[MOBY-guts] biomoby commit

Paul Gordon gordonp at dev.open-bio.org
Thu Oct 30 02:33:26 UTC 2008


gordonp
Wed Oct 29 22:33:25 EDT 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv10500/xmls

Modified Files:
	junit.xml project.pom seahawkBuild.xml 
Log Message:
Updates related to SAWSDL wrapping Web Service implementation
moby-live/Java/xmls junit.xml,1.5,1.6 project.pom,1.12,1.13 seahawkBuild.xml,1.17,1.18
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/junit.xml,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/xmls/junit.xml	2008/03/17 23:48:01	1.5
+++ /home/repository/moby/moby-live/Java/xmls/junit.xml	2008/10/30 02:33:25	1.6
@@ -36,7 +36,7 @@
   
 <!-- this is the core: here is the testing done -->
 <!-- [ maintained by Paul Gordon ]              -->
-<target name="do-junit" if="junit.is.present" depends="junit-present">
+<target name="do-junit" if="junit.is.present" depends="junit-present,compile">
 
   <junit
     printsummary="yes"
@@ -46,19 +46,23 @@
 
     <batchtest fork="no" todir="${test.report.dir}">
       <fileset dir="${src.main}">
-        <!--<include name="org/biomoby/shared/data/test/MobyDataDateTimeTestCase.java"/>-->
-        <!--<include name="org/biomoby/service/test/MobyServletTestCase.java"/>-->
-        <!--<include name="org/biomoby/client/test/AsyncClientTestCase.java"/>-->
-        <!--<include name="org/omg/lsae/sax/test/AnalysisEventTestCase.java"/>-->
-        <!--<include name="org/soap/sax/test/SOAPFaultTestCase.java"/>-->
-        <!--<include name="ca/ucalgary/services/util/test/ACDFileTestCase.java"/>-->
+<!--        <include name="org/biomoby/shared/data/test/MobyDataDateTimeTestCase.java"/>
+        <include name="org/biomoby/service/test/MobyServletTestCase.java"/>
+        <include name="org/biomoby/client/test/AsyncClientTestCase.java"/>
+        <include name="org/omg/lsae/sax/test/AnalysisEventTestCase.java"/>
+        <include name="org/soap/sax/test/SOAPFaultTestCase.java"/>
+        <include name="ca/ucalgary/services/util/test/ACDFileTestCase.java"/>
         <include name="ca/ucalgary/services/util/test/XHTMLFormTestCase.java"/>
-        <!--<include name="ca/ucalgary/services/test/ACDServiceTestCase.java"/>-->
-        <!--<include name="ca/ucalgary/seahawk/util/test/DataRecorderTestCase.java"/>-->
-        <!--<include name="ca/ucalgary/seahawk/gui/test/SeahawkTestCase.java"/>-->
-        <!--<include name="ca/ucalgary/seahawk/services/test/MobyClientTestCase.java"/>-->
-        <!--<include name="ca/ucalgary/seahawk/services/test/RegexParserTestCase.java"/>-->
-        <!--<include name="ca/ucalgary/seahawk/services/test/TextClientTestCase.java"/>-->
+        <include name="ca/ucalgary/services/util/test/WSDLConfigTestCase.java"/> 
+        <include name="ca/ucalgary/services/test/WSDLServiceTestCase.java"/>  
+        <include name="org/biomoby/shared/test/MobyNamespaceTestCase.java"/>
+        <include name="org/biomoby/shared/test/LSIDResolverTestCase.java"/>
+        <include name="ca/ucalgary/services/test/ACDServiceTestCase.java"/>
+        <include name="ca/ucalgary/seahawk/util/test/DataRecorderTestCase.java"/>-->
+        <include name="ca/ucalgary/seahawk/gui/test/SeahawkTestCase.java"/><!--
+        <include name="ca/ucalgary/seahawk/services/test/MobyClientTestCase.java"/>
+        <include name="ca/ucalgary/seahawk/services/test/RegexParserTestCase.java"/>
+        <include name="ca/ucalgary/seahawk/services/test/TextClientTestCase.java"/>-->
       </fileset>
     </batchtest>
 

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2008/08/13 15:12:38	1.12
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2008/10/30 02:33:25	1.13
@@ -46,6 +46,11 @@
       <layout>legacy</layout>
     </repository>
     <repository>
+      <id>maven2-repository.dev.java.net</id>
+      <name>Java.net Repository for Maven 2</name>
+      <url>http://download.java.net/maven/2/</url>
+    </repository>
+    <repository>
       <id>bio.maven.repository</id>
       <url>http://biomoby.org/m2repo/</url>
     </repository>
@@ -88,7 +93,6 @@
 
