build script updated

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4326 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/DEPENDENCY b/DEPENDENCY
index b22fbef..cddf8b6 100644 (file)
--- a/DEPENDENCY
+++ b/DEPENDENCY
@@ -1,4 +1,14 @@
 Compile time Dependencies of this project are: \r
 \r
 compbio-annotations-1.0.jar\r
-compbio-util-1.0.jar\r
+compbio-util-1.4.jar\r
+\r
+source.jar (includes compbio-annotations and compbio-util) depends on\r
+ \r
+Apache log 4j\r
+DRMAA library\r
+Servlet 2.5\r
+\r
+datamodel source depends on\r
+\r
+Apache log 4j
\ No newline at end of file

diff --git a/build.xml b/build.xml
index d30dc9f..4e9dd87 100644 (file)
--- a/build.xml
+++ b/build.xml
@@ -8,12 +8,24 @@
        <!-- Distributive file names-->\r
        <property name="distdir" value="website/archive"/>\r
        <mkdir dir="${distdir}" />\r
-       <property name="datamodel" value="${distdir}/datamodel-1.2.jar"/>\r
-       <property name="datamodel-src" value="${distdir}/datamodel-src-1.2.jar"/>\r
-       <property name="min-jaba-client" value="${distdir}/min-jaba-client.jar"/>\r
+       \r
+       <!-- projects details -->\r
+       <property name="project.url" value="http://www.compbio.dundee.ac.uk/jabaws"/>\r
+       <property name="product" value="Java Bioinformatics Analyses Web Services"/>\r
+       <property name="author" value="Peter Troshin"/>\r
+       \r
+       <!-- dependencies on other compbio projects  -->\r
+       <property name="compbio-annotation" value="compbio-annotations-1.0.jar"/>\r
+       <property name="compbio-util" value="compbio-util-1.4.jar"/>\r
+       \r
+       <!-- products -->\r
+       <property name="jaba_version" value="2.0"/>\r
+       <property name="datamodel" value="${distdir}/datamodel-${jaba_version}.jar"/>\r
+       <property name="datamodel-src" value="${distdir}/datamodel-src-${jaba_version}.jar"/>\r
+       <property name="min-jaba-client" value="${distdir}/min-jaba-client-${jaba_version}.jar"/>\r
        <property name="aacon-ws-client" value="${distdir}/aacon-ws-client.jar"/>\r
-       <property name="full-jaba-client" value="${distdir}/full-jaba-client.jar"/>\r
-       <property name="jaba-source-jar" value="${distdir}/jaba-source.jar"/>\r
+       <property name="full-jaba-client" value="${distdir}/full-jaba-client-${jaba_version}.jar"/>\r
+       <property name="jaba-source-jar" value="${distdir}/jabaws-src-${jaba_version}.jar"/>\r
        <property name="full-jaba-client-pack" value="${distdir}/full-jaba-client-pack.zip"/>\r
        <property name="jaba-no-jaxws" value="${distdir}/jaba-no-jaxws.war"/>\r
        <property name="jaba-no-jaxws-windows" value="${distdir}/jaba-no-jaxws-windows.war"/>\r
@@ -57,6 +69,7 @@
                <pathelement location="${classes}" />\r
        </path>\r
 \r
+\r
        <!-- The compilation order is \r
        1. datamodel \r
        2. engine\r
@@ -154,18 +167,19 @@
                </delete>\r
                <jar jarfile="${basedir}/${datamodel}">\r
                        <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >\r
-                               <include name="compbio-util-1.4.jar"/>\r
+                               <include name="${compbio-util}"/>\r
+                               <include name="${compbio-annotation}"/>\r
                        </zipgroupfileset>\r
                        <fileset dir="${basedir}/WEB-INF/classes/">\r
                                <include name="compbio/data/sequence/*.class"/>\r
                                <include name="compbio/metadata/*.class"/>\r
                        </fileset>\r
                        <manifest>\r
-                               <attribute name="Built-By" value="Peter Troshin" />\r
+                               <attribute name="Built-By" value="${author}" />\r
                                <attribute name="Class-Path" value="." />\r
-                               <attribute name="Implementation-Title" value="Datamodel for Java Bioinformatics Analyses Web Services " />\r
-                               <attribute name="Implementation-Vendor" value="Peter Troshin" />\r
-                               <attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />\r
+                               <attribute name="Implementation-Title" value="Datamodel for ${product} " />\r
+                               <attribute name="Implementation-Vendor" value="${author}" />\r
+                               <attribute name="Implementation-URL" value="${project.url}" />\r
                        </manifest>\r
                </jar>\r
        </target>\r
@@ -183,12 +197,12 @@
                                <include name="compbio/ws/client/**"/>\r
                        </fileset>\r
                        <manifest>\r
-                               <attribute name="Built-By" value="Peter Troshin" />\r
+                               <attribute name="Built-By" value="${author}" />\r
                                <attribute name="Main-Class" value="compbio.ws.client.Jws2Client" />\r
                                <attribute name="Class-Path" value="." />\r
-                               <attribute name="Implementation-Title" value="Minimal Java Bioinformatics Analyses Web Services Client" />\r
-                               <attribute name="Implementation-Vendor" value="Peter Troshin" />\r
-                               <attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />\r
