Refactor:

relocate getLimit() method from Util client to Util engine as  SkeletalExecutable (part of the engine depends on it)

Update compile ant task to get rid of warnings.
However, ant still does not complile due to cast issue. TODO later
Updating version of utils and datamodel as it includes the utils

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3967 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/.classpath b/.classpath
index 59011e3..6d71866 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -10,8 +10,8 @@
        <classpathentry kind="lib" path="testsrc/lib/testng-5.10-jdk15.jar"/>\r
        <classpathentry kind="lib" path="lib/servlet-api.jar"/>\r
        <classpathentry kind="lib" path="WEB-INF/lib/drmaa.jar"/>\r
-       <classpathentry kind="lib" path="WEB-INF/lib/compbio-util-1.3.jar"/>\r
        <classpathentry kind="lib" path="WEB-INF/lib/compbio-annotations-1.0.jar"/>\r
        <classpathentry kind="lib" path="WEB-INF/lib/derby.jar"/>\r
+       <classpathentry kind="lib" path="WEB-INF/lib/compbio-util-1.4.jar"/>\r
        <classpathentry kind="output" path="WEB-INF/classes"/>\r
 </classpath>\r

diff --git a/TODO.txt b/TODO.txt
index e08270c..a0a2706 100644 (file)
--- a/TODO.txt
+++ b/TODO.txt
@@ -1,5 +1,11 @@
 TODO: \r
 \r
+add to help text: To disable a web service remove it from WEB-INF/sun-jaxws.xml descriptor\r
+\r
+add to help: VirtualBox 4.0.4 works fine with JABAWS update links \r
+\r
+rename jaba.war to jabaws.war and make sure jabaws context path is used throughout. \r
+\r
 Current stat collector has to rely on file dates! \r
 \r
 Test all WS as names from Executables were removed\r

diff --git a/WEB-INF/lib/compbio-util-1.3.jar b/WEB-INF/lib/compbio-util-1.3.jar
deleted file mode 100644 (file)
index 9042b5a..0000000
Binary files a/WEB-INF/lib/compbio-util-1.3.jar and /dev/null differ

diff --git a/WEB-INF/lib/compbio-util-1.4.jar b/WEB-INF/lib/compbio-util-1.4.jar
new file mode 100644 (file)
index 0000000..7abd95e
Binary files /dev/null and b/WEB-INF/lib/compbio-util-1.4.jar differ

