From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Tue, 19 Nov 2013 15:28:58 +0000 (+0000)
Subject: PROT-6 A first working, but not tested ant-based build system prepared
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=808275f7712732177ad1973ef3be7d0ec46ccd88;p=proteocache.git

PROT-6 A first working, but not tested ant-based build system prepared
---

diff --git a/.classpath b/.classpath
index e01f61b..38a76ef 100644
--- a/.classpath
+++ b/.classpath
@@ -4,7 +4,6 @@
 	<classpathentry kind="src" path="engine"/>
 	<classpathentry kind="src" path="server"/>
 	<classpathentry excluding="testdata/" kind="src" path="testsrc"/>
-	<classpathentry kind="lib" path="testsrc/lib/testng-5.10-jdk15.jar"/>
 	<classpathentry kind="lib" path="WEB-INF/lib/log4j-1.2.16.jar"/>
 	<classpathentry kind="lib" path="WEB-INF/lib/cassandra-driver-core-2.0.0-beta3-SNAPSHOT.jar" sourcepath="WEB-INF/lib/cassandra-driver-core-2.0.0-beta3-SNAPSHOT-sources.jar"/>
 	<classpathentry kind="lib" path="WEB-INF/lib/lz4-1.2.0.jar"/>
@@ -17,13 +16,14 @@
 	<classpathentry kind="lib" path="WEB-INF/lib/displaytag-1.2.jar"/>
 	<classpathentry kind="lib" path="WEB-INF/lib/jabaws-core-2.1.0.jar" sourcepath="WEB-INF/lib/jabaws-core-src-2.1.0.jar"/>
 	<classpathentry kind="lib" path="WEB-INF/lib/jstl-1.2.jar"/>
+	<classpathentry kind="lib" path="WEB-INF/lib/jcommon-1.0.20.jar"/>
+	<classpathentry kind="lib" path="WEB-INF/lib/jfreechart-1.0.16.jar"/>
+	<classpathentry kind="lib" path="testsrc/lib/testng-6.8.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jst.server.core.container/org.eclipse.jst.server.tomcat.runtimeTarget/Apache Tomcat v7.0">
 		<attributes>
 			<attribute name="owner.project.facets" value="jst.web"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jdk1.7.0_45"/>
-	<classpathentry kind="lib" path="/home/natasha/workspace/proteocache/jfreechart-1.0.16/lib/jfreechart-1.0.16.jar"/>
-	<classpathentry kind="lib" path="/home/natasha/workspace/proteocache/jfreechart-1.0.16/lib/jcommon-1.0.20.jar"/>
 	<classpathentry kind="output" path="WEB-INF/classes"/>
 </classpath>
diff --git a/.gitignore b/.gitignore
index 01f344e..26664ec 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,5 +2,5 @@
 /testsrc/testdata/*.written
 /testsrc/testdata/alirna.ps
 /WEB-INF/classes/
-
+/distribution/
 
diff --git a/build.xml b/build.xml
index 50bdbac..e381cfc 100644
--- a/build.xml
+++ b/build.xml
@@ -1,94 +1,52 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<project default="proteocache" name="Build ProteoCache - Results repository for the Dundee Resource" basedir=".">
-
-	<property name="LD_LIBRARY_PATH" value="/gridware/sge/lib/lx24-amd64"/>
-
-	<!-- Distributive file names-->
-	<property name="distdir" value="distro"/>
-	<mkdir dir="${distdir}" />
+<project default="proteocache" name="Build ProteoCache - Caching framework for the Dundee Resource" basedir=".">
 