+                               <attribute name="Implementation-Title" value="Minimal ${product} Client" />\r
+                               <attribute name="Implementation-Vendor" value="${author}" />\r
+                               <attribute name="Implementation-URL" value="${project.url}" />\r
                        </manifest>\r
                </jar>\r
        </target>\r
@@ -205,23 +219,21 @@
                                <include name="compbio/ws/client/**"/>\r
                        </fileset>\r
                        <manifest>\r
-                               <attribute name="Built-By" value="Peter Troshin" />\r
+                               <attribute name="Built-By" value="${author}" />\r
                                <attribute name="Main-Class" value="compbio.ws.client.AAConClient" />\r
                                <attribute name="Class-Path" value="." />\r
                                <attribute name="Implementation-Title" value="AACon Client" />\r
-                               <attribute name="Implementation-Vendor" value="Peter Troshin" />\r
+                               <attribute name="Implementation-Vendor" value="${author}" />\r
                                <attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk/aacon" />\r
                        </manifest>\r
                </jar>\r
        </target>\r
 \r
-       <target name="source-jar" description="Pack java sources" depends="compile">\r
+       <target name="source-jar" description="Pack java sources" depends="datamodel-source-jar">\r
                <delete file="${basedir}/${jaba-source-jar}">\r
                </delete>\r
                <jar jarfile="${basedir}/${jaba-source-jar}">\r
-                       <fileset dir="${basedir}/datamodel">\r
-                               <include name="**"/>\r
-                       </fileset>\r
+                       <zipgroupfileset  excludes="META-INF/*.MF" file="${datamodel-src}"/>\r
                        <fileset dir="${basedir}/runner">\r
                                <include name="**"/>\r
                        </fileset>\r
@@ -232,14 +244,13 @@
                                <include name="**"/>\r
                        </fileset>\r
                        <manifest>\r
-                               <attribute name="Built-By" value="Peter Troshin" />\r
+                               <attribute name="Built-By" value="${author}" />\r
                                <attribute name="Class-Path" value="." />\r
-                               <attribute name="Implementation-Title" value="Java Bioinformatics Analyses Web Services Source Code Archive" />\r
-                               <attribute name="Implementation-Vendor" value="Peter Troshin" />\r
-                               <attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />\r
+                               <attribute name="Implementation-Title" value="${product} Source Code Archive" />\r
+                               <attribute name="Implementation-Vendor" value="${author}" />\r
+                               <attribute name="Implementation-URL" value="${project.url}" />\r
                        </manifest>\r
                </jar>\r
-\r
        </target>\r
        \r
        <target name="datamodel-source-jar" description="Pack java sources" depends="compile">\r
@@ -249,11 +260,14 @@
                                <fileset dir="${basedir}/datamodel">\r
                                        <include name="**"/>\r
                                </fileset>\r
+                               <zipgroupfileset excludes="META-INF/*.MF" dir="${lib.path}/src">\r
+                                       <include name="**"/>\r
+                               </zipgroupfileset>\r
                                <manifest>\r
-                                       <attribute name="Built-By" value="Peter Troshin" />\r
-                                       <attribute name="Implementation-Title" value="Java Bioinformatics Analyses Web Services Datamodel Source Code Archive" />\r
-                                       <attribute name="Implementation-Vendor" value="Peter Troshin" />\r
-                                       <attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk/jabaws" />\r
+                                       <attribute name="Built-By" value="${author}" />\r
+                                       <attribute name="Implementation-Title" value="${product} Datamodel Source Code Archive" />\r
+                                       <attribute name="Implementation-Vendor" value="${author}" />\r
+                                       <attribute name="Implementation-URL" value="${project.url}" />\r
                                </manifest>\r
                        </jar>\r
                </target>\r
@@ -275,17 +289,17 @@
                <jar jarfile="${full-jaba-client}">\r
                        <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >\r
                                <include name="log4j-1.2.15.jar"/>\r
-                               <include name="compbio-util-1.3.jar"/>\r
-                               <include name="compbio-annotations-1.0.jar"/>\r
+                               <include name="${compbio-util}"/>\r
+                               <include name="${compbio-annotation}"/>\r
                                <include name="drmaa.jar"/>\r
                        </zipgroupfileset>\r
                        <fileset refid="fullclient"/>\r
