From 1b7b48c7ec2b6694cd1f06b9838a0b8cfd0b9910 Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Thu, 23 Jun 2011 14:11:27 +0000
Subject: [PATCH] build script updated

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4326 e3abac25-378b-4346-85de-24260fe3988d
---
 DEPENDENCY |   12 ++++-
 build.xml  |  168 +++++++++++++++++++++++-------------------------------------
 2 files changed, 76 insertions(+), 104 deletions(-)

diff --git a/DEPENDENCY b/DEPENDENCY
index b22fbef..cddf8b6 100644
--- a/DEPENDENCY
+++ b/DEPENDENCY
@@ -1,4 +1,14 @@
 Compile time Dependencies of this project are: 
 
 compbio-annotations-1.0.jar
-compbio-util-1.0.jar
+compbio-util-1.4.jar
+
+source.jar (includes compbio-annotations and compbio-util) depends on
+ 
+Apache log 4j
+DRMAA library
+Servlet 2.5
+
+datamodel source depends on
+
+Apache log 4j
\ No newline at end of file
diff --git a/build.xml b/build.xml
index d30dc9f..4e9dd87 100644
--- a/build.xml
+++ b/build.xml
@@ -8,12 +8,24 @@
 	<!-- Distributive file names-->
 	<property name="distdir" value="website/archive"/>
 	<mkdir dir="${distdir}" />
-	<property name="datamodel" value="${distdir}/datamodel-1.2.jar"/>
-	<property name="datamodel-src" value="${distdir}/datamodel-src-1.2.jar"/>
-	<property name="min-jaba-client" value="${distdir}/min-jaba-client.jar"/>
+	
+	<!-- projects details -->
+	<property name="project.url" value="http://www.compbio.dundee.ac.uk/jabaws"/>
+	<property name="product" value="Java Bioinformatics Analyses Web Services"/>
+	<property name="author" value="Peter Troshin"/>
+	
+	<!-- 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"/>
+	
+	<!-- 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="aacon-ws-client" value="${distdir}/aacon-ws-client.jar"/>
-	<property name="full-jaba-client" value="${distdir}/full-jaba-client.jar"/>
-	<property name="jaba-source-jar" value="${distdir}/jaba-source.jar"/>
+	<property name="full-jaba-client" value="${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"/>
@@ -57,6 +69,7 @@
 		<pathelement location="${classes}" />
 	</path>
 
+
 	<!-- The compilation order is 
 	1. datamodel 
 	2. engine
@@ -154,18 +167,19 @@
 		</delete>
 		<jar jarfile="${basedir}/${datamodel}">
 			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
-				<include name="compbio-util-1.4.jar"/>
+				<include name="${compbio-util}"/>
+				<include name="${compbio-annotation}"/>
 			</zipgroupfileset>
 			<fileset dir="${basedir}/WEB-INF/classes/">
 				<include name="compbio/data/sequence/*.class"/>
 				<include name="compbio/metadata/*.class"/>
 			</fileset>
 			<manifest>
-				<attribute name="Built-By" value="Peter Troshin" />
+				<attribute name="Built-By" value="${author}" />
 				<attribute name="Class-Path" value="." />
-				<attribute name="Implementation-Title" value="Datamodel for Java Bioinformatics Analyses Web Services " />
-				<attribute name="Implementation-Vendor" value="Peter Troshin" />
-				<attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />
+				<attribute name="Implementation-Title" value="Datamodel for ${product} " />
+				<attribute name="Implementation-Vendor" value="${author}" />
+				<attribute name="Implementation-URL" value="${project.url}" />
 			</manifest>
 		</jar>
 	</target>
@@ -183,12 +197,12 @@
 				<include name="compbio/ws/client/**"/>
 			</fileset>
 			<manifest>
-				<attribute name="Built-By" value="Peter Troshin" />
+				<attribute name="Built-By" value="${author}" />
 				<attribute name="Main-Class" value="compbio.ws.client.Jws2Client" />
 				<attribute name="Class-Path" value="." />
-				<attribute name="Implementation-Title" value="Minimal Java Bioinformatics Analyses Web Services Client" />
-				<attribute name="Implementation-Vendor" value="Peter Troshin" />
-				<attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />
+				<attribute name="Implementation-Title" value="Minimal ${product} Client" />
+				<attribute name="Implementation-Vendor" value="${author}" />
+				<attribute name="Implementation-URL" value="${project.url}" />
 			</manifest>
 		</jar>
 	</target>
@@ -205,23 +219,21 @@
 				<include name="compbio/ws/client/**"/>
 			</fileset>
 			<manifest>
-				<attribute name="Built-By" value="Peter Troshin" />
+				<attribute name="Built-By" value="${author}" />
 				<attribute name="Main-Class" value="compbio.ws.client.AAConClient" />
 				<attribute name="Class-Path" value="." />
 				<attribute name="Implementation-Title" value="AACon Client" />
-				<attribute name="Implementation-Vendor" value="Peter Troshin" />
+				<attribute name="Implementation-Vendor" value="${author}" />
 				<attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk/aacon" />
 			</manifest>
 		</jar>
 	</target>
 