 	<!-- projects details -->
+	<property name="proteocache_version" value="0.1.0"/>
 	<property name="project.url" value="http://www.compbio.dundee.ac.uk/proteocache"/>
 	<property name="product" value="ProteoCache"/>
 	<property name="author" value="Alexander Sherstnev"/>
-
-	<!-- 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"/>
-
+	<!-- Distributive file names-->
+	<property name="distdir" value="distribution"/>
+	<mkdir dir="${distdir}" />
 	<!-- products -->
-	<property name="proteocache_version" value="2.1.0"/>
-	<property name="datamodel" value="${distdir}/datamodel-${proteocache_version}.jar"/>
-	<property name="datamodel-src" value="${distdir}/datamodel-src-${proteocache_version}.jar"/>
-	<property name="min-proteocache-client" value="${distdir}/min-proteocache-client-${proteocache_version}.jar"/>
-	<property name="min-proteocache-client-nolog" value="${distdir}/min-proteocache-client-nolog-${proteocache_version}.jar"/>
-	<property name="proteocache-client-src" value="${distdir}/proteocache-client-src-${proteocache_version}.jar"/>
-	<property name="aacon-ws-client" value="${distdir}/aacon-ws-client.jar"/>
-	<property name="full-proteocache-client" value="${distdir}/full-proteocache-client-${proteocache_version}.jar"/>
+	<property name="proteocache-war" value="${distdir}/proteocache-${proteocache_version}.war"/>
+	<property name="proteocache-jar" value="${distdir}/proteocache-${proteocache_version}.jar"/>
 	<property name="proteocache-source-jar" value="${distdir}/proteocache-src-${proteocache_version}.jar"/>
-	<property name="full-proteocache-client-pack" value="${distdir}/full-proteocache-client-${proteocache_version}-pack.zip"/>
-	<property name="proteocache" value="${distdir}/proteocache.war"/>
-	<!-- TODO 
-	<property name="proteocache-dundee" value="${distdir}/proteocache-dundee.war"/>
-	-->
-	<property name="proteocache-no-binaries" value="${distdir}/proteocache-no-binaries.war"/>
-	<property name="binaries" value="${distdir}/binaries.zip"/>
-	<property name="proteocache-devel-web" value="${distdir}/proteocache-devel-website.zip"/>
-
-	<!--Whole project archive -->
 	<property name="proteocache-project" value="${distdir}/proteocache-project.zip"/>
-
 	<!-- java -->
-	<property name="test.src" location="${basedir}/testsrc" />
 	<property name="classes" location="${basedir}/WEB-INF/classes" />
-	<property name="lib.path" location="${basedir}/lib" />
+	<property name="ext.lib.path" location="${basedir}/lib" />
 	<property name="web.lib.path" location="${basedir}/WEB-INF/lib" />
-	<property name="test.lib.path" location="${basedir}/testsrc/lib" />
-	<property name="activity.log" location="${basedir}/activity.log" />
 
-	<!-- add libraries -->
+	<!-- add external and internal libraries -->
 	<path id="project.classpath">
-		<fileset dir="${lib.path}">
-			<include name="*.jar" />
-		</fileset>
 		<fileset dir="${web.lib.path}">
 			<include name="*.jar" />
 		</fileset>
-	</path>
-
-	<!-- add test classes -->
-	<path id="test.classpath">
-		<fileset dir="${test.lib.path}">
+		<fileset dir="${ext.lib.path}">
 			<include name="*.jar" />
 		</fileset>
-		<pathelement location="${classes}" />
 	</path>
 
-	<fileset dir="${basedir}/WEB-INF/classes/" id="fullclient">
-		<!-- Datamodel -->
-		<include name="compbio/data/**"/>
-		<include name="compbio/metadata/**"/>
-		<!-- Engine -->
+	<fileset dir="${basedir}/WEB-INF/classes/" id="allcodes">
+		<include name="compbio/datadb/**"/>
 		<include name="compbio/engine/**"/>
-		<!-- Casscode -->
-		<include name="compbio/casscode/**"/>
-		<!-- Logging configuration -->
+		<include name="compbio/server/**"/>
 	</fileset>
 