diff --git a/build.xml b/build.xml
index 5597457..f368ec3 100644 (file)
--- a/build.xml
+++ b/build.xml
@@ -1,14 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>\r
 \r
 <project default="minimal-jaba-client-jar" name="Build minimal client for Java Bioinformatics Analysis Web Services" basedir=".">\r
-       \r
+\r
        <property name="basedir" location="${basedir}/log" />\r
        <property name="LD_LIBRARY_PATH" value="/gridware/sge/lib/lx24-amd64"/>\r
-       \r
+\r
        <!-- Distributive file names-->\r
        <property name="distdir" value="website/archive"/>\r
        <mkdir dir="${distdir}" />\r
-       <property name="datamodel" value="${distdir}/datamodel-1.0.jar"/>\r
+       <property name="datamodel" value="${distdir}/datamodel-1.1.jar"/>\r
        <property name="min-jaba-client" value="${distdir}/min-jaba-client.jar"/>\r
        <property name="aacon-ws-client" value="${distdir}/aacon-ws-client.jar"/>\r
        <property name="full-jaba-client" value="${distdir}/full-jaba-client.jar"/>\r
@@ -27,8 +27,8 @@
        <property name="jaxws-lib" value="${distdir}/jaxws-lib.zip"/>\r
        <!--Whole project archive -->\r
        <property name="jaba-project" value="${distdir}/jaba-project.zip"/>\r
-       \r
-       \r
+\r
+\r
        <!-- java -->\r
        <property name="test.src" location="${basedir}/testsrc" />\r
        <property name="classes" location="${basedir}/WEB-INF/classes" />\r
@@ -43,7 +43,7 @@
                        <include name="*.jar" />\r
                </fileset>\r
                <fileset dir="${web.lib.path}">\r
-                                       <include name="*.jar" />\r
+                       <include name="*.jar" />\r
                </fileset>\r
        </path>\r
 \r
@@ -72,41 +72,41 @@
                <!-- Complile the datamodel first -->\r
                <javac srcdir="${basedir}/datamodel" destdir="${classes}" target="1.6"\r
                                source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >\r
-                               <compilerarg value="-Xlint:unchecked"/>\r
-                               <classpath refid="project.classpath" />\r
+                       <compilerarg value="-Xlint:unchecked"/>\r
+                       <classpath refid="project.classpath" />\r
                </javac>\r
                <!-- Complile the engines -->\r
                <javac srcdir="${basedir}/engine" destdir="${classes}" target="1.6"\r
                                source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >\r
-                               <compilerarg value="-Xlint:unchecked"/>\r
-                               <classpath refid="project.classpath" />\r
+                       <compilerarg value="-Xlint:unchecked"/>\r
+                       <classpath refid="project.classpath" />\r
                </javac>\r
                <!-- Complile the runners -->\r
                <javac srcdir="${basedir}/runner" destdir="${classes}" target="1.6"\r
                                source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >\r
-                               <compilerarg value="-Xlint:unchecked"/>\r
-                               <classpath refid="project.classpath" />\r
+                       <compilerarg value="-Xlint:unchecked"/>\r
+                       <classpath refid="project.classpath" />\r
                </javac>\r
                <!-- Complile the webservices -->\r
                <javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6"\r
                                source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >\r
-                               <compilerarg value="-Xlint:unchecked"/>\r
-                               <classpath refid="project.classpath" />\r
+                       <compilerarg value="-Xlint:unchecked"/>\r
+                       <classpath refid="project.classpath" />\r
                </javac>\r
                <!-- Complile the tests -->\r
                <javac srcdir="${basedir}/testsrc" destdir="${classes}" target="1.6"\r
                                source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >\r
-                               <compilerarg value="-Xlint:unchecked"/>\r
-                               <classpath refid="project.classpath" />\r
-                               <classpath refid="test.classpath" />\r
+                       <compilerarg value="-Xlint:unchecked"/>\r
+                       <classpath refid="project.classpath" />\r
+                       <classpath refid="test.classpath" />\r
                </javac>\r
        </target>\r
 \r
- <!-- Clean temp directories -->\r
-    <target name="clean">\r
-        <delete dir="${classes}" />\r
-        <mkdir dir="${classes}" />\r
-    </target>\r
+       <!-- Clean temp directories -->\r
+       <target name="clean">\r
+               <delete dir="${classes}" />\r
+               <mkdir dir="${classes}" />\r
+       </target>\r
 \r
        <!--\r
        Compile with optimisation. Do not compile testsrc \r
@@ -123,60 +123,60 @@
                <!-- copy files to class path-->\r
                <copy file="${basedir}/conf/log4j.properties" tofile="${classes}/log4j.properties" />\r
                <!-- Complile the datamodel first -->\r
-               <javac srcdir="${basedir}/datamodel" destdir="${classes}" target="1.6"\r
-                               source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true" >\r
-                               <compilerarg value="-Xlint:unchecked"/>\r
-                               <classpath refid="project.classpath" />\r
+               <javac srcdir="${basedir}/datamodel" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">\r
+                       <compilerarg value="-Xlint:-unchecked" />\r
+                       <classpath refid="project.classpath" />\r
                </javac>\r
                <!-- Complile the engines -->\r
-               <javac srcdir="${basedir}/engine" destdir="${classes}" target="1.6"\r
-                               source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true" >\r
-                               <compilerarg value="-Xlint:unchecked"/>\r
-                               <classpath refid="project.classpath" />\r
+               <javac srcdir="${basedir}/engine" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">\r
+                       <compilerarg value="-Xlint:-all" />\r
+                       <compilerarg value="-Xlint:-unchecked" />\r
+                       <classpath refid="project.classpath" />\r
                </javac>\r
                <!-- Complile the runners -->\r
-               <javac srcdir="${basedir}/runner" destdir="${classes}" target="1.6"\r
-                               source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true" >\r
-                               <compilerarg value="-Xlint:unchecked"/>\r
-                               <classpath refid="project.classpath" />\r
+               <javac srcdir="${basedir}/runner" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">\r
+                       <compilerarg value="-Xlint:-unchecked" />\r
+                       <classpath refid="project.classpath" />\r
                </javac>\r
                <!-- Complile the webservices -->\r
-               <javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6"\r
-                               source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true" >\r
-                               <compilerarg value="-Xlint:unchecked"/>\r
-                               <classpath refid="project.classpath" />\r
+               <javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">\r
+                       <compilerarg value="-Xlint:-unchecked" />\r
+                       <classpath refid="project.classpath" />\r
                </javac>\r
+\r
        </target>\r
 \r
 \r
        <target name="datamodel-jar" description="Pack data model classes" depends="compile">\r
-                       <echo>Jar file: Minimal WS client jar</echo>\r
-                       <delete file="${basedir}/${datamodel}"></delete>\r
-                       <jar jarfile="${basedir}/${datamodel}">\r
-                               <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >\r
-                                       <include name="compbio-util-1.3.jar"/>\r
-                               </zipgroupfileset>\r
-                               <fileset dir="${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="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
-                               </manifest>\r
-                       </jar>\r
-               </target>\r
-       \r
-       \r
+               <echo>Jar file: Minimal WS client jar</echo>\r
+               <delete file="${basedir}/${datamodel}">\r
+               </delete>\r
+               <jar jarfile="${basedir}/${datamodel}">\r
+                       <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >\r
+                               <include name="compbio-util-1.4.jar"/>\r
+                       </zipgroupfileset>\r
+                       <fileset dir="${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="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
+                       </manifest>\r
+               </jar>\r
+       </target>\r
+\r
+\r
        <target name="minimal-jaba-client-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class" depends="compile, datamodel-jar">\r
                <echo>Jar file: Minimal WS client jar</echo>\r
-               <delete file="${basedir}/${min-jaba-client}"></delete>\r
+               <delete file="${basedir}/${min-jaba-client}">\r
+               </delete>\r
                <jar jarfile="${basedir}/${min-jaba-client}">\r
                        <zipgroupfileset excludes="META-INF/*.SF" dir="" includes="${datamodel}" />\r
-                       <fileset dir="${basedir}/WEB-INF/classes/"> \r
+                       <fileset dir="${basedir}/WEB-INF/classes/">\r
                                <!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->\r
                                <include name="compbio/data/msa/**"/>\r
                                <include name="compbio/ws/client/**"/>\r
@@ -191,41 +191,43 @@
                        </manifest>\r
                </jar>\r
        </target>\r
-       \r
+\r
        <target name="aacon-ws-client-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class" depends="compile, datamodel-jar">\r
-                       <echo>Jar file: AAConWS client jar</echo>\r
-                       <delete file="${basedir}/${aacon-ws-client}"></delete>\r
-                       <jar jarfile="${basedir}/${aacon-ws-client}">\r
-                               <zipgroupfileset excludes="META-INF/*.SF" dir="" includes="${datamodel}" />\r
-                               <fileset dir="${basedir}/WEB-INF/classes/"> \r
-                                       <!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->\r
-                                       <include name="compbio/data/msa/**"/>\r
-                                       <include name="compbio/ws/client/**"/>\r
-                               </fileset>\r
-                               <manifest>\r
-                                       <attribute name="Built-By" value="Peter Troshin" />\r
-                                       <attribute name="Main-Class" value="compbio.ws.client.AAConClient" />\r
-                                       <attribute name="Class-Path" value="." />\r
-                                       <attribute name="Implementation-Title" value="AACon Client" />\r
-                                       <attribute name="Implementation-Vendor" value="Peter Troshin" />\r
-                                       <attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk/aacon" />\r
-                               </manifest>\r
-                       </jar>\r
+               <echo>Jar file: AAConWS client jar</echo>\r
+               <delete file="${basedir}/${aacon-ws-client}">\r
+               </delete>\r
+               <jar jarfile="${basedir}/${aacon-ws-client}">\r
+                       <zipgroupfileset excludes="META-INF/*.SF" dir="" includes="${datamodel}" />\r
+                       <fileset dir="${basedir}/WEB-INF/classes/">\r
+                               <!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->\r
+                               <include name="compbio/data/msa/**"/>\r
+                               <include name="compbio/ws/client/**"/>\r
+                       </fileset>\r
+                       <manifest>\r
+                               <attribute name="Built-By" value="Peter Troshin" />\r
+                               <attribute name="Main-Class" value="compbio.ws.client.AAConClient" />\r
+                               <attribute name="Class-Path" value="." />\r
+                               <attribute name="Implementation-Title" value="AACon Client" />\r
+                               <attribute name="Implementation-Vendor" value="Peter Troshin" />\r
+                               <attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk/aacon" />\r
+                       </manifest>\r
+               </jar>\r
        </target>\r
 \r
        <target name="source-jar" description="Pack java sources" depends="compile">\r
-               <delete file="${basedir}/${jaba-source-jar}"></delete>\r
+               <delete file="${basedir}/${jaba-source-jar}">\r
+               </delete>\r
                <jar jarfile="${basedir}/${jaba-source-jar}">\r
-                       <fileset dir="${basedir}/datamodel"> \r
+                       <fileset dir="${basedir}/datamodel">\r
                                <include name="**"/>\r
                        </fileset>\r
-                       <fileset dir="${basedir}/runner"> \r
+                       <fileset dir="${basedir}/runner">\r
                                <include name="**"/>\r
                        </fileset>\r
-                       <fileset dir="${basedir}/engine"> \r
+                       <fileset dir="${basedir}/engine">\r
                                <include name="**"/>\r
                        </fileset>\r
-                       <fileset dir="${basedir}/webservices/"> \r
+                       <fileset dir="${basedir}/webservices/">\r
                                <include name="**"/>\r
                        </fileset>\r
                        <manifest>\r
@@ -236,10 +238,10 @@
                                <attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />\r
                        </manifest>\r
                </jar>\r
-               \r
+\r
        </target>\r
-       \r
-       <fileset dir="${basedir}/WEB-INF/classes/" id="fullclient"> \r
+\r
+       <fileset dir="${basedir}/WEB-INF/classes/" id="fullclient">\r
                <!-- Datamodel -->\r
                <include name="compbio/data/**"/>\r
                <include name="compbio/metadata/**"/>\r
@@ -250,26 +252,27 @@
        </fileset>\r
 \r
        <target name="full-jaba-client-jar" description="Pack datamodel, engine and runners" depends="compile">\r
-                       <echo>Jar file: Full WS client jar</echo>\r
-                       <delete file="${full-jaba-client}"></delete>\r
-                       <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="drmaa.jar"/>\r
-                               </zipgroupfileset>\r
-                               <fileset refid="fullclient"/>\r
-                               <manifest>\r
-                                       <attribute name="Built-By" value="Peter Troshin" />\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
-                               </manifest>\r
-                       </jar>\r
-               </target>\r
-       \r
+               <echo>Jar file: Full WS client jar</echo>\r
+               <delete file="${full-jaba-client}">\r
+               </delete>\r
+               <jar jarfile="${full-jaba-client}">\r
+                       <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >\r
+                               <include name="log4j-1.2.15.jar"/>\r
+                               <include name="compbio-util-1.3.jar"/>\r
+                               <include name="compbio-annotations-1.0.jar"/>\r
+                               <include name="drmaa.jar"/>\r
+                       </zipgroupfileset>\r
+                       <fileset refid="fullclient"/>\r
+                       <manifest>\r
+                               <attribute name="Built-By" value="Peter Troshin" />\r
+                               <attribute name="Class-Path" value="." />\r
+                               <attribute name="Implementation-Title" value="Full Java Bioinformatics Analyses Web Services Client" />\r
+                               <attribute name="Implementation-Vendor" value="Peter Troshin" />\r
+                               <attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />\r
+                       </manifest>\r
+               </jar>\r
+       </target>\r
+\r
        <target name="full-jaba-client" description="Pack binaries with sources and configuration files" \r
                        depends="full-jaba-client-jar, pack-binaries">\r
                <echo>Packing binaries, and configuration files</echo>\r
@@ -280,51 +283,53 @@
                </zip>\r
        </target>\r
 \r
-       \r
+\r
        <target name="full-jaba-jar" description="Pack datamodel, engine, runners, configuration, binaries and webservices" depends="compile">\r
-                       <echo>Jar file: Full WS client jar</echo>\r
-                       <delete file="${full-jaba-client}"></delete>\r
-                       <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="drmaa.jar"/>\r
-                               </zipgroupfileset>\r
-                               <fileset refid="fullclient"></fileset>\r
-                               <fileset dir="${basedir}/WEB-INF/classes/">\r
-                                       <!-- Web services-->\r
-                                       <include name="compbio/ws/**"/>\r
-                               </fileset>\r
-                               <!-- Set WSTester as main to help user to test their deployments -->\r
-                               <manifest>\r
-                                       <attribute name="Built-By" value="Peter Troshin" />\r
-                                       <attribute name="Class-Path" value="." />\r
-                                       <attribute name="Main-Class" value="compbio.ws.client.WSTester" />\r
-                                       <attribute name="Implementation-Title" value="Java Bioinformatics Analyses Web Services" />\r
-                                       <attribute name="Implementation-Vendor" value="Peter Troshin" />\r
-                                       <attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />\r
-                               </manifest>\r
-                       </jar>\r
+               <echo>Jar file: Full WS client jar</echo>\r
+               <delete file="${full-jaba-client}">\r
+               </delete>\r
+               <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="drmaa.jar"/>\r
+                       </zipgroupfileset>\r
+                       <fileset refid="fullclient">\r
+                       </fileset>\r
+                       <fileset dir="${basedir}/WEB-INF/classes/">\r
+                               <!-- Web services-->\r
+                               <include name="compbio/ws/**"/>\r
+                       </fileset>\r
+                       <!-- Set WSTester as main to help user to test their deployments -->\r
+                       <manifest>\r
+                               <attribute name="Built-By" value="Peter Troshin" />\r
+                               <attribute name="Class-Path" value="." />\r
+                               <attribute name="Main-Class" value="compbio.ws.client.WSTester" />\r
+                               <attribute name="Implementation-Title" value="Java Bioinformatics Analyses Web Services" />\r
+                               <attribute name="Implementation-Vendor" value="Peter Troshin" />\r
+                               <attribute name="Implementation-URL" value="http://www.compbio.dundee.ac.uk" />\r
+                       </manifest>\r
+               </jar>\r
        </target>\r
 \r
-       <target name="pack-binaries" description="Zip all binary files"> \r
+       <target name="pack-binaries" description="Zip all binary files">\r
                <delete file="${binaries}" failonerror="false"/>\r
                <zip destfile="${binaries}" >\r
                        <zipfileset dir="${basedir}/binaries" prefix="binaries" excludes="**/linux*/**"/>\r
                </zip>\r
        </target>\r
-       \r
-       <target name="pack-jaxws" description="Zip all JAXWS libraries"> \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="${web.lib.path}" includes="webservices-api.jar"  prefix="WEB-INF/lib" />\r
+                       <zipfileset dir="${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
-       <target name="pack-windows-binaries" description="Zip only windows binary files"> \r
+\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
                        <zipfileset dir="${basedir}/binaries" prefix="binaries" >\r
@@ -336,101 +341,108 @@
        </target>\r
 \r
        <target name="jaba-no-jaxws-no-binaries" description="Prepare JWS2 war file without runtime dependency - JAXWS jars and native binaries" depends="full-jaba-jar">\r
-                               <echo>Preparing war file without JAXWS and binaries</echo>\r
-               <delete file="${jaba}"></delete>        \r
-               <delete file="${jaba-no-jaxws-no-binaries}"></delete>\r
-                               <zip destfile="${jaba-no-jaxws-no-binaries}" whenempty="create">\r
-                                       <zipfileset dir="${basedir}/WEB-INF" prefix="WEB-INF">\r
-                                               <include name="web.xml"/>\r
-                                               <include name="sun-jaxws.xml"/>\r
-                                               <exclude name="classes"/>\r
-                                               <exclude name="lib"/>\r
-                                       </zipfileset>\r
-                                       <zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="**/*"/>\r
-                                       <zipfileset dir="${basedir}/conf" prefix="conf" excludes="**/log4j.properties*"/>\r
-                                       <!-- Add JSW2 web site apart from the binary archive -->\r
-                                       <zipfileset dir="${basedir}/website" excludes="archive/**, full_javadoc/**, devel*.html, tests/**, template.html"/>\r
-                                       <zipfileset dir="." includes="${full-jaba-client}" fullpath="WEB-INF/lib/jaba-client.jar"/>\r
-                                       <!-- Put a copy of log4j configuration file where it can be used  -->\r
-                                       <zipfileset dir="conf" includes="log4j.properties" prefix="WEB-INF/classes"/>\r
-                                       <!-- This is runtime dependency must be supplied by the container -->\r
-                                       <!-- zipfileset dir="${web.lib.path}" includes="servlet-api.jar" prefix="WEB-INF/lib" / -->\r
-                               </zip>\r
-       </target> \r
+               <echo>Preparing war file without JAXWS and binaries</echo>\r
+               <delete file="${jaba}">\r
+               </delete>\r
+               <delete file="${jaba-no-jaxws-no-binaries}">\r