 
   <dependencies>
-
     <dependency>
       <groupId>org.apache.axis</groupId>
       <artifactId>axis</artifactId>
@@ -266,6 +270,12 @@
     </dependency>
 
     <dependency>
+      <groupId>com.sun.xml.ws</groupId>
+      <artifactId>jaxws-rt</artifactId>
+      <version>2.1.4</version>
+    </dependency>
+
+    <dependency>
       <groupId>jdom</groupId>
       <artifactId>jdom</artifactId>
       <version>1.0</version>
@@ -280,13 +290,13 @@
     <dependency>
       <groupId>javax.xml</groupId>
       <artifactId>jaxb-impl</artifactId>
-      <version>2.0EA3</version>
+      <version>2.1</version>
     </dependency>
 
     <dependency>
-      <groupId>javax.xml</groupId>
+      <groupId>com.sun.xml.bind</groupId>
       <artifactId>jaxb-xjc</artifactId>
-      <version>2.0EA3</version>
+      <version>2.1</version>
     </dependency>
 
     <dependency>
@@ -305,11 +315,11 @@
       </exclusions> 
     </dependency>
 
-    <dependency>
+    <!--<dependency>
       <groupId>javax.xml</groupId>
       <artifactId>jaxrpc-api</artifactId>
       <version>1.1</version>
-    </dependency>
+    </dependency>-->
 
     <dependency>
       <groupId>com.toedter</groupId>
@@ -368,11 +378,11 @@
       <version>1.0-MR1</version>
     </dependency>
 
-    <dependency>
+    <!--<dependency>
       <groupId>javax.annotation</groupId>
       <artifactId>jsr250-api</artifactId>
       <version>1.0</version>
-    </dependency>
+    </dependency>-->
 
     <dependency>
       <groupId>org.openoffice</groupId>
@@ -417,8 +427,13 @@
       <groupId>org.jvnet.staxex</groupId>
       <artifactId>stax-ex</artifactId>
       <version>1.2</version>
+    </dependency>-->
+
+    <dependency>
+      <groupId>org.codehaus.woodstox</groupId>
+      <artifactId>wstx-asl</artifactId>
+      <version>3.2.1</version>
     </dependency>
-    -->
 
     <dependency>
       <groupId>org.tulsoft</groupId>

===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml	2008/02/14 10:19:46	1.17
+++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml	2008/10/30 02:33:25	1.18
@@ -32,6 +32,11 @@
   <property name="acdservlet.warname" value="ACDServlet"/>
   <property name="acdservlet.web.xml" value="acdweb.xml"/>
 
+  <property name="wsdlservlet.auto.classname" value="ca.ucalgary.services.test.WSDLServiceTestCase"/>
+  <property name="wsdlservlet.classname" value="ca.ucalgary.servlets.WSDLService"/>
+  <property name="wsdlservlet.warname" value="SAWSDLServlet"/>
+  <property name="wsdlservlet.web.xml" value="wsdlweb.xml"/>
+
   <property name="cgiservlet.auto.classname" value="ca.ucalgary.services.test.CGIServiceTestCase"/>
   <property name="cgiservlet.classname" value="ca.ucalgary.servlets.CGIService"/>
   <property name="cgiservlet.warname" value="CGIServlet"/>
@@ -50,8 +55,8 @@
   <!-- The following should be the path to a JRE install with nothing but the
 	default libraries, so that we don't miss classes in the jar making because
 	they're part of our system's custom Java. -->
-  <!--<property name="jarmaker.virgin_jvm" location="/export/data/programs/jdk1.6.0_04/bin/java"/>-->
-  <property name="jarmaker.virgin_jvm" location="/export/data/programs/jdk1.5.0_06/bin/java"/>
+  <property name="jarmaker.virgin_jvm" location="/export/data/programs/jdk1.6.0_04/bin/java"/>
+  <!--<property name="jarmaker.virgin_jvm" location="/export/data/programs/jdk1.5.0_06/bin/java"/>-->
   <!--<property name="jarmaker.virgin_jvm" location="/usr/bin/java"/>-->
   
   <target name="seahawk-init" depends="init">
@@ -83,11 +88,12 @@
       <classpath>
 	<pathelement path="${jarmaker.dir}"/>
       </classpath>
+        <!--<jvmarg value="-Dverbose.class=true"/>-->
 	<jvmarg value="-D${jarmaker.classPathProperty}=${scp}"/>
 	<jvmarg value="-D${jarmaker.manifestMainClassProperty}=${seahawk.classname}"/>
 	<!-- The following is a list of classes that aren't picked up by the unit
 	     tests, but which the applet might need.  -->
-	<jvmarg value="-D${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/**ErrorHandler.class:org/apache/log4j/spi/*.class:org/apache/axis/**:org/apache/**.properties:javax/**/soap/*.class:org/jdom/*.class"/>
+	<jvmarg value="-D${jarmaker.extraClassesProperty}=META-INF/**: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/**ErrorHandler.class:org/apache/log4j/spi/*.class:org/apache/axis/**:org/apache/**.properties:javax/**/soap/*.class:org/jdom/*.class:com/ibm/icu/**.class"/>
 