                        <manifest>\r
-                               <attribute name="Built-By" value="Peter Troshin" />\r
+                               <attribute name="Built-By" value="${author}" />\r
                                <attribute name="Class-Path" value="." />\r
-                               <attribute name="Implementation-Title" value="Full Java Bioinformatics Analyses Web Services Client" />\r
-                               <attribute name="Implementation-Vendor" value="Peter Troshin" />\r
-                               <attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />\r
+                               <attribute name="Implementation-Title" value="Full ${product} Client" />\r
+                               <attribute name="Implementation-Vendor" value="${author}" />\r
+                               <attribute name="Implementation-URL" value="${project.url}" />\r
                        </manifest>\r
                </jar>\r
        </target>\r
@@ -308,24 +322,26 @@
                <jar jarfile="${full-jaba-client}">\r
                        <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >\r
                                <include name="log4j-1.2.15.jar"/>\r
-                               <include name="compbio-util-1.3.jar"/>\r
-                               <include name="compbio-annotations-1.0.jar"/>\r
+                               <include name="${compbio-util}"/>\r
+                               <include name="${compbio-annotation}"/>\r
                                <include name="drmaa.jar"/>\r
                        </zipgroupfileset>\r
                        <fileset refid="fullclient">\r
                        </fileset>\r
                        <fileset dir="${basedir}/WEB-INF/classes/">\r
+                               <!-- Statistics web application -->\r
+                               <include name="compbio/stat/**"/>\r
                                <!-- Web services-->\r
                                <include name="compbio/ws/**"/>\r
                        </fileset>\r
                        <!-- Set WSTester as main to help user to test their deployments -->\r
                        <manifest>\r
-                               <attribute name="Built-By" value="Peter Troshin" />\r
+                               <attribute name="Built-By" value="${author}" />\r
                                <attribute name="Class-Path" value="." />\r
                                <attribute name="Main-Class" value="compbio.ws.client.WSTester" />\r
-                               <attribute name="Implementation-Title" value="Java Bioinformatics Analyses Web Services" />\r
-                               <attribute name="Implementation-Vendor" value="Peter Troshin" />\r
-                               <attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />\r
+                               <attribute name="Implementation-Title" value="${product}" />\r
+                               <attribute name="Implementation-Vendor" value="${author}" />\r
+                               <attribute name="Implementation-URL" value="${project.url}" />\r
                        </manifest>\r
                </jar>\r
        </target>\r
@@ -356,9 +372,8 @@
                <delete file="${win-binaries}" failonerror="false" />\r
                <zip destfile="${win-binaries}">\r
                        <zipfileset dir="${basedir}/binaries" prefix="binaries" >\r
-                               <include name="clustalw2.exe"/>\r
-                               <include name="muscle.exe"/>\r
                                <include name="matrices/*" />\r
+                               <include name="windows/*" />\r
                        </zipfileset>\r
                </zip>\r
        </target>\r
@@ -379,7 +394,7 @@
                        <zipfileset dir="${basedir}/ExecutionStatistic" prefix="ExecutionStatistic" />\r
                        <zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="**/*"/>\r
                        <zipfileset dir="${basedir}/conf" prefix="conf" excludes="**/log4j.properties*"/>\r
-                       <!-- Add JSW2 web site apart from the binary archive -->\r
+                       <!-- Add JABAWS web site apart from the binary archive -->\r
                        <zipfileset dir="${basedir}/website" excludes="archive/**, full_javadoc/**, devel*.html, tests/**, template.html"/>\r
                        <zipfileset dir="." includes="${full-jaba-client}" fullpath="WEB-INF/lib/jaba-client.jar"/>\r
                        <!-- Put a copy of log4j configuration file where it can be used  -->\r
@@ -394,7 +409,7 @@
                <delete file="${jaba-devel-web}">\r
                </delete>\r
                <zip destfile="${jaba-devel-web}" whenempty="create">\r
-                       <!-- Add JSW2 web site apart from the binary archive -->\r
+                       <!-- Add JABAWS web site apart from the binary archive -->\r
                        <zipfileset dir="${basedir}/website" excludes="template.html, download.html, index.html, manual.html, howto.html, archive/**, prog_docs/**"/>\r
                </zip>\r
        </target>\r
@@ -410,7 +425,7 @@
        </target>\r
 \r
        <target name="jaba-without-jaxws-windows" description="Prepare JWS2 war file without runtime dependency - JAXWS jars" \r
-               depends="full-jaba-jar, pack-windows-binaries">\r
