X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=04f80a4a2fdfcf93204f752be427bb07fd14a7af;hb=14c406769ac5cd4acfbc4819bb3dc967a51e4bb6;hp=208fcbf2c27a9d69e5d02490051e23e170b011c5;hpb=5a05ba47cfe2ecc186fa78f00ac29b2680d36aeb;p=jabaws.git

diff --git a/build.xml b/build.xml
index 208fcbf..04f80a4 100644
--- a/build.xml
+++ b/build.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<project default="minimal-jaba-client-jar" name="Build minimal client for Java Bioinformatics Analysis Web Services" basedir=".">
+<project default="jabaws" name="Build Java Bioinformatics Analysis Web Services" basedir=".">
 
 	<property name="basedir" location="${basedir}/log" />
 	<property name="LD_LIBRARY_PATH" value="/gridware/sge/lib/lx24-amd64"/>
@@ -17,9 +17,10 @@
 	<!-- 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="jaba_version" value="2.1"/>
 	<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"/>
@@ -29,7 +30,7 @@
 	<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="${distdir}/full-jaba-client-pack.zip"/>
-	<property name="jaba" value="${distdir}/jaba.war"/>
+	<property name="jaba" value="${distdir}/jabaws.war"/>
 	<!-- TODO  
 	<property name="jaba-dundee" value="${distdir}/jaba-dundee.war"/>
 	 -->
@@ -40,7 +41,6 @@
 	<!--Whole project archive -->
 	<property name="jaba-project" value="${distdir}/jaba-project.zip"/>
 
-
 	<!-- java -->
 	<property name="test.src" location="${basedir}/testsrc" />
 	<property name="classes" location="${basedir}/WEB-INF/classes" />
@@ -59,7 +59,6 @@
 		</fileset>
 	</path>
 
-
 	<!-- add test classes -->
 	<path id="test.classpath">
 		<fileset dir="${test.lib.path}">
@@ -68,8 +67,47 @@
 		<pathelement location="${classes}" />
 	</path>
 
+	<fileset dir="${basedir}/WEB-INF/classes/" id="fullclient">
+		<!-- Datamodel -->
+		<include name="compbio/data/**"/>
+		<include name="compbio/metadata/**"/>
+		<!-- Engines -->
+		<include name="compbio/engine/**"/>
+		<!-- Runners -->
+		<include name="compbio/runner/**"/>
+		<!-- Logging configuration -->
+	</fileset>
+
+	<!-- Clean temp directories -->
+	<target name="clean">
+		<delete dir="${classes}" />
+		<delete file="${distdir}/binaries.zip" />
+		<delete file="${basedir}/activity.log" />
+		<delete file="${basedir}/derby.log" />
+		<mkdir dir="${classes}" />
+		<copy file="${basedir}/conf/log4j.properties" tofile="${classes}/log4j.properties" />
+	</target>
+
+	<!-- Clean up temp directories and dist directory (all jar, zip, and war files deleted) -->
+	<target name="full-clean" depends="clean">
+		<delete>
+			<fileset dir="${distdir}">
+				<include name="*.jar"/>
+				<include name="*.zip"/>
+				<include name="*.war"/>
+			</fileset>
+		</delete>
+	</target>
+
+	<target name="clearStatDB" description="Remove all records from statistics database">
+		<echo>Cleaning Statistics database</echo>
+		<java classname="compbio.stat.collector.StatDB" fork="false" failonerror="true" classpath="${classes}">
+		<classpath refid="project.classpath" />
+		</java>
+	</target>
 