+               </delete>\r
+               <zip destfile="${jaba-no-jaxws-no-binaries}" whenempty="create">\r
+                       <zipfileset dir="${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
+                       <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
+                       <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
+                       <zipfileset dir="conf" includes="log4j.properties" prefix="WEB-INF/classes"/>\r
+                       <!-- This is runtime dependency must be supplied by the container -->\r
+                       <!-- zipfileset dir="${web.lib.path}" includes="servlet-api.jar" prefix="WEB-INF/lib" / -->\r
+               </zip>\r
+       </target>\r
 \r
        <target name="build-devel-website" description="Pack developement related pages, tests, javadoc" >\r
-                               <echo>Packing data for internal web site</echo>\r
-                               <delete file="${jaba-devel-web}"></delete>      \r
-                               <zip destfile="${jaba-devel-web}" whenempty="create">\r
-                                       <!-- Add JSW2 web site apart from the binary archive -->\r
-                                       <zipfileset dir="${basedir}/website" excludes="template.html, download.html, index.html, manual.html, howto.html, archive/**, prog_docs/**"/>\r
-                               </zip>\r
-       </target> \r
-       \r
+               <echo>Packing data for internal web site</echo>\r
+               <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
+                       <zipfileset dir="${basedir}/website" excludes="template.html, download.html, index.html, manual.html, howto.html, archive/**, prog_docs/**"/>\r
+               </zip>\r
+       </target>\r
+\r
        <target name="jaba-without-jaxws" description="Prepare JWS2 war file without runtime dependency - JAXWS jars" depends="jaba-no-jaxws-no-binaries, pack-binaries">\r
-                               <echo>Preparing war file without JAXWS</echo>\r
-               <delete file="${jaba-no-jaxws}"></delete>       \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="${binaries}" />\r
+                       <zipgroupfileset file="${binaries}" />\r
                </zip>\r
-       </target> \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">\r
-                               <echo>Preparing war file without JAXWS</echo>\r
-               <delete file="${jaba-windows}"></delete>        \r
+               <echo>Preparing war file without JAXWS</echo>\r
+               <delete file="${jaba-windows}">\r
+               </delete>\r
                <delete dir="${basedir}/jobsout/*"/>\r
-               <delete file="${jaba-no-jaxws-windows}"></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 JSW2 web site apart from the binary archive -->\r
-                                       <zipfileset dir="${basedir}/website" excludes="archive/**, full_javadoc/**, devel*.html, tests/**, template.html"/>\r
-                               </zip>\r
-       </target> \r
-\r
-       \r
-       \r
+               <delete file="${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 JSW2 web site apart from the binary archive -->\r
+                       <zipfileset dir="${basedir}/website" excludes="archive/**, full_javadoc/**, devel*.html, tests/**, template.html"/>\r
+               </zip>\r
+       </target>\r
+\r
+\r
+\r
        <target name="jaba-complete" description="Prepare JWS2 war file" depends="jaba-without-jaxws, pack-jaxws">\r
-                       <echo>Preparing a complete war file</echo>\r
-                       <copy tofile="${jaba}" file="${jaba-no-jaxws}"/>\r
-                       <zip destfile="${jaba}" update="true" >\r
-                               <zipgroupfileset file="${jaxws-lib}"/>\r
-                       </zip>\r
-       </target> \r
+               <echo>Preparing a complete war file</echo>\r
+               <copy tofile="${jaba}" file="${jaba-no-jaxws}"/>\r
+               <zip destfile="${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="${jaxws-lib}"/>\r
-                       </zip>  \r
-       </target> \r
+               <echo>Preparing a complete war file</echo>\r
+               <copy tofile="${jaba-no-binaries}" file="${jaba-no-jaxws-no-binaries}"/>\r
+               <zip destfile="${jaba-no-binaries}" update="true" >\r
+                       <zipgroupfileset file="${jaxws-lib}"/>\r
+               </zip>\r
+       </target>\r
 \r
        <target name="jaba-complete-windows" description="Prepare JWS2 war file for windows" depends="jaba-without-jaxws-windows, pack-jaxws">\r
-                               <echo>Preparing a complete war file</echo>\r
-                               <copy tofile="${jaba-windows}" file="${jaba-no-jaxws-windows}"/>\r
-                               <zip destfile="${jaba-windows}" update="true" >\r
-                                       <zipgroupfileset file="${jaxws-lib}"/>\r
-                               </zip>\r
-       </target> \r
-       \r
+               <echo>Preparing a complete war file</echo>\r
+               <copy tofile="${jaba-windows}" file="${jaba-no-jaxws-windows}"/>\r
+               <zip destfile="${jaba-windows}" update="true" >\r
+                       <zipgroupfileset file="${jaxws-lib}"/>\r
+               </zip>\r
+       </target>\r
+\r
        <target name="build-all" description="Build-all the distributives"\r
                depends="full-jaba-client, minimal-jaba-client-jar, jaba-no-jaxws-no-binaries, jaba-no-binaries, jaba-complete, jaba-complete-windows"/>\r
 \r
        <!-- This task does not really depends on compile, but it is better to make sure that the code is sound -->\r
        <target name="archive-project" description="Pack everything in the project for those who do not have access to SVN" depends="compile">\r
-               <delete file="${jaba-project}"></delete>        \r
+               <delete file="${jaba-project}">\r
+               </delete>\r
                <zip destfile="${jaba-project}" whenempty="create" >\r
                        <fileset dir="." excludes="${distdir}/**, jobsout/**, test-output/**, **.svn, dundee-conf/**, TODO.txt, IDEAS.txt, ${activity.log}, **/*.zip, **/*.war"/>\r
                        <!-- Add jobsout directory but no content -->\r
@@ -455,142 +467,143 @@
                    </junit>\r
                </target>\r
        -->\r
-       \r
+\r
        <taskdef name="testNG" classname="org.testng.TestNGAntTask">\r
-               <classpath refid="test.classpath"></classpath>\r
+               <classpath refid="test.classpath">\r
+               </classpath>\r
        </taskdef>\r
-               \r
+\r
        <target name="CustomTest" depends="compile_with_debug">\r
-                       <delete file="${activity.log}"/> \r
-                       <testNG haltonfailure="true" enableassert="true" >\r
-                                       <jvmarg value="-server" />\r
-                                       <jvmarg value="-enableassertions" />\r
-                                       <jvmarg value="-Xms1024m" />\r
-                                       <jvmarg value="-Xmx1024m" />\r
-                                               <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>\r
-                                       <classpath refid="test.classpath" />\r
-                                       <classpath refid="project.classpath" />\r
-                                               <xmlfileset dir="." includes="temp-testng-customsuite.xml"/>\r
-                                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
-                   </testNG>\r
+               <delete file="${activity.log}"/>\r
+               <testNG haltonfailure="true" enableassert="true" >\r
+                       <jvmarg value="-server" />\r
+                       <jvmarg value="-enableassertions" />\r
+                       <jvmarg value="-Xms1024m" />\r
+                       <jvmarg value="-Xmx1024m" />\r
+                       <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>\r
+                       <classpath refid="test.classpath" />\r
+                       <classpath refid="project.classpath" />\r
+                       <xmlfileset dir="." includes="temp-testng-customsuite.xml"/>\r
+                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
+               </testNG>\r
        </target>\r
 \r
        <target name="Run_cluster_dependent_test" depends="compile_with_debug">\r
-                               <delete file="${activity.log}"/> \r
-                               <testNG groups="cluster" haltonfailure="true" enableassert="true" parallel="false" verbose="3">\r
-                                               <jvmarg value="-server" />\r
-                                               <jvmarg value="-enableassertions" />\r
-                                               <jvmarg value="-Xms1024m" />\r
-                                               <jvmarg value="-Xmx1024m" />\r
-                                                       <classfileset dir="${classes}" includes="**/*.class" />\r
-                                                       <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>\r
-                                               <classpath refid="test.classpath" />\r
-                                               <classpath refid="project.classpath" />\r
-                                               <sysproperty key="TestingDataPath" value="${data.src}"/>\r
-                           </testNG>\r
-               </target>\r
-       \r
+               <delete file="${activity.log}"/>\r
+               <testNG groups="cluster" haltonfailure="true" enableassert="true" parallel="false" verbose="3">\r
+                       <jvmarg value="-server" />\r
+                       <jvmarg value="-enableassertions" />\r
+                       <jvmarg value="-Xms1024m" />\r
+                       <jvmarg value="-Xmx1024m" />\r
+                       <classfileset dir="${classes}" includes="**/*.class" />\r
+                       <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>\r
+                       <classpath refid="test.classpath" />\r
+                       <classpath refid="project.classpath" />\r
+                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
+               </testNG>\r
+       </target>\r
+\r
        <target name="Test" depends="compile_with_debug">\r
-                               <delete file="${activity.log}"/> \r
-                               <testNG haltonfailure="true" enableassert="true" verbose="3" excludedgroups="performance" >\r
-                                               <jvmarg value="-server" />\r
-                                               <jvmarg value="-enableassertions" />\r
-                                               <jvmarg value="-Xms1024m" />\r
-                                               <jvmarg value="-Xmx1024m" />\r
-                                                       <classfileset dir="${classes}" includes="**/*.class" />\r
-                                                       <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>\r
-                                               <classpath refid="test.classpath" />\r
-                                               <classpath refid="project.classpath" />\r
-                                               <sysproperty key="TestingDataPath" value="${data.src}"/>\r
-                           </testNG>\r
-               </target>\r
+               <delete file="${activity.log}"/>\r
+               <testNG haltonfailure="true" enableassert="true" verbose="3" excludedgroups="performance" >\r
+                       <jvmarg value="-server" />\r
+                       <jvmarg value="-enableassertions" />\r
+                       <jvmarg value="-Xms1024m" />\r
+                       <jvmarg value="-Xmx1024m" />\r
+                       <classfileset dir="${classes}" includes="**/*.class" />\r
+                       <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>\r
+                       <classpath refid="test.classpath" />\r
+                       <classpath refid="project.classpath" />\r
+                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
+               </testNG>\r
+       </target>\r
 \r
        <target name="Performance_tests" depends="compile_with_debug">\r
-                                       <delete file="${activity.log}"/> \r
-                                       <testNG haltonfailure="true" enableassert="true" verbose="3" groups="performance" >\r
-                                                       <jvmarg value="-server" />\r
-                                                       <jvmarg value="-enableassertions" />\r
-                                                       <jvmarg value="-Xms1024m" />\r
-                                                       <jvmarg value="-Xmx1024m" />\r
-                                                               <classfileset dir="${classes}" includes="**/*.class" />\r
-                                                               <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>\r
-                                                       <classpath refid="test.classpath" />\r
-                                                       <classpath refid="project.classpath" />\r
-                                                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
-                                   </testNG>\r
+               <delete file="${activity.log}"/>\r
+               <testNG haltonfailure="true" enableassert="true" verbose="3" groups="performance" >\r
+                       <jvmarg value="-server" />\r
+                       <jvmarg value="-enableassertions" />\r
+                       <jvmarg value="-Xms1024m" />\r
+                       <jvmarg value="-Xmx1024m" />\r
+                       <classfileset dir="${classes}" includes="**/*.class" />\r
+                       <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>\r
+                       <classpath refid="test.classpath" />\r
+                       <classpath refid="project.classpath" />\r
+                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
+               </testNG>\r
        </target>\r
 \r
        <target name="Test_runners" depends="compile_with_debug">\r
-                       <delete file="${activity.log}"/> \r
-                       <testNG groups="runner" haltonfailure="true" verbose="3" enableassert="true" >\r
-                                       <jvmarg value="-server" />\r
-                                       <jvmarg value="-enableassertions" />\r
-                                       <jvmarg value="-Xms1024m" />\r
-                                       <jvmarg value="-Xmx1024m" />\r
-                                               <classfileset dir="${classes}" includes="**/*.class" />\r
-                                               <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>\r
-                                       <classpath refid="test.classpath" />\r
-                                       <classpath refid="project.classpath" />\r
-                                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
-                   </testNG>\r
+               <delete file="${activity.log}"/>\r
+               <testNG groups="runner" haltonfailure="true" verbose="3" enableassert="true" >\r
+                       <jvmarg value="-server" />\r
+                       <jvmarg value="-enableassertions" />\r
+                       <jvmarg value="-Xms1024m" />\r
+                       <jvmarg value="-Xmx1024m" />\r
+                       <classfileset dir="${classes}" includes="**/*.class" />\r
+                       <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>\r
+                       <classpath refid="test.classpath" />\r
+                       <classpath refid="project.classpath" />\r
+                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
+               </testNG>\r
        </target>\r
 \r
        <target name="Test_engines" depends="compile_with_debug">\r
-                       <delete file="${activity.log}"/> \r
-                       <testNG groups="engine" haltonfailure="true" verbose="3" enableassert="true" >\r
-                                       <jvmarg value="-server" />\r
-                                       <jvmarg value="-enableassertions" />\r
-                                       <jvmarg value="-Xms1024m" />\r
-                                       <jvmarg value="-Xmx1024m" />\r
-                                               <classfileset dir="${classes}" includes="**/*.class" />\r
-                                               <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>\r
-                                       <classpath refid="test.classpath" />\r
-                                       <classpath refid="project.classpath" />\r
-                                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
-                   </testNG>\r
+               <delete file="${activity.log}"/>\r
+               <testNG groups="engine" haltonfailure="true" verbose="3" enableassert="true" >\r
+                       <jvmarg value="-server" />\r
+                       <jvmarg value="-enableassertions" />\r
+                       <jvmarg value="-Xms1024m" />\r
+                       <jvmarg value="-Xmx1024m" />\r
+                       <classfileset dir="${classes}" includes="**/*.class" />\r
+                       <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>\r
+                       <classpath refid="test.classpath" />\r
+                       <classpath refid="project.classpath" />\r
+                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
+               </testNG>\r
        </target>\r
 \r
        <target name="All_cluster_independent_windows_only_tests" depends="compile_with_debug">\r
-                       <delete file="${activity.log}" failonerror="false"/> \r
-                       <testNG excludedgroups="cluster, non_windows" haltonfailure="true" verbose="3" enableassert="true"  >\r
-                                       <jvmarg value="-server" />\r
-                                       <jvmarg value="-enableassertions" />\r
-                                       <jvmarg value="-Xms1024m" />\r
-                                       <jvmarg value="-Xmx1024m" />\r
-                                               <classfileset dir="${classes}" includes="**/*.class" />\r
-                                               <classpath refid="test.classpath" />\r
-                                       <classpath refid="project.classpath" />\r
-                                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
-                   </testNG>\r
+               <delete file="${activity.log}" failonerror="false"/>\r
+               <testNG excludedgroups="cluster, non_windows" haltonfailure="true" verbose="3" enableassert="true"  >\r
+                       <jvmarg value="-server" />\r
+                       <jvmarg value="-enableassertions" />\r
+                       <jvmarg value="-Xms1024m" />\r
+                       <jvmarg value="-Xmx1024m" />\r
+                       <classfileset dir="${classes}" includes="**/*.class" />\r
+                       <classpath refid="test.classpath" />\r
+                       <classpath refid="project.classpath" />\r
+                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
+               </testNG>\r
        </target>\r
 \r
        <target name="All_cluster_independent_tests" depends="compile_with_debug">\r
-                       <delete file="${activity.log}" failonerror="false"/> \r
-                       <testNG excludedgroups="cluster, performance" haltonfailure="true" verbose="3" enableassert="true"  >\r
-                                       <jvmarg value="-server" />\r
-                                       <jvmarg value="-enableassertions" />\r
-                                       <jvmarg value="-Xms1024m" />\r
-                                       <jvmarg value="-Xmx1024m" />\r
-                                               <classfileset dir="${classes}" includes="**/*.class" />\r
-                                               <classpath refid="test.classpath" />\r
-                                       <classpath refid="project.classpath" />\r
-                                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
-                   </testNG>\r
+               <delete file="${activity.log}" failonerror="false"/>\r
+               <testNG excludedgroups="cluster, performance" haltonfailure="true" verbose="3" enableassert="true"  >\r
+                       <jvmarg value="-server" />\r
+                       <jvmarg value="-enableassertions" />\r
+                       <jvmarg value="-Xms1024m" />\r
+                       <jvmarg value="-Xmx1024m" />\r
+                       <classfileset dir="${classes}" includes="**/*.class" />\r
+                       <classpath refid="test.classpath" />\r
+                       <classpath refid="project.classpath" />\r
+                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
+               </testNG>\r
        </target>\r
 \r
        <target name="Rerun_failed_tests" depends="compile_with_debug">\r
-                       <delete file="${activity.log}" failonerror="false"/> \r
-                       <testNG haltonfailure="true" enableassert="true" verbose="9" >\r
-                                       <jvmarg value="-server" />\r
-                                       <jvmarg value="-enableassertions" />\r
-                                       <jvmarg value="-Xms1024m" />\r
-                                       <jvmarg value="-Xmx1024m" />\r
-                                               <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>\r
-                                       <classpath refid="test.classpath" />\r
-                                       <classpath refid="project.classpath" />\r
-                                               <xmlfileset dir="." includes="test-output/testng-failed.xml"/>\r
-                                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
-                   </testNG>\r
+               <delete file="${activity.log}" failonerror="false"/>\r
+               <testNG haltonfailure="true" enableassert="true" verbose="9" >\r
+                       <jvmarg value="-server" />\r
+                       <jvmarg value="-enableassertions" />\r
+                       <jvmarg value="-Xms1024m" />\r
+                       <jvmarg value="-Xmx1024m" />\r
+                       <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>\r
+                       <classpath refid="test.classpath" />\r
+                       <classpath refid="project.classpath" />\r
+                       <xmlfileset dir="." includes="test-output/testng-failed.xml"/>\r
+                       <sysproperty key="TestingDataPath" value="${data.src}"/>\r
+               </testNG>\r
        </target>\r
 \r
        <!-- <zipfileset excludes="META-INF/*.SF" src="jarfilename.jar"/> \r
@@ -631,7 +644,7 @@
                </target>\r
                \r
                -->\r
-       \r
+\r
        <!--\r
                <target name="run-client-jar" description="EXAMPLE TASK ONLY">\r
                        <java jar="${basedir}/resources/wsclient.jar" fork="true"\r
@@ -648,5 +661,5 @@
                        </java>\r
                </target>\r
        -->\r
-       \r
+\r
 </project>
\ No newline at end of file