 	<arg value="${build.clients.absolute}/${seahawk.jarname}.jar"/>
 	<arg value="${seahawk.auto.classname}"/>
@@ -107,8 +113,8 @@
       <classpath>
 	<pathelement path="${jarmaker.dir}"/>
       </classpath>
-        <!--<jvmarg value="-verbose:class"/>
-        <jvmarg value="-Dverbose.class=true"/>-->
+        <!--<jvmarg value="-verbose:class"/>-->
+        <jvmarg value="-Dverbose.class=true"/>
 	<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
@@ -203,6 +209,60 @@
     
   </target>
 
+  <target name="sawsdlservlet-war" depends="seahawk-init, compile, make_maker" description="(User) Builds the SAWSDLServlet WAR for MOBY-S service creation based on wrapping SAWSDL and moby-annotated WSDL documents">
+    <echo message="Building SAWSDL servlet standalone WAR to ${build.clients.absolute}"/>
+
+    <mkdir dir="${jarmaker.dir}/WEB-INF"/>
+    <copy file="${src.webapps}/WEB-INF/${wsdlservlet.web.xml}" tofile="${jarmaker.dir}/WEB-INF/web.xml" overwrite="true"/>
+    <java dir="${jarmaker.dir}" jvm="${jarmaker.virgin_jvm}" classname="${jarmaker.fullname}" fork="true">
+      <classpath>
+	<pathelement path="${jarmaker.dir}"/>
+      </classpath>
+	<sysproperty key="log4j.configuration" value="log4j.properties"/>
+	<jvmarg value="-Dmoby.debug=1"/>
+	<!--<jvmarg value="-Dverbose.class=true"/>-->
+        <jvmarg value="-D${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${jarmaker.extraClassesProperty}=javax/xml/**.class:javax/activation/**.class:javax/jws/**.class:com/sun/org/apache/xml/**.class:org/apache/xerces/xs/*PSVI.class:org/biomoby/**Exception.class:org/apache/**Exception.class:org/apache/**Error.class:org/apache/**ErrorResources.class:org/apache/**Messages.class:org/apache/log4j/spi/*.class:org/apache/xalan/**.class:org/apache/xpath/**.class:org/apache/axis/**.class:org/apache/log4j/*.class:org/apache/**.properties:javax/**/soap/*.class:org/jdom/*.class"/>
+
+	<arg value="${build.clients.absolute}/${wsdlservlet.warname}.war"/>
+	<arg value="${wsdlservlet.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}/${wsdlservlet.warname}.war" dest="${build.classes}/WEB-INF/classes"/>
+        <copy file="${src.webapps}/WEB-INF/${wsdlservlet.web.xml}" tofile="${build.classes}/WEB-INF/web.xml"/>
+
+	<jar destfile="${build.clients.absolute}/${wsdlservlet.warname}.war"
+		filesonly="true"
+		update="true"
+		compress="true"
+	        includes="WEB-INF/**"
+	        excludes="WEB-INF/classes/javax/servlet/**"
+		basedir="${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="SAWSDLServlet: A Framework for providing MOBY-S Web Services based on wrapping SAWSDL and moby-annotation WSDL documents"/>
+		<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 SAWSDL servlet standalone WAR is ${build.clients.absolute}/${wsdlservlet.warname}.war"/>
+    
+  </target>
+
+
   <target name="cgiservlet-war" depends="seahawk-init, compile, make_maker" description="(User) Builds the CGIServlet WAR for MOBY-S service creation based on wrapping moby-annotated HTML CGI forms on the Web">
     <echo message="Building CGI servlet standalone WAR to ${build.clients.absolute}"/>
 
@@ -212,7 +272,7 @@
       <classpath>
 	<pathelement path="${jarmaker.dir}"/>
       </classpath>
-	<sysproperty key="log4j.configuration" value="file:${log4j.configuration}"/>
+	<sysproperty key="log4j.configuration" value="log4j.properties"/>
 	<jvmarg value="-Dmoby.debug=1"/>
         <jvmarg value="-D${jarmaker.classPathProperty}=${scp}:${src.webapps}"/>
 	<jvmarg value="-D${jarmaker.manifestMainClassProperty}=${servlet.tester.classname}"/>




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