-	<target name="source-jar" description="Pack java sources" depends="compile">
+	<target name="source-jar" description="Pack java sources" depends="datamodel-source-jar">
 		<delete file="${basedir}/${jaba-source-jar}">
 		</delete>
 		<jar jarfile="${basedir}/${jaba-source-jar}">
-			<fileset dir="${basedir}/datamodel">
-				<include name="**"/>
-			</fileset>
+			<zipgroupfileset  excludes="META-INF/*.MF" file="${datamodel-src}"/>
 			<fileset dir="${basedir}/runner">
 				<include name="**"/>
 			</fileset>
@@ -232,14 +244,13 @@
 				<include name="**"/>
 			</fileset>
 			<manifest>
-				<attribute name="Built-By" value="Peter Troshin" />
+				<attribute name="Built-By" value="${author}" />
 				<attribute name="Class-Path" value="." />
-				<attribute name="Implementation-Title" value="Java Bioinformatics Analyses Web Services Source Code Archive" />
-				<attribute name="Implementation-Vendor" value="Peter Troshin" />
-				<attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />
+				<attribute name="Implementation-Title" value="${product} Source Code Archive" />
+				<attribute name="Implementation-Vendor" value="${author}" />
+				<attribute name="Implementation-URL" value="${project.url}" />
 			</manifest>
 		</jar>
-
 	</target>
 	