diff --git a/engine/compbio/engine/client/PathValidator.java b/engine/compbio/engine/client/PathValidator.java
index c59c957..97b5315 100644 (file)
--- a/engine/compbio/engine/client/PathValidator.java
+++ b/engine/compbio/engine/client/PathValidator.java
@@ -46,6 +46,9 @@ public final class PathValidator {
                }\r
        }\r
 \r
+       /*\r
+        * TODO move to Utils\r
+        */\r
        public static boolean isValidDirectory(String directory) {\r
                if (Util.isEmpty(directory)) {\r
                        return false;\r

diff --git a/engine/compbio/engine/client/SkeletalExecutable.java b/engine/compbio/engine/client/SkeletalExecutable.java
index 19fde7e..744bb33 100644 (file)
--- a/engine/compbio/engine/client/SkeletalExecutable.java
+++ b/engine/compbio/engine/client/SkeletalExecutable.java
@@ -323,7 +323,7 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
        public LimitsManager<T> getLimits() {\r
                synchronized (SkeletalExecutable.class) {\r
                        if (limits == null) {\r
-                               limits = compbio.runner.Util.getLimits(this.getType());\r
+                               limits = compbio.engine.client.Util.getLimits(this.getType());\r
                        }\r
                }\r
                return limits;\r