+<!-- ###################################################################################################################################### -->
+<!-- Main targets -->
+
 	<!-- Clean temp directories -->
 	<target name="clean">
 		<delete dir="${classes}" />
-		<delete dir="${basedir}/logs" />
-		<delete file="${distdir}/binaries.zip" />
-		<delete file="${basedir}/activity.log" />
-		<delete file="${basedir}/derby.log" />
 		<mkdir dir="${classes}" />
 		<copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
 	</target>
 
-	<!-- Clean up temp directories and dist directory (all jar, zip, and war files deleted) -->
+	<!-- Clean up temporary directories and dist directory (all jar, zip, and war files deleted) -->
 	<target name="full-clean" depends="clean">
 		<delete>
 			<fileset dir="${distdir}">
@@ -99,205 +57,44 @@
 		</delete>
 	</target>
 
-	<target name="clearStatDB" description="Remove all records from statistics database">
-		<echo>Cleaning Statistics database</echo>
-		<java classname="compbio.stat.collector.StatDB" fork="true" failonerror="true" classpath="${classes}">
-			<jvmarg value="-Dlog4j.configuration=file:log/log4j.properties.statdb" />
-			<classpath refid="project.classpath" />
-		</java>
-	</target>
-
 	<!--
-	The compilation order is 
-	1. datamodel 
-	2. engine
-	3. casscode
-	4. testscr
-	5. webservices
-	Packages of the lower order could not have dependencies on the packages on the next layer. 
-	So, casscode (layer 3) depends on the enginesand the datamodel but engine does not depend on 
-	anything in casscode or any other layers above. Testsrc is not allowed to test webservices. 
+	Compile with optimisation. testsrc is not compiled
+	Packages of the lower order should not have dependencies on the packages 
+	on the next layer. So datadb (layer 3) depends on the engine classes but 
+	engine does not depend on anything in datadb
 	-->
-	<target name="compile_with_debug" depends="clean" description="Perform a multiple step compilation to ensure layered structure is preserved. Debug enabled.">
+	<target name="compile" depends="clean" description="Multiple step compilation to ensure layered structure is preserved. Debug disabled, optimisation enabled.">
 		<!-- copy files to class path-->
 		<copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
-		<!-- Complile the datamodel first -->
-		<javac srcdir="${basedir}/datamodel" destdir="${classes}" target="1.6"
-				source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
-			<compilerarg value="-Xlint:unchecked"/>
-			<classpath refid="project.classpath" />
-		</javac>
-		<!-- Complile the engines -->
-		<javac srcdir="${basedir}/engine" destdir="${classes}" target="1.6"
-				source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
-			<compilerarg value="-Xlint:unchecked"/>
-			<classpath refid="project.classpath" />
-		</javac>
-		<!-- Complile the casscode -->
-		<javac srcdir="${basedir}/casscode" destdir="${classes}" target="1.6"
-				source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
-			<compilerarg value="-Xlint:unchecked"/>
-			<classpath refid="project.classpath" />
-		</javac>
-		<!-- Complile the webservices -->
-		<javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6"
-				source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
-			<compilerarg value="-Xlint:unchecked"/>
-			<classpath refid="project.classpath" />
-		</javac>
-		<!-- Complile the tests -->
-		<javac srcdir="${basedir}/testsrc" destdir="${classes}" target="1.6"
-				source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
-			<compilerarg value="-Xlint:unchecked"/>
-			<classpath refid="project.classpath" />
-			<classpath refid="test.classpath" />
-		</javac>
-	</target>
-
-	<!--
-	Compile with optimisation. Do not compile testsrc
-	The compilation order is 
-	1. datamodel 
-	2. engine
-	3. casscode
-	4. webservices
-	Packages of the lower order could not have dependencies on the packages on the next layer. 
-	So casscode (layer 3) depends on the engine and the datamodel but engine does not depend 
-	on anything in casscode or any other layers above.
-	-->
-	<target name="compile" depends="clean" description="Perform a multiple step compilation to ensure layered structure is preserved. Debug disabled, optimisation enabled. Tests are not compiled.">
-		<!-- copy files to class path-->
-		<copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
