[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Fri Jun  8 10:04:27 EDT 2007
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv28675/xmls

Modified Files:
	seahawkBuild.xml 
Log Message:
Commit of Seahawk 1.0 updates and associated core updates
moby-live/Java/xmls seahawkBuild.xml,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml	2006/12/15 04:39:52	1.7
+++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml	2007/06/08 14:04:27	1.8
@@ -25,6 +25,10 @@
   <property name="servlet.tester.classname" value="org.biomoby.service.test.ServletTester"/>
   <property name="servlet.warname" value="MobyServlet"/>
 
+  <property name="acdservlet.auto.classname" value="ca.ucalgary.services.test.ACDServiceTestCase"/>
+  <property name="acdservlet.classname" value="ca.ucalgary.servlets.ACDService"/>
+  <property name="acdservlet.warname" value="ACDServlet"/>
+
   <property name="jarmaker.dir" location="${build.dir}/jarmaker"/>
   <property name="jarmaker.fullname" value="ca.ucalgary.seahawk.util.MinJarMaker"/>
   <property name="jarmaker.name" value="MinJarMaker"/>
@@ -87,7 +91,7 @@
 	<pathelement path="${jarmaker.dir}"/>
       </classpath>
 	<jvmarg value="-D${jarmaker.classPathProperty}=${scp}:${src.webapps}"/>
-	<jvmarg value="-D${jarmaker.manifestMainClassProperty}=${servlet.classname}"/>
+	<jvmarg value="-D${jarmaker.manifestMainClassProperty}=${servlet.tester.classname}"/>
 	<!-- The following is a list of classes that aren't picked up by the unit
 	     tests, but which the applet might need.  -->
 	<jvmarg value="-D${jarmaker.extraClassesProperty}=org/apache/xerces/xs/*PSVI.class:org/biomoby/**Exception.class:org/apache/**Exception.class:org/apache/**Error.class:org/apache/**ErrorResources.class:org/apache/**Messages.class:org/apache/log4j/spi/*.class:org/apache/axis/utils/*.class:org/apache/**.properties:javax/**/soap/*.class:org/jdom/*.class"/>
@@ -129,10 +133,63 @@
     
   </target>
 
+  <target name="acdservlet-war" depends="compile, make_maker" description="(User) Builds the ACDServlet WAR for MOBY-S service creation based on wrapping EMBOSS command-line programs described by ACD files">
+    <echo message="Building ACD servlet standalone WAR to ${build.clients.absolute}"/>
+
+    <mkdir dir="${jarmaker.dir}/WEB-INF"/>
+    <copy file="${src.webapps}/WEB-INF/acdweb.xml" tofile="${jarmaker.dir}/WEB-INF/web.xml"/>
+    <java dir="${jarmaker.dir}" jvm="${jarmaker.virgin_jvm}" classname="${jarmaker.fullname}" fork="true">
+      <classpath>
+	<pathelement path="${jarmaker.dir}"/>
+      </classpath>
+	<jvmarg value="-Dmoby.debug=1"/>
+        <jvmarg value="-D${jarmaker.classPathProperty}=${scp}:${src.webapps}"/>
+	<jvmarg value="-D${jarmaker.manifestMainClassProperty}=${servlet.tester.classname}"/>
+	<!-- The following is a list of classes that aren't picked up by the unit
+	     tests, but which the applet might need.  -->
+	<jvmarg value="-D${jarmaker.extraClassesProperty}=org/apache/xerces/xs/*PSVI.class:org/biomoby/**Exception.class:org/apache/**Exception.class:org/apache/**Error.class:org/apache/**ErrorResources.class:org/apache/**Messages.class:org/apache/log4j/spi/*.class:org/apache/axis/utils/*.class:org/apache/**.properties:javax/**/soap/*.class:org/jdom/*.class"/>
+
+	<arg value="${build.clients.absolute}/${acdservlet.warname}.war"/>
+	<arg value="${acdservlet.auto.classname}"/>
+    </java>
+
+	<mkdir dir="${build.classes}/WEB-INF"/>
+	<mkdir dir="${build.classes}/WEB-INF/classes"/>
+	<mkdir dir="${build.classes}/WEB-INF/lib"/>
+	<unjar src="${build.clients.absolute}/${acdservlet.warname}.war" dest="${build.classes}/WEB-INF/classes"/>
+        <copy file="${src.webapps}/WEB-INF/acdweb.xml" tofile="${build.classes}/WEB-INF/web.xml"/>
+
+	<jar destfile="${build.clients.absolute}/${acdservlet.warname}.war"
+		filesonly="true"
+		update="true"
+		compress="true"
+	        includes="WEB-INF/**"
+	        excludes="WEB-INF/classes/javax/servlet/**"
+		basedir="${build.classes}">
+            <manifest>
+		<attribute name="Built-By" value="${user.name}"/>
+		<attribute name="Main-Class" value="${servlet.tester.classname}"/>
+		<section name="common">
+		<attribute name="Implementation-Title" value="ACDServlet: A Framework for providing MOBY-S Web Services based on wrapping EMBOSS ACD-file-described command-line programs"/>
+		<attribute name="Implementation-Version" value="${version}"/>
+		<attribute name="Implementation-Vendor"
+                   value="University of Calgary, Sun Center of Excellence for Visual Genomics"/>
+		</section>
+    	    </manifest>
+        </jar>
+	
+	<delete dir="${build.classes}/WEB-INF"/>
+
+	<echo message="The ACD servlet standalone WAR is ${build.clients.absolute}/${acdservlet.warname}.war"/>
+    
+  </target>
+
+  <property name="url" value=""/>
   <target name="seahawk" depends="compile" description="(User) Run the Seahawk MOBY client interface as a standalone application">
       <java classname="${seahawk.classname}" classpathref="seahawk.build.classpath" fork="true">
 	<jvmarg value="-Dmoby.debug=1"/>
-	<jvmarg value="-Dcom.sun.management.jmxremote=1"/>
+	<!--<jvmarg value="-Dcom.sun.management.jmxremote=1"/>-->
+        <arg value="${url}"/>
     </java>
   </target>