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 (file)
--- 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.  \r
 Can be done once JABAWS 1 is replaced with 2. \r
 \r
-Globprot need a proper reference to bio python and sav_gol binaries -> they should be \r
-somehow taken from disembl. \r
-\r
 \r
 ? Replace conservation.Method with server.ws.Method and try building WS. If this does not work - get rid of Method\r
 \r
-Output file parsing for stat reporting\r
-install cluster engine stat of www-jws2 user\r
-\r
 integrate the above to tweak the size of the local job\r
 \r
 Good toString method for Limits (test with command line client -limits)\r

diff --git a/WEB-INF/lib/biojava.jar b/WEB-INF/lib/biojava.jar
deleted file mode 100644 (file)
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 (file)
--- 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 \r
+within servlet container e.g. tomcat\r
+\r
 webservices-rt.jar\r
 webservices-tools.jar \r
 webservices-api.jar \r
 \r
-is to satisfy compile dependencies for web services. \r
-Once they are compiled this library is not needed. \r
-They are required to run a web service within servlet container - tomcat  \r
-Standard JDK6 has this library in, it is relocated here to be able to use Ant tasks (WsGen, wsimport) for WS compilation\r
-and make the project less dependant on the environment\r
+JABAWS Statistics web application dependencies:  \r
 \r
-display tag 1.2 dependencies\r
+- Display Tag 1.2 dependencies\r
 \r
 commons-beanutils-1.7.0.jar\r
 commons-collections-3.2.jar\r
@@ -19,4 +18,7 @@ displaytag-export-poi-1.2.jar
 itext-1.4.7.jar\r
 jstl-1.1.2.jar\r
 poi-3.2-FINAL-20081019.jar\r
-standard-1.1.2.jar
\ No newline at end of file
+standard-1.1.2.jar\r
+\r
+- Derby database driver for statistics database \r
+derby.jar 
\ No newline at end of file

diff --git a/build.xml b/build.xml
index 4e9dd87..884ee5e 100644 (file)
--- a/build.xml
+++ b/build.xml
@@ -27,17 +27,14 @@
        <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="${distdir}/jaba-no-jaxws-windows.war"/>\r
        <property name="jaba" value="${distdir}/jaba.war"/>\r
+       <!-- TODO  \r
        <property name="jaba-dundee" value="${distdir}/jaba-dundee.war"/>\r
-       <property name="jaba-no-jaxws-no-binaries" value="${distdir}/jaba-no-jaxws-no-binaries.war"/>\r
+        -->\r
        <property name="jaba-no-binaries" value="${distdir}/jaba-no-binaries.war"/>\r
-       <property name="jaba-windows" value="${distdir}/jaba-windows.war"/>\r
        <property name="binaries" value="${distdir}/binaries.zip"/>\r
-       <property name="win-binaries" value="${distdir}/win-binaries.zip"/>\r
        <property name="jaba-devel-web" value="${distdir}/jaba-devel-website.zip"/>\r
-       <property name="jaxws-lib" value="${distdir}/jaxws-lib.zip"/>\r
+\r
        <!--Whole project archive -->\r
        <property name="jaba-project" value="${distdir}/jaba-project.zip"/>\r
 \r
@@ -309,8 +306,10 @@
                <echo>Packing binaries, and configuration files</echo>\r
                <zip destfile="${full-jaba-client-pack}" >\r
                        <zipgroupfileset file="${binaries}" />\r
-                       <zipfileset dir="${basedir}/conf" prefix="conf"/>\r
-                       <fileset dir="." includes="${full-jaba-client}" />\r
+                       <zipfileset dir="conf" prefix="conf">\r
+                               <exclude name="**/temp/**"/>\r
+                       </zipfileset>\r
+                       <fileset file="${full-jaba-client}" />\r
                </zip>\r
        </target>\r
 \r
@@ -359,15 +358,7 @@
                </zip>\r
        </target>\r
 \r
-       <target name="pack-jaxws" description="Zip all JAXWS libraries">\r
-               <delete file="${jaxws-lib}" failonerror="false"/>\r
-               <zip destfile="${jaxws-lib}" update="false" >\r
-                       <zipfileset dir="${web.lib.path}" includes="webservices-tools.jar"  prefix="WEB-INF/lib"  />\r
-                       <zipfileset dir="${web.lib.path}" includes="webservices-rt.jar"   prefix="WEB-INF/lib" />\r
-                       <zipfileset dir="${web.lib.path}" includes="webservices-api.jar"  prefix="WEB-INF/lib" />\r
-               </zip>\r
-       </target>\r
-\r
+<!-- DEPRICATED \r
        <target name="pack-windows-binaries" description="Zip only windows binary files">\r
                <delete file="${win-binaries}" failonerror="false" />\r
                <zip destfile="${win-binaries}">\r
@@ -377,25 +368,30 @@