-	<!-- The compilation order is 
+	<!--
+	The compilation order is 
 	1. datamodel 
 	2. engine
 	3. runner
@@ -77,7 +115,7 @@
 	5. webservices
 	Packages of the lower order could not have dependencies on the packages on the next layer. 
 	So runners (layer 3) depends on the engines and the datamodel but engines does not depend on 
-	anything in runners or any other layers above. Testscr is not allowed to test webservices. 
+	anything in runners or any other layers above. Testsrc is not allowed to test webservices. 
 	-->
 	<target name="compile_with_debug" depends="clean" description="Perform a multiple step compilation to ensure layered structure is preserved. Debug enabled.">
 		<!-- copy files to class path-->
@@ -115,22 +153,16 @@
 		</javac>
 	</target>
 
-	<!-- Clean temp directories -->
-	<target name="clean">
-		<delete dir="${classes}" />
-		<mkdir dir="${classes}" />
-	</target>
-
 	<!--
-	Compile with optimisation. Do not compile testsrc 
+	Compile with optimisation. Do not compile testsrc
 	The compilation order is 
 	1. datamodel 
 	2. engine
 	3. runner
 	4. webservices
 	Packages of the lower order could not have dependencies on the packages on the next layer. 
-	So runners (layer 3) depends on the engines and the datamodel but engines does not depend on 
-	anything in runners or any other layers above.  
+	So runners (layer 3) depends on the engines and the datamodel but engines does not depend 
+	on anything in runners or any other layers above.
 	-->
 	<target name="compile" depends="clean" description="Perform a multiple step compilation to ensure layered structure is preserved. Debug disabled, optimisation enabled. Tests are not compiled.">
 		<!-- copy files to class path-->
@@ -156,11 +188,9 @@
 			<compilerarg value="-Xlint:-unchecked" />
 			<classpath refid="project.classpath" />
 		</javac>
-
 	</target>
 
-
-	<target name="datamodel-jar" description="Pack data model classes" depends="compile">
+	<target name="datamodel-jar" depends="compile" description="Pack data model classes">
 		<echo>Jar file: Minimal WS client jar</echo>
 		<delete file="${basedir}/${datamodel}">
 		</delete>
@@ -183,29 +213,29 @@
 		</jar>
 	</target>
 
-	<target name="jaba-client-src-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class" depends="datamodel-source-jar">
+	<target name="jaba-client-src-jar" depends="datamodel-source-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class">
 		<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>
+			<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="${project.url}" />
+			</manifest>
+		</jar>
 	</target>
-	
-	<target name="minimal-jaba-client-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class" depends="compile, datamodel-jar">
+
+	<target name="minimal-jaba-client-jar" depends="compile, datamodel-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class">
 		<echo>Jar file: Minimal WS client jar</echo>
 		<delete file="${basedir}/${min-jaba-client}">
 		</delete>
@@ -216,6 +246,7 @@
 				<include name="compbio/data/msa/**"/>
 				<include name="compbio/ws/client/**"/>
 			</fileset>
+			<zipgroupfileset excludes="META-INF/*" dir="" includes="WEB-INF/lib/log4j-1.2.15.jar" />
 			<manifest>
 				<attribute name="Built-By" value="${author}" />
 				<attribute name="Main-Class" value="compbio.ws.client.Jws2Client" />
@@ -227,7 +258,28 @@
 		</jar>
 	</target>
 
-	<target name="aacon-ws-client-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class" depends="compile, datamodel-jar">
+	<target name="full-jaba-client-jar" depends="compile" description="Pack datamodel, engine and runners">
+		<echo>Jar file: Full WS client jar</echo>
+		<delete file="${full-jaba-client}">
+		</delete>
+		<jar jarfile="${full-jaba-client}">
+			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
+				<include name="${compbio-util}"/>
+				<include name="${compbio-annotation}"/>
+				<include name="drmaa.jar"/>
+			</zipgroupfileset>
+			<fileset refid="fullclient"/>
+			<manifest>
+				<attribute name="Built-By" value="${author}" />
+				<attribute name="Class-Path" value="." />
+				<attribute name="Implementation-Title" value="Full ${product} Client" />
+				<attribute name="Implementation-Vendor" value="${author}" />
+				<attribute name="Implementation-URL" value="${project.url}" />
+			</manifest>
+		</jar>
+	</target>
+
+	<target name="aacon-ws-client-jar" depends="compile, datamodel-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class">
 		<echo>Jar file: AAConWS client jar</echo>
 		<delete file="${basedir}/${aacon-ws-client}">
 		</delete>
@@ -249,7 +301,19 @@
 		</jar>
 	</target>
 