 	<target name="datamodel-source-jar" description="Pack java sources" depends="compile">
@@ -249,11 +260,14 @@
 				<fileset dir="${basedir}/datamodel">
 					<include name="**"/>
 				</fileset>
+				<zipgroupfileset excludes="META-INF/*.MF" dir="${lib.path}/src">
+					<include name="**"/>
+				</zipgroupfileset>
 				<manifest>
-					<attribute name="Built-By" value="Peter Troshin" />
-					<attribute name="Implementation-Title" value="Java Bioinformatics Analyses Web Services Datamodel Source Code Archive" />
-					<attribute name="Implementation-Vendor" value="Peter Troshin" />
-					<attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk/jabaws" />
+					<attribute name="Built-By" value="${author}" />
+					<attribute name="Implementation-Title" value="${product} Datamodel Source Code Archive" />
+					<attribute name="Implementation-Vendor" value="${author}" />
+					<attribute name="Implementation-URL" value="${project.url}" />
 				</manifest>
 			</jar>
 		</target>
@@ -275,17 +289,17 @@
 		<jar jarfile="${full-jaba-client}">
 			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
 				<include name="log4j-1.2.15.jar"/>
-				<include name="compbio-util-1.3.jar"/>
-				<include name="compbio-annotations-1.0.jar"/>
+				<include name="${compbio-util}"/>
+				<include name="${compbio-annotation}"/>
 				<include name="drmaa.jar"/>
 			</zipgroupfileset>
 			<fileset refid="fullclient"/>
 			<manifest>
-				<attribute name="Built-By" value="Peter Troshin" />
+				<attribute name="Built-By" value="${author}" />
 				<attribute name="Class-Path" value="." />
-				<attribute name="Implementation-Title" value="Full Java Bioinformatics Analyses Web Services Client" />
-				<attribute name="Implementation-Vendor" value="Peter Troshin" />
-				<attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />
+				<attribute name="Implementation-Title" value="Full ${product} Client" />
+				<attribute name="Implementation-Vendor" value="${author}" />
+				<attribute name="Implementation-URL" value="${project.url}" />
 			</manifest>
 		</jar>
 	</target>
@@ -308,24 +322,26 @@
 		<jar jarfile="${full-jaba-client}">
 			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
 				<include name="log4j-1.2.15.jar"/>
-				<include name="compbio-util-1.3.jar"/>
-				<include name="compbio-annotations-1.0.jar"/>
+				<include name="${compbio-util}"/>
+				<include name="${compbio-annotation}"/>
 				<include name="drmaa.jar"/>
 			</zipgroupfileset>
 			<fileset refid="fullclient">
 			</fileset>
 			<fileset dir="${basedir}/WEB-INF/classes/">
+				<!-- Statistics web application -->
+				<include name="compbio/stat/**"/>
 				<!-- Web services-->
 				<include name="compbio/ws/**"/>
 			</fileset>
 			<!-- Set WSTester as main to help user to test their deployments -->
 			<manifest>
-				<attribute name="Built-By" value="Peter Troshin" />
+				<attribute name="Built-By" value="${author}" />
 				<attribute name="Class-Path" value="." />
 				<attribute name="Main-Class" value="compbio.ws.client.WSTester" />
-				<attribute name="Implementation-Title" value="Java Bioinformatics Analyses Web Services" />
-				<attribute name="Implementation-Vendor" value="Peter Troshin" />
-				<attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />
+				<attribute name="Implementation-Title" value="${product}" />
+				<attribute name="Implementation-Vendor" value="${author}" />
+				<attribute name="Implementation-URL" value="${project.url}" />
 			</manifest>
 		</jar>
 	</target>
@@ -356,9 +372,8 @@
 		<delete file="${win-binaries}" failonerror="false" />
 		<zip destfile="${win-binaries}">
 			<zipfileset dir="${basedir}/binaries" prefix="binaries" >
-				<include name="clustalw2.exe"/>
-				<include name="muscle.exe"/>
 				<include name="matrices/*" />
+				<include name="windows/*" />
 			</zipfileset>
 		</zip>
 	</target>
@@ -379,7 +394,7 @@
 			<zipfileset dir="${basedir}/ExecutionStatistic" prefix="ExecutionStatistic" />
 			<zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="**/*"/>
 			<zipfileset dir="${basedir}/conf" prefix="conf" excludes="**/log4j.properties*"/>
-			<!-- Add JSW2 web site apart from the binary archive -->
+			<!-- Add JABAWS web site apart from the binary archive -->
 			<zipfileset dir="${basedir}/website" excludes="archive/**, full_javadoc/**, devel*.html, tests/**, template.html"/>
 			<zipfileset dir="." includes="${full-jaba-client}" fullpath="WEB-INF/lib/jaba-client.jar"/>
 			<!-- Put a copy of log4j configuration file where it can be used  -->
@@ -394,7 +409,7 @@
 		<delete file="${jaba-devel-web}">
 		</delete>
 		<zip destfile="${jaba-devel-web}" whenempty="create">
-			<!-- Add JSW2 web site apart from the binary archive -->
+			<!-- Add JABAWS web site apart from the binary archive -->
 			<zipfileset dir="${basedir}/website" excludes="template.html, download.html, index.html, manual.html, howto.html, archive/**, prog_docs/**"/>
 		</zip>
 	</target>
@@ -410,7 +425,7 @@
 	</target>
 