+               depends="full-jaba-jar, pack-windows-binaries, clearStatDB">\r
                <echo>Preparing war file without JAXWS</echo>\r
                <delete file="${jaba-windows}">\r
                </delete>\r
@@ -429,7 +444,7 @@
                        <zipfileset dir="${basedir}/conf" prefix="conf" excludes="**/log4j.properties*"/>\r
                        <zipfileset dir="." includes="${full-jaba-client}" fullpath="WEB-INF/lib/jaba-client.jar"/>\r
                        <zipfileset dir="conf" includes="log4j.properties" prefix="WEB-INF/classes"/>\r
-                       <!-- Add JSW2 web site apart from the binary archive -->\r
+                       <!-- Add JABAWS web site apart from the binary archive -->\r
                        <zipfileset dir="${basedir}/website" excludes="archive/**, full_javadoc/**, devel*.html, tests/**, template.html"/>\r
                </zip>\r
        </target>\r
@@ -461,7 +476,9 @@
        </target>\r
 \r
        <target name="build-all" description="Build-all the distributives"\r
-               depends="full-jaba-client, minimal-jaba-client-jar, jaba-no-jaxws-no-binaries, jaba-no-binaries, jaba-complete, jaba-complete-windows"/>\r
+               depends="full-jaba-client, minimal-jaba-client-jar, jaba-no-jaxws-no-binaries,\r
+                jaba-no-binaries, jaba-complete, jaba-complete-windows,\r
+                datamodel-jar, datamodel-source-jar, source-jar"/>\r
 \r
        <!-- This task does not really depends on compile, but it is better to make sure that the code is sound -->\r
        <target name="archive-project" description="Pack everything in the project for those who do not have access to SVN" depends="compile">\r
@@ -630,60 +647,5 @@
                </testNG>\r
        </target>\r
 \r
-       <!-- <zipfileset excludes="META-INF/*.SF" src="jarfilename.jar"/> \r
-               \r
-               <target name="build-jar" description="Pack cluster  and runners into a jar" depends="compile">\r
-                       <echo>Jar file: integration</echo>\r
-                       <delete file="${basedir}/.jar"></delete>\r
-                       <copy file="${basedir}/conf/" tofile="${classes}/log4j.properties" />\r
-                       <jar jarfile="${basedir}/.jar">\r
-                               <fileset dir="${basedir}/WEB-INF/classes/" includes="compbio/**" />\r
-                               <manifest>\r
-                                       <attribute name="Built-By" value="Peter Troshin" />\r
-                                       <attribute name="Main-Class" value="compbio.clust..JobStatus" />\r
-                                       <attribute name="Class-Path" value=" . /gridware/sge/lib/drmaa.jar" />\r
-                                       <attribute name="Implementation-Title" value="Cluster Submission Engine" />\r
-                                       <attribute name="Implementation-Vendor" value="Peter Troshin" />\r
-                                       <attribute name="Implementation-URL" value="xxx" />\r
-                               </manifest>\r
-                       </jar>\r
-               </target>\r
-               \r
-               \r
-               <target name="build-jar-local" description="Pack cluster  and runners with dependencies" depends="compile">\r
-                       <echo>Jar file: integration</echo>\r
-                       <delete file="${basedir}/.jar"></delete>\r
-                       <jar jarfile="${basedir}/.jar">\r
-                               <zipgroupfileset excludes="META-INF/*.SF" dir="${lib.path}"></zipgroupfileset>\r
-                               <fileset dir="${basedir}/WEB-INF/classes/" includes="**" />\r
-                               <manifest>\r
-                                       <attribute name="Built-By" value="Peter Troshin" />\r
-                                       <attribute name="Main-Class" value="compbio..cluster.JobStatus" />\r
-                                       <attribute name="Class-Path" value="." />\r
-                                       <attribute name="Implementation-Title" value="Cluster Submission Engine" />\r
-                                       <attribute name="Implementation-Vendor" value="Peter Troshin" />\r
-                                       <attribute name="Implementation-URL" value="xxx" />\r
-                               </manifest>\r
-                       </jar>\r
-               </target>\r
-               \r
-               -->\r
-\r
-       <!--\r
-               <target name="run-client-jar" description="EXAMPLE TASK ONLY">\r
-                       <java jar="${basedir}/resources/wsclient.jar" fork="true"\r
-                               failonerror="true" maxmemory="256m">\r
-                               <arg\r
-                                       value="C:/Documents and Settings/pvt43/Desktop/Leeds Sequencing/Copy of Files to up load" />\r
-                       </java>\r
-               </target>\r
-               <target name="run-client-class" description="EXAMPLE TASK ONLY">\r
-                       <java classname="org.pimslims.ws.client.FileUploadClient" fork="true"\r
-                               failonerror="true" maxmemory="256m">\r
-                               <classpath refid="project.classpath" />\r
-                               <classpath refid="instrument.classpath" />\r
-                       </java>\r
-               </target>\r
-       -->\r
 \r
 </project>
\ No newline at end of file