                        </zipfileset>\r
                </zip>\r
        </target>\r
+-->\r
 \r
-       <target name="jaba-no-jaxws-no-binaries" description="Prepare JWS2 war file without runtime dependency - JAXWS jars and native binaries" depends="full-jaba-jar">\r
-               <echo>Preparing war file without JAXWS and binaries</echo>\r
-               <delete file="${jaba}">\r
+       <target name="jaba-no-binaries" description="Prepare JABAWS war file without native binaries" depends="full-jaba-jar">\r
+               <echo>Preparing a war file without binaries</echo>\r
+               <delete file="${jaba-no-binaries}">\r
                </delete>\r
-               <delete file="${jaba-no-jaxws-no-binaries}">\r
-               </delete>\r
-               <zip destfile="${jaba-no-jaxws-no-binaries}" whenempty="create">\r
+               <zip destfile="${jaba-no-binaries}" whenempty="create">\r
                        <zipfileset dir="${basedir}/WEB-INF" prefix="WEB-INF">\r
+                               <exclude name="classes"/>\r
+                               <!-- These are included into JABA client so exclude the jars -->\r
+                               <exclude name="lib/drmaa.jar"/>\r
+                               <exclude name="lib/log4j-1.2.15.jar"/>\r
+                               <exclude name="lib/${compbio-annotation}"/>\r
+                               <exclude name="lib/${compbio-util}"/>\r
+                               \r
                                <include name="web.xml"/>\r
                                <include name="sun-jaxws.xml"/>\r
-                               <exclude name="classes"/>\r
-                               <exclude name="lib"/>\r
+                               <include name="lib/*"/>\r
                        </zipfileset>\r
                        <zipfileset dir="${basedir}/ExecutionStatistic" prefix="ExecutionStatistic" />\r
                        <zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="**/*"/>\r
                        <zipfileset dir="${basedir}/conf" prefix="conf" excludes="**/log4j.properties*"/>\r
                        <!-- Add JABAWS web site apart from the binary archive -->\r
-                       <zipfileset dir="${basedir}/website" excludes="archive/**, full_javadoc/**, devel*.html, tests/**, template.html"/>\r
+                       <zipfileset dir="${basedir}/website" excludes="archive/**, devel*.html, tests/**, template.html"/>\r
                        <zipfileset dir="." includes="${full-jaba-client}" fullpath="WEB-INF/lib/jaba-client.jar"/>\r
                        <!-- Put a copy of log4j configuration file where it can be used  -->\r
                        <zipfileset dir="conf" includes="log4j.properties" prefix="WEB-INF/classes"/>\r
@@ -414,71 +410,30 @@
                </zip>\r
        </target>\r
 \r
-       <target name="jaba-without-jaxws" description="Prepare JWS2 war file without runtime dependency - JAXWS jars" depends="jaba-no-jaxws-no-binaries, pack-binaries">\r
-               <echo>Preparing war file without JAXWS</echo>\r
-               <delete file="${jaba-no-jaxws}">\r
-               </delete>\r
-               <copy tofile="${jaba-no-jaxws}" file="${jaba-no-jaxws-no-binaries}"/>\r
-               <zip destfile="${jaba-no-jaxws}" update="true" >\r
-                       <zipgroupfileset file="${binaries}" />\r
-               </zip>\r
-       </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, clearStatDB">\r
-               <echo>Preparing war file without JAXWS</echo>\r
-               <delete file="${jaba-windows}">\r
-               </delete>\r
-               <delete dir="${basedir}/jobsout/*"/>\r
-               <delete file="${jaba-no-jaxws-windows}">\r
-               </delete>\r
-               <zip destfile="${jaba-no-jaxws-windows}" >\r
-                       <zipfileset dir="${basedir}/WEB-INF" prefix="WEB-INF">\r
-                               <include name="web.xml"/>\r
-                               <include name="sun-jaxws.xml"/>\r
-                               <exclude name="classes"/>\r
-                               <exclude name="lib"/>\r
-                       </zipfileset>\r
-                       <zipgroupfileset file="${win-binaries}" />\r
-                       <zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="**/*"/>\r
-                       <zipfileset dir="${basedir}/conf" prefix="conf" excludes="**/log4j.properties*"/>\r
-                       <zipfileset dir="." includes="${full-jaba-client}" fullpath="WEB-INF/lib/jaba-client.jar"/>\r