-		<!-- Complile the datamodel -->
-		<javac srcdir="${basedir}/datamodel" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
+		<!-- Complile engine -->
+		<javac srcdir="${basedir}/engine" destdir="${classes}" target="1.7" source="1.7" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
 			<compilerarg value="-Xlint:-unchecked" />
 			<classpath refid="project.classpath" />
 		</javac>
-		<!-- Complile the engine -->
-		<javac srcdir="${basedir}/engine" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
-			<compilerarg value="-Xlint:-all" />
+		<!-- Complile database code -->
+		<javac srcdir="${basedir}/datadb" destdir="${classes}" target="1.7" source="1.7" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
+			<compilerarg value="-Xlint:all" />
 			<compilerarg value="-Xlint:-unchecked" />
 			<classpath refid="project.classpath" />
 		</javac>
-		<!-- Complile the casscode -->
-		<javac srcdir="${basedir}/casscode" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
+		<!-- Complile the server -->
+		<javac srcdir="${basedir}/server" destdir="${classes}" target="1.7" source="1.7" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
 			<compilerarg value="-Xlint:-unchecked" />
 			<classpath refid="project.classpath" />
 		</javac>
-		<!-- Complile the webservices -->
-		<javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
-			<compilerarg value="-Xlint:-unchecked" />
-			<classpath refid="project.classpath" />
-		</javac>
-	</target>
-
-	<target name="datamodel-jar" depends="compile" description="Pack data model classes">
-		<echo>Jar file: Minimal WS client jar</echo>
-		<delete file="${basedir}/${datamodel}">
-		</delete>
-		<jar jarfile="${basedir}/${datamodel}">
-			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
-				<include name="${compbio-util}"/>
-				<include name="${compbio-annotation}"/>
-			</zipgroupfileset>
-			<fileset dir="${basedir}/WEB-INF/classes/">
-				<include name="compbio/data/sequence/*.class"/>
-				<include name="compbio/metadata/*.class"/>
-			</fileset>
-			<manifest>
-				<attribute name="Built-By" value="${author}" />
-				<attribute name="Class-Path" value="." />
-				<attribute name="Implementation-Title" value="Datamodel for ${product} " />
-				<attribute name="Implementation-Vendor" value="${author}" />
-				<attribute name="Implementation-URL" value="${project.url}" />
-			</manifest>
-		</jar>
-	</target>
-
-	<target name="minimal-proteocache-client-jar" depends="compile, datamodel-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class">
-		<echo>Jar file: Minimal WS client jar</echo>
-		<delete file="${basedir}/${min-proteocache-client}"></delete>
-		<jar jarfile="${basedir}/${min-proteocache-client}">
-			<zipgroupfileset excludes="META-INF/*.SF" dir="" includes="${datamodel}" />
-			<fileset dir="${basedir}/WEB-INF/classes/">
-				<!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->
-				<include name="compbio/data/msa/**"/>
-				<include name="compbio/ws/client/**"/>
-			</fileset>
-			<zipgroupfileset excludes="META-INF/*" dir="" includes="WEB-INF/lib/log4j-1.2.15.jar" />
-			<manifest>
-				<attribute name="Built-By" value="${author}" />
-				<attribute name="Main-Class" value="compbio.ws.client.Jws2Client" />
-				<attribute name="Class-Path" value="." />
-				<attribute name="Implementation-Title" value="Minimal ${product} Client" />
-				<attribute name="Implementation-Vendor" value="${author}" />
-				<attribute name="Implementation-URL" value="${project.url}" />
-			</manifest>
-		</jar>
-		<delete file="${basedir}/${min-proteocache-client-nolog}"></delete>
-		<jar jarfile="${basedir}/${min-proteocache-client-nolog}">
-			<zipgroupfileset excludes="META-INF/*.SF" dir="" includes="${datamodel}" />
-			<fileset dir="${basedir}/WEB-INF/classes/">
-				<!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->
-				<include name="compbio/data/msa/**"/>
-				<include name="compbio/ws/client/**"/>
-			</fileset>
-			<manifest>
-				<attribute name="Built-By" value="${author}" />
-				<attribute name="Main-Class" value="compbio.ws.client.Jws2Client" />
-				<attribute name="Class-Path" value="." />
-				<attribute name="Implementation-Title" value="Minimal ${product} Client" />
-				<attribute name="Implementation-Vendor" value="${author}" />
-				<attribute name="Implementation-URL" value="${project.url}" />
-			</manifest>
-		</jar>
 	</target>
 
