset dir="${basedir}/website" excludes="archive/**, full_javadoc/**, devel*.html, tests/**, template.html"/>
-		</zip>
-	</target>
-
-
-
-	<target name="jaba-complete" description="Prepare JWS2 war file" depends="jaba-without-jaxws, pack-jaxws">
+	<target name="jaba-complete" description="Prepare JABAWS war file without runtime dependency - JAXWS jars" depends="jaba-no-binaries, pack-binaries">
 		<echo>Preparing a complete war file</echo>
-		<copy tofile="${jaba}" file="${jaba-no-jaxws}"/>
+		<delete file="${jaba}">
+		</delete>
+		<copy tofile="${jaba}" file="${jaba-no-binaries}"/>
 		<zip destfile="${jaba}" update="true" >
-			<zipgroupfileset file="${jaxws-lib}"/>
-		</zip>
-	</target>
-
-	<target name="jaba-no-binaries" description="Prepare JWS2 war file without native binaries" depends="jaba-no-jaxws-no-binaries, pack-jaxws">
-		<echo>Preparing a complete war file</echo>
-		<copy tofile="${jaba-no-binaries}" file="${jaba-no-jaxws-no-binaries}"/>
-		<zip destfile="${jaba-no-binaries}" update="true" >
-			<zipgroupfileset file="${jaxws-lib}"/>
+			<zipgroupfileset file="${binaries}" />
 		</zip>
 	</target>
 
-	<target name="jaba-complete-windows" description="Prepare JWS2 war file for windows" depends="jaba-without-jaxws-windows, pack-jaxws">
+<!-- DEPRICATED - STANDARD JABA WAR WILL WORK FOR WINDOWS JUST FINE, DOWNLOAD SPACE SAVING IS NOT WORTH THE 
+  ADDITIONAL COMPLEXITY 
+	<target name="jaba-complete-windows" description="Prepare JABAWS war file for windows" depends="jaba-no-binaries">
 		<echo>Preparing a complete war file</echo>
-		<copy tofile="${jaba-windows}" file="${jaba-no-jaxws-windows}"/>
+		<copy tofile="${jaba-windows}" file="${jaba-no-binaries}"/>
 		<zip destfile="${jaba-windows}" update="true" >
-			<zipgroupfileset file="${jaxws-lib}"/>
+			<zipgroupfileset file="${win-binaries}" />
 		</zip>
 	</target>
-
+-->
+ 
 	<target name="build-all" description="Build-all the distributives"
-		depends="full-jaba-client, minimal-jaba-client-jar, jaba-no-jaxws-no-binaries,
-		 jaba-no-binaries, jaba-complete, jaba-complete-windows,
-		 datamodel-jar, datamodel-source-jar, source-jar"/>
+		depends="full-jaba-client, minimal-jaba-client-jar, jaba-no-binaries,
+		 jaba-complete, datamodel-jar, datamodel-source-jar, source-jar, jaba-client-src-jar"/>
 
 	<!-- This task does not really depends on compile, but it is better to make sure that the code is sound -->
 	<target name="archive-project" description="Pack everything in the project for those who do not have access to SVN" depends="compile">
@@ -491,23 +473,6 @@
 		</zip>
 	</target>
 
-	<!-- This is JUNIT test 
-	<target name="testEngine" depends="compileTest">
-			<delete file="${activity.log}"/> 
-			<junit filtertrace="false" haltonfailure="true" haltonerror="true" fork="true" forkmode="once">
-		        <jvmarg value="-server" />
-		        <jvmarg value="-enableassertions" />
-		        <jvmarg value="-Xms512m" />
-		        <jvmarg value="-Xmx512m" />
-				<env key="LD_LIBRARY_PATH" value="/gridware/sge/lib/lx24-amd64"/>
-		        <classpath refid="test.classpath" />
-		    	<classpath refid="project.classpath" />
-		        <formatter type="plain" usefile="false" />
-		        <test name="compbio.engine.cluster.AllTestSuit" />
-		        <sysproperty key="TestingDataPath" value="${data.src}"/>
-		    </junit>
-		</target>
-	-->
 
 	<taskdef name="testNG" classname="org.testng.TestNGAntTask">
 		<classpath refid="test.classpath">