 	<target name="jaba-without-jaxws-windows" description="Prepare JWS2 war file without runtime dependency - JAXWS jars" 
-		depends="full-jaba-jar, pack-windows-binaries">
+		depends="full-jaba-jar, pack-windows-binaries, clearStatDB">
 		<echo>Preparing war file without JAXWS</echo>
 		<delete file="${jaba-windows}">
 		</delete>
@@ -429,7 +444,7 @@
 			<zipfileset dir="${basedir}/conf" prefix="conf" excludes="**/log4j.properties*"/>
 			<zipfileset dir="." includes="${full-jaba-client}" fullpath="WEB-INF/lib/jaba-client.jar"/>
 			<zipfileset dir="conf" includes="log4j.properties" prefix="WEB-INF/classes"/>
-			<!-- Add JSW2 web site apart from the binary archive -->
+			<!-- Add JABAWS web site apart from the binary archive -->
 			<zipfileset dir="${basedir}/website" excludes="archive/**, full_javadoc/**, devel*.html, tests/**, template.html"/>
 		</zip>
 	</target>
@@ -461,7 +476,9 @@
 	</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"/>
+		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"/>
 
 	<!-- 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">
@@ -630,60 +647,5 @@
 		</testNG>
 	</target>
 
-	<!-- <zipfileset excludes="META-INF/*.SF" src="jarfilename.jar"/> 
-		
-		<target name="build-jar" description="Pack cluster  and runners into a jar" depends="compile">
-			<echo>Jar file: integration</echo>
-			<delete file="${basedir}/.jar"></delete>
-			<copy file="${basedir}/conf/" tofile="${classes}/log4j.properties" />
-			<jar jarfile="${basedir}/.jar">
-				<fileset dir="${basedir}/WEB-INF/classes/" includes="compbio/**" />
-				<manifest>
-					<attribute name="Built-By" value="Peter Troshin" />
-					<attribute name="Main-Class" value="compbio.clust..JobStatus" />
-					<attribute name="Class-Path" value=" . /gridware/sge/lib/drmaa.jar" />
-					<attribute name="Implementation-Title" value="Cluster Submission Engine" />
-					<attribute name="Implementation-Vendor" value="Peter Troshin" />
-					<attribute name="Implementation-URL" value="xxx" />
-				</manifest>
-			</jar>
-		</target>
-		
-		
-		<target name="build-jar-local" description="Pack cluster  and runners with dependencies" depends="compile">
-			<echo>Jar file: integration</echo>
-			<delete file="${basedir}/.jar"></delete>
-			<jar jarfile="${basedir}/.jar">
-				<zipgroupfileset excludes="META-INF/*.SF" dir="${lib.path}"></zipgroupfileset>
-				<fileset dir="${basedir}/WEB-INF/classes/" includes="**" />
-				<manifest>
-					<attribute name="Built-By" value="Peter Troshin" />
-					<attribute name="Main-Class" value="compbio..cluster.JobStatus" />
-					<attribute name="Class-Path" value="." />
-					<attribute name="Implementation-Title" value="Cluster Submission Engine" />
-					<attribute name="Implementation-Vendor" value="Peter Troshin" />
-					<attribute name="Implementation-URL" value="xxx" />
-				</manifest>
-			</jar>
-		</target>
-		
-		-->
-
-	<!--
-		<target name="run-client-jar" description="EXAMPLE TASK ONLY">
-			<java jar="${basedir}/resources/wsclient.jar" fork="true"
-				failonerror="true" maxmemory="256m">
-				<arg
-					value="C:/Documents and Settings/pvt43/Desktop/Leeds Sequencing/Copy of Files to up load" />
-			</java>
-		</target>
-		<target name="run-client-class" description="EXAMPLE TASK ONLY">
-			<java classname="org.pimslims.ws.client.FileUploadClient" fork="true"
-				failonerror="true" maxmemory="256m">
-				<classpath refid="project.classpath" />
-				<classpath refid="instrument.classpath" />
-			</java>
-		</target>
-	-->
 
 </project>
\ No newline at end of file
-- 
1.7.10.2