diff --git a/engine/compbio/engine/client/Util.java b/engine/compbio/engine/client/Util.java
index afe2b6c..63181ea 100644 (file)
--- a/engine/compbio/engine/client/Util.java
+++ b/engine/compbio/engine/client/Util.java
@@ -32,6 +32,7 @@ import compbio.engine.client.Executable.ExecProvider;
 import compbio.engine.conf.DirectoryManager;\r
 import compbio.engine.conf.PropertyHelperManager;\r
 import compbio.metadata.JobStatus;\r
+import compbio.metadata.LimitsManager;\r
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.util.FileUtil;\r
 import compbio.util.PropertyHelper;\r
@@ -303,4 +304,37 @@ public final class Util {
                return exec;\r
        }\r
 \r
+       /**\r
+        * For now just assume that all parameters which came in needs setting it\r
+        * will be a client responsibility to prepare RunnerConfig object then\r
+        * \r
+        * @param rconfig\r
+        * @return\r
+        * \r
+        *         public static List<String> toOptionString(RunnerConfig<?>\r
+        *         rconfig) { String option = ""; List<String> options = new\r
+        *         ArrayList<String>(); for (Parameter<?> par :\r
+        *         rconfig.getParameters()) { if (par.getPossibleValues().isEmpty())\r
+        *         { option = par.getOptionName(); } else { option =\r
+        *         par.getOptionName() + "=" + par.getPossibleValues().get(0); } //\r
+        *         separate options options.add(option); } return options; }\r
+        */\r
+       \r
+       public static <T> LimitsManager<T> getLimits(Class<Executable<T>> clazz) {\r
+               LimitsManager<T> limits = null;\r
+               try {\r
+                       limits = ConfExecutable.getRunnerLimits(clazz);\r
+               } catch (FileNotFoundException e) {\r
+                       Util.log.warn(\r
+                                       "No limits are found for " + clazz + " executable! "\r
+                                                       + e.getLocalizedMessage(), e.getCause());\r
+                       // its ok, limit may not be initialized\r
+               } catch (IOException e) {\r
+                       Util.log.warn("IO exception while attempting to read limits for "\r
+                                       + clazz + " executable! " + e.getLocalizedMessage(),\r
+                                       e.getCause());\r
+               }\r
+               return limits;\r
+       }\r
+\r
 }\r