-	<target name="source-jar" description="Pack java sources" depends="datamodel-source-jar">
+	<target name="full-jaba-client" depends="full-jaba-client-jar, pack-binaries" description="Pack binaries with sources and configuration files">
+		<echo>Packing binaries, and configuration files</echo>
+		<zip destfile="${full-jaba-client-pack}" >
+			<zipgroupfileset file="${binaries}" />
+			<zipfileset dir="conf" prefix="conf" >
+				<exclude name="**/temp/**"/>
+			</zipfileset>
+			<fileset file="${full-jaba-client}" />
+		</zip>
+	</target>
+
+
+	<target name="source-jar" depends="datamodel-source-jar" description="Pack java sources">
 		<delete file="${basedir}/${jaba-source-jar}">
 		</delete>
 		<jar jarfile="${basedir}/${jaba-source-jar}">
@@ -272,72 +336,27 @@
 			</manifest>
 		</jar>
 	</target>
-	
-	<target name="datamodel-source-jar" description="Pack java sources" depends="compile">
-			<delete file="${datamodel-src}">
-			</delete>
-			<jar jarfile="${datamodel-src}">
-				<fileset dir="${basedir}/datamodel">
-					<include name="**"/>
-				</fileset>
-				<zipgroupfileset excludes="META-INF/*.MF" dir="${lib.path}/src">
-					<include name="**"/>
-				</zipgroupfileset>
-				<manifest>
-					<attribute name="Built-By" value="${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>
 
-	<fileset dir="${basedir}/WEB-INF/classes/" id="fullclient">
-		<!-- Datamodel -->
-		<include name="compbio/data/**"/>
-		<include name="compbio/metadata/**"/>
-		<!-- Engines -->
-		<include name="compbio/engine/**"/>
-		<!-- Runners -->
-		<include name="compbio/runner/**"/>
-	</fileset>
-
-	<target name="full-jaba-client-jar" description="Pack datamodel, engine and runners" depends="compile">
-		<echo>Jar file: Full WS client jar</echo>
-		<delete file="${full-jaba-client}">
+	<target name="datamodel-source-jar" depends="compile" description="Pack java sources">
+		<delete file="${datamodel-src}">
 		</delete>
-		<jar jarfile="${full-jaba-client}">
-			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
-				<include name="log4j-1.2.15.jar"/>
-				<include name="${compbio-util}"/>
-				<include name="${compbio-annotation}"/>
-				<include name="drmaa.jar"/>
+		<jar jarfile="${datamodel-src}">
+			<fileset dir="${basedir}/datamodel">
+				<include name="**"/>
+			</fileset>
+			<zipgroupfileset excludes="META-INF/*.MF" dir="${lib.path}/src">
+				<include name="**"/>
 			</zipgroupfileset>
-			<fileset refid="fullclient"/>
 			<manifest>
 				<attribute name="Built-By" value="${author}" />
-				<attribute name="Class-Path" value="." />
-				<attribute name="Implementation-Title" value="Full ${product} Client" />
+				<attribute name="Implementation-Title" value="${product} Datamodel Source Code Archive" />
 				<attribute name="Implementation-Vendor" value="${author}" />
 				<attribute name="Implementation-URL" value="${project.url}" />
 			</manifest>
 		</jar>
 	</target>
 
