From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Fri, 24 Jun 2011 17:17:29 +0000 (+0000)
Subject: Further simplification of build tasks
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b92afa441493a3c675fa0e63977aa7d5f0e17d8e;p=jabaws.git

Further simplification of build tasks
get rid of biojava jar as it's not in use

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4328 e3abac25-378b-4346-85de-24260fe3988d
---

diff --git a/TODO.txt b/TODO.txt
index b2060ce..5d66c70 100644
--- a/TODO.txt
+++ b/TODO.txt
@@ -21,15 +21,9 @@ To change this you need
 2) Update the code to get the date out of the file.  
 Can be done once JABAWS 1 is replaced with 2. 
 
-Globprot need a proper reference to bio python and sav_gol binaries -> they should be 
-somehow taken from disembl. 
-
 
 ? Replace conservation.Method with server.ws.Method and try building WS. If this does not work - get rid of Method
 
-Output file parsing for stat reporting
-install cluster engine stat of www-jws2 user
-
 integrate the above to tweak the size of the local job
 
 Good toString method for Limits (test with command line client -limits)
diff --git a/WEB-INF/lib/biojava.jar b/WEB-INF/lib/biojava.jar
deleted file mode 100644
index 9c306c8..0000000
Binary files a/WEB-INF/lib/biojava.jar and /dev/null differ
diff --git a/WEB-INF/lib/readme.txt b/WEB-INF/lib/readme.txt
index 2736669..9992096 100644
--- a/WEB-INF/lib/readme.txt
+++ b/WEB-INF/lib/readme.txt
@@ -1,14 +1,13 @@
+Runtime dependency for web services. They are required to run a web service 
+within servlet container e.g. tomcat
+
 webservices-rt.jar
 webservices-tools.jar 
 webservices-api.jar 
 
-is to satisfy compile dependencies for web services. 
-Once they are compiled this library is not needed. 
-They are required to run a web service within servlet container - tomcat  
-Standard JDK6 has this library in, it is relocated here to be able to use Ant tasks (WsGen, wsimport) for WS compilation
-and make the project less dependant on the environment
+JABAWS Statistics web application dependencies:  
 
-display tag 1.2 dependencies
+- Display Tag 1.2 dependencies
 
 commons-beanutils-1.7.0.jar
 commons-collections-3.2.jar
@@ -19,4 +18,7 @@ displaytag-export-poi-1.2.jar
 itext-1.4.7.jar
 jstl-1.1.2.jar
 poi-3.2-FINAL-20081019.jar
-standard-1.1.2.jar
\ No newline at end of file
+standard-1.1.2.jar
+
+- Derby database driver for statistics database 
+derby.jar 
\ No newline at end of file
diff --git a/build.xml b/build.xml
index 4e9dd87..884ee5e 100644
--- a/build.xml
+++ b/build.xml
@@ -27,17 +27,14 @@
 	<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"/>
 
@@ -309,8 +306,10 @@
 		<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>
 
@@ -359,15 +358,7 @@
 		</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}">
@@ -377,25 +368,30 @@
 			</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="${jaba}">
+	<target name="jaba-no-binaries" description="Prepare JABAWS war file without native binaries" depends="full-jaba-jar">
+		<echo>Preparing a war file without binaries</echo>
+		<delete file="${jaba-no-binaries}">
 		</delete>
-		<delete file="${jaba-no-jaxws-no-binaries}">
-		</delete>
-		<zip destfile="${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}/jobsout" prefix="jobsout" excludes="**/*"/>
 			<zipfileset dir="${basedir}/conf" prefix="conf" excludes="**/log4j.properties*"/>
 			<!-- Add JABAWS web site apart from the binary archive -->
-			<zipfileset dir="${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"/>
@@ -414,71 +410,30 @@
 		</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"/>
 
 	<!-- 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 +446,6 @@
 		</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">