diff --git a/runner/compbio/runner/Util.java b/runner/compbio/runner/Util.java
index bfced2a..47f169b 100644 (file)
--- a/runner/compbio/runner/Util.java
+++ b/runner/compbio/runner/Util.java
@@ -37,53 +37,19 @@ import compbio.engine.client.ConfExecutable;
 import compbio.engine.client.ConfiguredExecutable;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.conf.PropertyHelperManager;\r
-import compbio.metadata.LimitsManager;\r
 import compbio.metadata.PresetManager;\r
 import compbio.metadata.RunnerConfig;\r
 import compbio.util.PropertyHelper;\r
 \r
 public final class Util {\r
 \r
-       private static Logger log = Logger.getLogger(Util.class);\r
+       public static Logger log = Logger.getLogger(Util.class);\r
 \r
        private static final PropertyHelper ph = PropertyHelperManager\r
                        .getPropertyHelper();\r
 \r
        public static final String SPACE = " ";\r
 \r
-       /**\r
-        * For now just assume that all parameters which came in needs setting it\r
-        * will be a client responsibility to prepare RunnerConfig object then\r
-        * \r
-        * @param rconfig\r
-        * @return\r
-        * \r
-        *         public static List<String> toOptionString(RunnerConfig<?>\r
-        *         rconfig) { String option = ""; List<String> options = new\r
-        *         ArrayList<String>(); for (Parameter<?> par :\r
-        *         rconfig.getParameters()) { if (par.getPossibleValues().isEmpty())\r
-        *         { option = par.getOptionName(); } else { option =\r
-        *         par.getOptionName() + "=" + par.getPossibleValues().get(0); } //\r
-        *         separate options options.add(option); } return options; }\r
-        */\r
-\r
-       public static <T> LimitsManager<T> getLimits(Class<Executable<T>> clazz) {\r
-               LimitsManager<T> limits = null;\r
-               try {\r
-                       limits = ConfExecutable.getRunnerLimits(clazz);\r
-               } catch (FileNotFoundException e) {\r
-                       log.warn(\r
-                                       "No limits are found for " + clazz + " executable! "\r
-                                                       + e.getLocalizedMessage(), e.getCause());\r
-                       // its ok, limit may not be initialized\r
-               } catch (IOException e) {\r
-                       log.warn("IO exception while attempting to read limits for "\r
-                                       + clazz + " executable! " + e.getLocalizedMessage(),\r
-                                       e.getCause());\r
-               }\r
-               return limits;\r
-       }\r
-\r
        public static synchronized <T> RunnerConfig<T> getSupportedOptions(\r
                        Class<? extends Executable<T>> clazz) {\r
                try {\r