-	<target name="full-jaba-client" description="Pack binaries with sources and configuration files" 
-			depends="full-jaba-client-jar, pack-binaries">
-		<echo>Packing binaries, and configuration files</echo>
-		<zip destfile="${full-jaba-client-pack}" >
-			<zipgroupfileset file="${binaries}" />
-			<zipfileset dir="conf" prefix="conf" >
-				<exclude name="**/temp/**"/>
-			</zipfileset>
-			<fileset file="${full-jaba-client}" />
-		</zip>
-	</target>
-
-	
-	<target name="full-jaba-jar" description="Pack datamodel, engine, runners, configuration, binaries and webservices" depends="compile">
+	<target name="full-jaba-jar" depends="compile" description="Pack datamodel, engine, runners, configuration, binaries and webservices">
 		<echo>Jar file: Full WS client jar</echo>
 		<delete file="${full-jaba-client}">
 		</delete>
@@ -368,13 +387,6 @@
 		</jar>
 	</target>
 
-	<target name="clearStatDB" description="Remove all records from statistics database">
-		 <echo>Cleaning Statistics database</echo>
-		 <java classname="compbio.stat.collector.StatDB" fork="false" failonerror="true" classpath="${classes}">
-	            <classpath refid="project.classpath" />
-	     </java>
-	</target>
-	
 	<target name="pack-binaries" description="Zip all binary files">
 		<delete file="${binaries}" failonerror="false"/>
 		<zip destfile="${binaries}" >
@@ -382,19 +394,7 @@
 		</zip>
 	</target>
 
-<!-- DEPRICATED 
-	<target name="pack-windows-binaries" description="Zip only windows binary files">
-		<delete file="${win-binaries}" failonerror="false" />
-		<zip destfile="${win-binaries}">
-			<zipfileset dir="${basedir}/binaries" prefix="binaries" >
-				<include name="matrices/*" />
-				<include name="windows/*" />
-			</zipfileset>
-		</zip>
-	</target>
--->
-
-	<target name="jaba-no-binaries" description="Prepare JABAWS war file without native binaries" depends="full-jaba-jar,  clearStatDB">
+	<target name="jaba-no-binaries" depends="full-jaba-jar, clearStatDB" description="Prepare JABAWS war file without native binaries">
 		<echo>Preparing a war file without binaries</echo>
 		<delete file="${jaba-no-binaries}">
 		</delete>
@@ -436,7 +436,7 @@
 		</zip>
 	</target>
 
-	<target name="jaba-complete" description="Prepare JABAWS war file without runtime dependency - JAXWS jars" depends="jaba-no-binaries, pack-binaries">
+	<target name="jaba-complete" depends="jaba-no-binaries, pack-binaries" description="Prepare JABAWS war file without runtime dependency - JAXWS jars">
 		<echo>Preparing a complete war file</echo>
 		<delete file="${jaba}">
 		</delete>
@@ -446,20 +446,7 @@
 		</zip>
 	</target>
 
-<!-- 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-binaries}"/>
-		<zip destfile="${jaba-windows}" update="true" >
-			<zipgroupfileset file="${win-binaries}" />
-		</zip>
-	</target>
--->
- 
-	<target name="build-all" description="Build-all the distributives"
-		depends="full-jaba-client, minimal-jaba-client-jar, jaba-no-binaries,
-		 jaba-complete, datamodel-jar, datamodel-source-jar, source-jar, jaba-client-src-jar"/>
+	<target name="build-all" depends="full-jaba-client, minimal-jaba-client-jar, jaba-no-binaries, jaba-complete, datamodel-jar, datamodel-source-jar, source-jar, jaba-client-src-jar" description="Build-all the distributives"/>
 
 	<!-- 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">
@@ -472,7 +459,7 @@
 		</zip>
 	</target>
 
-
+<!-- Test targets -->
 	<taskdef name="testNG" classname="org.testng.TestNGAntTask">
 		<classpath refid="test.classpath">
 		</classpath>
@@ -610,6 +597,4 @@
 			<sysproperty key="TestingDataPath" value="${data.src}"/>
 		</testNG>
 	</target>
-
-
-</project>
\ No newline at end of file
+</project>