-	<target name="full-proteocache-client-jar" depends="compile" description="Pack datamodel, engine and casscode">
-		<echo>Jar file: Full ProteoCache client jar</echo>
-		<delete file="${full-proteocache-client}">
+	<target name="source-jar" description="Pack java sources">
+		<delete file="${proteocache-source-jar}">
 		</delete>
-		<jar jarfile="${full-proteocache-client}">
-			<zipgroupfileset excludes="META-INF/*.SF" dir="${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="${project.url}" />
-			</manifest>
-		</jar>
-	</target>
-
-	<target name="full-proteocache-client" depends="full-proteocache-client-jar" description="Pack sources and configuration files">
-		<echo>Packing binaries, and configuration files</echo>
-		<zip destfile="${full-proteocache-client-pack}" >
-			<zipgroupfileset file="${binaries}" />
-			<zipfileset dir="conf" prefix="conf" >
-				<exclude name="**/temp/**"/>
-			</zipfileset>
-			<fileset file="${full-proteocache-client}" />
-		</zip>
-	</target>
-
-
-	<target name="source-jar" depends="datamodel-source-jar" description="Pack java sources">
-		<delete file="${basedir}/${proteocache-source-jar}">
-		</delete>
-		<jar jarfile="${basedir}/${proteocache-source-jar}">
-			<zipgroupfileset  excludes="META-INF/*.MF" file="${datamodel-src}"/>
-			<fileset dir="${basedir}/casscode">
+		<jar jarfile="${proteocache-source-jar}">
+			<fileset dir="${basedir}/datadb">
 				<include name="**"/>
 			</fileset>
 			<fileset dir="${basedir}/engine">
 				<include name="**"/>
 			</fileset>
-			<fileset dir="${basedir}/webservices/">
+			<fileset dir="${basedir}/server/">
 				<include name="**"/>
 			</fileset>
 			<manifest>
@@ -310,49 +107,18 @@
 		</jar>
 	</target>
 
-	<target name="datamodel-source-jar" depends="compile" description="Pack java sources">
-		<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>
-
-	<target name="full-proteocache-jar" depends="compile" description="Pack datamodel, engine, casscode, configuration, binaries and webservices">
-		<echo>Jar file: Full WS client jar</echo>
-		<delete file="${full-proteocache-client}">
-		</delete>
-		<jar jarfile="${full-proteocache-client}">
-			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
-				<include name="log4j-1.2.15.jar"/>
-				<include name="${compbio-util}"/>
-				<include name="${compbio-annotation}"/>
-				<include name="drmaa.jar"/>
-			</zipgroupfileset>
-			<fileset refid="fullclient">
-			</fileset>
-			<fileset dir="${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 -->
+	<target name="build-proteocache-jar" depends="compile" description="Pack all compiled codes, configuration, ...">
+		<echo>Build full jar</echo>
+		<delete file="${proteocache-jar}"></delete>
+		<jar jarfile="${proteocache-jar}">
+			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" ></zipgroupfileset>
+			<fileset refid="allcodes"></fileset>
+			<fileset dir="${basedir}/WEB-INF/classes/"></fileset>
+			<!-- Set compbio.server.MainTester as main to help user to test their deployments -->
 			<manifest>
 				<attribute name="Built-By" value="${author}" />
 				<attribute name="Class-Path" value="." />
-				<attribute name="Main-Class" value="compbio.ws.client.WSTester" />
+				<attribute name="Main-Class" value="compbio.server.MainTester" />
 				<attribute name="Implementation-Title" value="${product}" />
 				<attribute name="Implementation-Vendor" value="${author}" />
 				<attribute name="Implementation-URL" value="${project.url}" />
@@ -360,71 +126,78 @@
 		</jar>
 	</target>
 