-                       <zipfileset dir="conf" includes="log4j.properties" prefix="WEB-INF/classes"/>\r
-                       <!-- Add JABAWS web site apart from the binary archive -->\r
-                       <zipfileset dir="${basedir}/website" excludes="archive/**, full_javadoc/**, devel*.html, tests/**, template.html"/>\r
-               </zip>\r
-       </target>\r
-\r
-\r
-\r
-       <target name="jaba-complete" description="Prepare JWS2 war file" depends="jaba-without-jaxws, pack-jaxws">\r
+       <target name="jaba-complete" description="Prepare JABAWS war file without runtime dependency - JAXWS jars" depends="jaba-no-binaries, pack-binaries">\r
                <echo>Preparing a complete war file</echo>\r
-               <copy tofile="${jaba}" file="${jaba-no-jaxws}"/>\r
+               <delete file="${jaba}">\r
+               </delete>\r
+               <copy tofile="${jaba}" file="${jaba-no-binaries}"/>\r
                <zip destfile="${jaba}" update="true" >\r
-                       <zipgroupfileset file="${jaxws-lib}"/>\r
-               </zip>\r
-       </target>\r
-\r
-       <target name="jaba-no-binaries" description="Prepare JWS2 war file without native binaries" depends="jaba-no-jaxws-no-binaries, pack-jaxws">\r
-               <echo>Preparing a complete war file</echo>\r
-               <copy tofile="${jaba-no-binaries}" file="${jaba-no-jaxws-no-binaries}"/>\r
-               <zip destfile="${jaba-no-binaries}" update="true" >\r
-                       <zipgroupfileset file="${jaxws-lib}"/>\r
+                       <zipgroupfileset file="${binaries}" />\r
                </zip>\r
        </target>\r
 \r
-       <target name="jaba-complete-windows" description="Prepare JWS2 war file for windows" depends="jaba-without-jaxws-windows, pack-jaxws">\r
+<!-- DEPRICATED - STANDARD JABA WAR WILL WORK FOR WINDOWS JUST FINE, DOWNLOAD SPACE SAVING IS NOT WORTH THE \r
+  ADDITIONAL COMPLEXITY \r
+       <target name="jaba-complete-windows" description="Prepare JABAWS war file for windows" depends="jaba-no-binaries">\r
                <echo>Preparing a complete war file</echo>\r
-               <copy tofile="${jaba-windows}" file="${jaba-no-jaxws-windows}"/>\r
+               <copy tofile="${jaba-windows}" file="${jaba-no-binaries}"/>\r
                <zip destfile="${jaba-windows}" update="true" >\r
-                       <zipgroupfileset file="${jaxws-lib}"/>\r
+                       <zipgroupfileset file="${win-binaries}" />\r
                </zip>\r
        </target>\r
-\r
+-->\r
+ \r
        <target name="build-all" description="Build-all the distributives"\r
-               depends="full-jaba-client, minimal-jaba-client-jar, jaba-no-jaxws-no-binaries,\r
-                jaba-no-binaries, jaba-complete, jaba-complete-windows,\r
-                datamodel-jar, datamodel-source-jar, source-jar"/>\r
+               depends="full-jaba-client, minimal-jaba-client-jar, jaba-no-binaries,\r
+                jaba-complete, datamodel-jar, datamodel-source-jar, source-jar"/>\r
 \r
        <!-- This task does not really depends on compile, but it is better to make sure that the code is sound -->\r
        <target name="archive-project" description="Pack everything in the project for those who do not have access to SVN" depends="compile">\r
@@ -491,23 +446,6 @@
                </zip>\r
        </target>\r
 \r
-       <!-- This is JUNIT test \r
-       <target name="testEngine" depends="compileTest">\r
-                       <delete file="${activity.log}"/> \r
-                       <junit filtertrace="false" haltonfailure="true" haltonerror="true" fork="true" forkmode="once">\r
-                       <jvmarg value="-server" />\r
-                       <jvmarg value="-enableassertions" />\r
-                       <jvmarg value="-Xms512m" />\r
-                       <jvmarg value="-Xmx512m" />\r
-                               <env key="LD_LIBRARY_PATH" value="/gridware/sge/lib/lx24-amd64"/>\r
-                       <classpath refid="test.classpath" />\r
-                       <classpath refid="project.classpath" />\r
-                       <formatter type="plain" usefile="false" />\r
-                       <test name="compbio.engine.cluster.AllTestSuit" />\r
-                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
-                   </junit>\r
-               </target>\r
-       -->\r
 \r
        <taskdef name="testNG" classname="org.testng.TestNGAntTask">\r
                <classpath refid="test.classpath">\r