diff --git a/testsrc/compbio/metadata/AllTestSuit.java b/testsrc/compbio/metadata/AllTestSuit.java
index 794565a..24ca11d 100644 (file)
--- a/testsrc/compbio/metadata/AllTestSuit.java
+++ b/testsrc/compbio/metadata/AllTestSuit.java
@@ -32,21 +32,21 @@ public class AllTestSuit {
                        .getPresets(ClustalW.class);\r
        public static final RunnerConfig<ClustalW> CLUSTAL_PARAMETERS = Util\r
                        .getSupportedOptions(ClustalW.class);\r
-       public static final LimitsManager<ClustalW> CLUSTAL_LIMITS = Util\r
+       public static final LimitsManager<ClustalW> CLUSTAL_LIMITS = compbio.engine.client.Util\r
                        .getLimits(new ClustalW().getType());\r
 \r
        public static final PresetManager<Tcoffee> TCOFFEE_PRESETS = Util\r
                        .getPresets(Tcoffee.class);\r
        public static final RunnerConfig<Tcoffee> TCOFFEE_PARAMETERS = Util\r
                        .getSupportedOptions(Tcoffee.class);\r
-       public static final LimitsManager<Tcoffee> TCOFFEE_LIMITS = Util\r
+       public static final LimitsManager<Tcoffee> TCOFFEE_LIMITS = compbio.engine.client.Util\r
                        .getLimits(new Tcoffee().getType());\r
 \r
        public static final PresetManager<Muscle> MUSCLE_PRESETS = Util\r
                        .getPresets(Muscle.class);\r
        public static final RunnerConfig<Muscle> MUSCLE_PARAMETERS = Util\r
                        .getSupportedOptions(Muscle.class);\r
-       public static final LimitsManager<Muscle> MUSCLE_LIMITS = Util\r
+       public static final LimitsManager<Muscle> MUSCLE_LIMITS = compbio.engine.client.Util\r
                        .getLimits(new Muscle().getType());\r
 \r
        public final static String test_group_cluster = "cluster";\r

diff --git a/webservices/compbio/ws/server/AAConWS.java b/webservices/compbio/ws/server/AAConWS.java
index e6f8122..1ffbbf3 100644 (file)
--- a/webservices/compbio/ws/server/AAConWS.java
+++ b/webservices/compbio/ws/server/AAConWS.java
@@ -51,7 +51,7 @@ public class AAConWS implements SequenceAnnotation<AACon> {
        private static final PresetManager<AACon> aaconPresets = Util\r
                        .getPresets(AACon.class);\r
 \r
-       private static final LimitsManager<AACon> limitMan = compbio.runner.Util\r
+       private static final LimitsManager<AACon> limitMan = compbio.engine.client.Util\r
                        .getLimits(new AACon().getType());\r
 \r
        ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)\r