-	<target name="proteocache-no-binaries" depends="full-proteocache-jar, clearStatDB" description="Prepare proteocache war file without native binaries">
-		<echo>Preparing a war file without binaries</echo>
-		<delete file="${proteocache-no-binaries}">
-		</delete>
-		<zip destfile="${proteocache-no-binaries}" whenempty="create">
+	<target name="proteocache-server" depends="build-proteocache-jar" description="Prepare ProteoCache war file">
+		<echo>Prepare ProteoCache war file</echo>
+		<delete file="${proteocache-war}"></delete>
+		<zip destfile="${proteocache-war}" 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/${compbio-util}"/>
-				
 				<include name="web.xml"/>
-				<include name="sun-jaxws.xml"/>
 				<include name="lib/*"/>
 			</zipfileset>
-			<zipfileset dir="${basedir}/ExecutionStatistic" prefix="ExecutionStatistic" />
-			<zipfileset dir="${basedir}/statpages" prefix="statpages" />
-			<zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="**/*"/>
-			<zipfileset dir="conf" prefix="conf" >
-				<exclude name="**/temp/**"/>
-			</zipfileset>
-			<!-- Add proteocache web site apart from the binary archive -->
-			<zipfileset dir="${basedir}/website" excludes="archive/**, devel*.html, tests/**, template.html"/>
-			<zipfileset dir="." includes="${full-proteocache-client}" fullpath="WEB-INF/lib/proteocache-client.jar"/>
+			<zipfileset dir="conf" prefix="conf" />
+			<!-- Add ProteoCache static web site pages apart from the binary archive -->
+			<zipfileset dir="${basedir}/website" excludes="tests/**, template.html"/>
 			<!-- Put a copy of log4j configuration file where it can be used  -->
 			<zipfileset dir="log" includes="log4j.properties" prefix="WEB-INF/classes"/>
 		</zip>
 	</target>
 
-	<target name="build-devel-website" description="Pack developement related pages, tests, javadoc" >
-		<echo>Packing data for internal web site</echo>
-		<delete file="${proteocache-devel-web}">
-		</delete>
-		<zip destfile="${proteocache-devel-web}" whenempty="create">
-			<!-- Add proteocache web site apart from the binary archive -->
-			<zipfileset dir="${basedir}/website" excludes="template.html, download.html, index.html, manual.html, howto.html, archive/**, prog_docs/**"/>
-		</zip>
-	</target>
-
-	<target name="proteocache-complete" depends="proteocache-no-binaries" description="Prepare proteocache war file without runtime dependency - JAXWS jars">
-		<echo>Preparing a complete war file</echo>
-		<delete file="${proteocache}">
-		</delete>
-		<copy tofile="${proteocache}" file="${proteocache-no-binaries}"/>
-		<zip destfile="${proteocache}" update="true" >
-			<zipgroupfileset file="${binaries}" />
-		</zip>
-	</target>
-
-	<target name="build-all" depends="full-proteocache-client, minimal-proteocache-client-jar, proteocache-no-binaries, proteocache-complete, datamodel-jar, datamodel-source-jar, source-jar" description="Build-all the distributives"/>
+	<target name="all" depends="proteocache-server, source-jar" description="Build all files"/>
 
 	<!-- 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">
+	<target name="archive" description="Pack everything in the project for those who do not have access to SVN" depends="full-clean">
 		<delete file="${proteocache-project}">
 		</delete>
 		<zip destfile="${proteocache-project}" whenempty="create" >
-			<fileset dir="." excludes="${distdir}/**, jobsout/**, test-output/**, **.svn, dundee-conf/**, TODO.txt, IDEAS.txt, ${activity.log}, **/*.zip, **/*.war"/>
-			<!-- Add jobsout directory but no content -->
-			<zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="*/**"/>
+			<fileset dir="." excludes="${distdir}/**, **.git, **/*.zip, **/*.war"/>
 		</zip>
 	</target>
 
+<!-- ###################################################################################################################################### -->
 <!-- Test targets -->
+
+	<property name="LD_LIBRARY_PATH" value="/gridware/sge/lib/lx24-amd64"/>
+
+	<!-- add test library -->
+	<path id="test.classpath">
+		<fileset dir="${basedir}/testsrc/lib">
+			<include name="*.jar" />
+		</fileset>
+		<pathelement location="${classes}" />
+	</path>
+	<!--
+	Packages of the lower order should not have dependencies on the packages 
+	on the next layer. So datadb (layer 3) depends on the engine classes but 
+	engine does not depend on anything in datadb
+	-->
+	<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-->
+		<copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
+		<!-- Complile the engine classes -->
+		<javac srcdir="${basedir}/engine" destdir="${classes}" target="1.7" source="1.7" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
+			<compilerarg value="-Xlint:unchecked"/>
+			<classpath refid="project.classpath" />
+		</javac>
+		<!-- Complile the database classes -->
+		<javac srcdir="${basedir}/datadb" destdir="${classes}" target="1.7" source="1.7" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
+			<compilerarg value="-Xlint:unchecked"/>
+			<classpath refid="project.classpath" />
+		</javac>
+		<!-- Complile the server classes -->
+		<javac srcdir="${basedir}/server" destdir="${classes}" target="1.7" source="1.7" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
+			<compilerarg value="-Xlint:unchecked"/>
+			<classpath refid="project.classpath" />
+		</javac>
+		<!-- Complile the tests -->
+		<javac srcdir="${basedir}/testsrc" destdir="${classes}" target="1.7" source="1.7" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
+			<compilerarg value="-Xlint:unchecked"/>
+			<classpath refid="project.classpath" />
+			<classpath refid="test.classpath" />
+		</javac>
+	</target>
+
+
 	<taskdef name="testNG" classname="org.testng.TestNGAntTask">
 		<classpath refid="test.classpath">
 		</classpath>
@@ -505,21 +278,6 @@
 		</testNG>
 	</target>
 
-	<target name="Test_engines" depends="compile_with_debug">
-		<delete file="${activity.log}"/>
-		<testNG groups="engine" haltonfailure="true" verbose="3" enableassert="true" >
-			<jvmarg value="-server" />
-			<jvmarg value="-enableassertions" />
-			<jvmarg value="-Xms1024m" />
-			<jvmarg value="-Xmx1024m" />
-			<classfileset dir="${classes}" includes="**/*.class" />
-			<env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
-			<classpath refid="test.classpath" />
-			<classpath refid="project.classpath" />
-			<sysproperty key="TestingDataPath" value="${data.src}"/>
-		</testNG>
-	</target>
-
 	<target name="All_cluster_independent_windows_only_tests" depends="compile_with_debug">
 		<delete file="${activity.log}" failonerror="false"/>
 		<testNG excludedgroups="cluster, non_windows" haltonfailure="true" verbose="3" enableassert="true"  >
diff --git a/lib/servlet-api.jar b/lib/servlet-api.jar
new file mode 100644
index 0000000..c6273b9
Binary files /dev/null and b/lib/servlet-api.jar differ