diff --git a/webservices/compbio/ws/server/ClustalWS.java b/webservices/compbio/ws/server/ClustalWS.java
index a5fc701..93d0c7f 100644 (file)
--- a/webservices/compbio/ws/server/ClustalWS.java
+++ b/webservices/compbio/ws/server/ClustalWS.java
@@ -66,7 +66,7 @@ public class ClustalWS implements MsaWS<ClustalW> {
        private static final PresetManager<ClustalW> clustalPresets = Util\r
                        .getPresets(ClustalW.class);\r
 \r
-       private static final LimitsManager<ClustalW> limitMan = compbio.runner.Util\r
+       private static final LimitsManager<ClustalW> limitMan = compbio.engine.client.Util\r
                        .getLimits(new ClustalW().getType());\r
 \r
        /*\r

diff --git a/webservices/compbio/ws/server/DisemblWS.java b/webservices/compbio/ws/server/DisemblWS.java
index 62f70d3..213711c 100644 (file)
--- a/webservices/compbio/ws/server/DisemblWS.java
+++ b/webservices/compbio/ws/server/DisemblWS.java
@@ -47,7 +47,7 @@ public class DisemblWS implements SequenceAnnotation<Disembl> {
        private static final PresetManager<Disembl> disemblPresets = Util\r
                        .getPresets(Disembl.class);\r
 \r
-       private static final LimitsManager<Disembl> limitMan = compbio.runner.Util\r
+       private static final LimitsManager<Disembl> limitMan = compbio.engine.client.Util\r
                        .getLimits(new Disembl().getType());\r
 \r
        ConfiguredExecutable<Disembl> init(List<FastaSequence> sequences)\r

diff --git a/webservices/compbio/ws/server/GlobPlotWS.java b/webservices/compbio/ws/server/GlobPlotWS.java
index 603c7dd..affe48e 100644 (file)
--- a/webservices/compbio/ws/server/GlobPlotWS.java
+++ b/webservices/compbio/ws/server/GlobPlotWS.java
@@ -47,7 +47,7 @@ public class GlobPlotWS implements SequenceAnnotation<GlobPlot> {
        private static final PresetManager<GlobPlot> globPlotPresets = Util\r
                        .getPresets(GlobPlot.class);\r
 \r
-       private static final LimitsManager<GlobPlot> limitMan = compbio.runner.Util\r
+       private static final LimitsManager<GlobPlot> limitMan = compbio.engine.client.Util\r
                        .getLimits(new GlobPlot().getType());\r
 \r
        ConfiguredExecutable<GlobPlot> init(List<FastaSequence> sequences)\r

diff --git a/webservices/compbio/ws/server/JronnWS.java b/webservices/compbio/ws/server/JronnWS.java
index 202cad1..97d4ceb 100644 (file)
--- a/webservices/compbio/ws/server/JronnWS.java
+++ b/webservices/compbio/ws/server/JronnWS.java
@@ -49,7 +49,7 @@ public class JronnWS implements SequenceAnnotation<Jronn> {
        private static final PresetManager<Jronn> jronnPresets = Util\r
                        .getPresets(Jronn.class);\r
 \r
-       private static final LimitsManager<Jronn> limitMan = compbio.runner.Util\r
+       private static final LimitsManager<Jronn> limitMan = compbio.engine.client.Util\r
                        .getLimits(new Jronn().getType());\r
 \r
        ConfiguredExecutable<Jronn> init(List<FastaSequence> sequences)\r

diff --git a/webservices/compbio/ws/server/MafftWS.java b/webservices/compbio/ws/server/MafftWS.java
index d2de592..9b74ce6 100644 (file)
--- a/webservices/compbio/ws/server/MafftWS.java
+++ b/webservices/compbio/ws/server/MafftWS.java
@@ -64,7 +64,7 @@ public class MafftWS implements MsaWS<Mafft> {
        private static final PresetManager<Mafft> mafftPresets = Util\r
                        .getPresets(Mafft.class);\r
 \r
-       private static final LimitsManager<Mafft> limitMan = compbio.runner.Util\r
+       private static final LimitsManager<Mafft> limitMan = compbio.engine.client.Util\r
                        .getLimits(new Mafft().getType());\r
 \r
        @Override\r

diff --git a/webservices/compbio/ws/server/MuscleWS.java b/webservices/compbio/ws/server/MuscleWS.java
index d6a9ba1..80f67b2 100644 (file)
--- a/webservices/compbio/ws/server/MuscleWS.java
+++ b/webservices/compbio/ws/server/MuscleWS.java
@@ -64,7 +64,7 @@ public class MuscleWS implements MsaWS<Muscle> {
        private static final PresetManager<Muscle> musclePresets = Util\r
                        .getPresets(Muscle.class);\r
 \r
-       private static final LimitsManager<Muscle> limitMan = compbio.runner.Util\r
+       private static final LimitsManager<Muscle> limitMan = compbio.engine.client.Util\r
                        .getLimits(new Muscle().getType());\r
 \r
        @Override\r

diff --git a/webservices/compbio/ws/server/ProbconsWS.java b/webservices/compbio/ws/server/ProbconsWS.java
index 3600c46..586352b 100644 (file)
--- a/webservices/compbio/ws/server/ProbconsWS.java
+++ b/webservices/compbio/ws/server/ProbconsWS.java
@@ -61,7 +61,7 @@ public class ProbconsWS implements MsaWS<Probcons> {
        private static final RunnerConfig<Probcons> probconsOptions = Util\r
                        .getSupportedOptions(Probcons.class);\r
 \r
-       private static final LimitsManager<Probcons> limitMan = compbio.runner.Util\r
+       private static final LimitsManager<Probcons> limitMan = compbio.engine.client.Util\r
                        .getLimits(new Probcons().getType());\r
 \r
        @Override\r

diff --git a/webservices/compbio/ws/server/TcoffeeWS.java b/webservices/compbio/ws/server/TcoffeeWS.java
index 5608a53..feb35f0 100644 (file)
--- a/webservices/compbio/ws/server/TcoffeeWS.java
+++ b/webservices/compbio/ws/server/TcoffeeWS.java
@@ -66,7 +66,7 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
        private static final PresetManager<Tcoffee> tcoffeePresets = Util\r
                        .getPresets(Tcoffee.class);\r
 \r
-       private static final LimitsManager<Tcoffee> limitMan = compbio.runner.Util\r
+       private static final LimitsManager<Tcoffee> limitMan = compbio.engine.client.Util\r
                        .getLimits(new Tcoffee().getType());\r
 \r
        @Override\r

diff --git a/website/archive/datamodel-1.1.jar b/website/archive/datamodel-1.1.jar
new file mode 100644 (file)
index 0000000..36dfa7f
Binary files /dev/null and b/website/archive/datamodel-1.1.jar differ