From simont at pub.open-bio.org  Tue Jun  1 12:51:27 2004
From: simont at pub.open-bio.org (Simon Twigger)
Date: Tue Jun  1 12:37:20 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406011651.i51GpR7t003930@pub.open-bio.org>


simont
Tue Jun  1 12:51:26 EDT 2004
Update of /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege
In directory pub.open-bio.org:/tmp/cvs-serv3911

Modified Files:
	MOBY_Service_ontology.png 
Log Message:
update, no change to content

moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege MOBY_Service_ontology.png,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MOBY_Service_ontology.png,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
Binary files /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MOBY_Service_ontology.png	2004/04/28 18:48:41	1.2 and /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MOBY_Service_ontology.png	2004/06/01 16:51:26	1.3 differ
rcsdiff: /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MOBY_Service_ontology.png: diff failed

From gss at pub.open-bio.org  Thu Jun 10 14:47:42 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 14:32:36 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406101847.i5AIlger017252@pub.open-bio.org>


gss
Thu Jun 10 14:47:42 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files
In directory pub.open-bio.org:/tmp/cvs-serv17230/ref-impl/config-files

Removed Files:
	for-tomcat-conf-catalina.properties 
Log Message:
No longer needed

moby-live/S-MOBY/ref-impl/config-files for-tomcat-conf-catalina.properties,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files/RCS/for-tomcat-conf-catalina.properties,v: No such file or directory

From gss at pub.open-bio.org  Thu Jun 10 14:58:01 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 14:42:55 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406101858.i5AIw13A017320@pub.open-bio.org>


gss
Thu Jun 10 14:58:01 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files
In directory pub.open-bio.org:/tmp/cvs-serv17295/ref-impl/config-files

Modified Files:
	for-tomcat-conf-server.xml 
Added Files:
	for-hosts-file README 
Log Message:
Cleanup

moby-live/S-MOBY/ref-impl/config-files for-hosts-file,NONE,1.1 README,NONE,1.1 for-tomcat-conf-server.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files/for-tomcat-conf-server.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files/for-tomcat-conf-server.xml	2004/04/02 00:02:03	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files/for-tomcat-conf-server.xml	2004/06/10 18:58:01	1.2
@@ -1,32 +1,32 @@
 <!-- Put the following just after the last </Host> closing element
      in <tomcat-home>/conf/server.xml -->
 
-      <Host appBase="webapps" name="acmepubs.com">
+      <Host appBase="webapps/acmepubs.com" name="acmepubs.com">
           <Alias>www.acmepubs.com</Alias>
-          <Context path="" docBase="acmepubs.com" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="megapubs.com">
+      <Host appBase="webapps/megapubs.com" name="megapubs.com">
           <Alias>www.megapubs.com</Alias>
-          <Context path="" docBase="megapubs.com" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="go.org">
+      <Host appBase="webapps/go.org" name="go.org">
           <Alias>www.go.org</Alias>
-          <Context path="" docBase="go.org" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="sgd.org">
+      <Host appBase="webapps/sgd.org" name="sgd.org">
           <Alias>www.sgd.org</Alias>
-          <Context path="" docBase="sgd.org" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="pubs.org">
+      <Host appBase="webapps/pubs.org" name="pubs.org">
           <Alias>www.pubs.org</Alias>
-          <Context path="" docBase="pubs.org" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="s-moby.org">
+      <Host appBase="webapps/s-moby.org" name="s-moby.org">
           <Alias>www.s-moby.org</Alias>
-          <Context path="" docBase="s-moby.org" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>

From gss at pub.open-bio.org  Thu Jun 10 19:06:55 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 18:51:48 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102306.i5AN6tGb017989@pub.open-bio.org>


gss
Thu Jun 10 19:06:55 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv17968/ref-impl

Added Files:
	.cvsignore 
Log Message:
Ignore products of building the reference implementation

moby-live/S-MOBY/ref-impl .cvsignore,NONE,1.1
From gss at pub.open-bio.org  Thu Jun 10 19:09:39 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 18:54:32 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102309.i5AN9dXo018072@pub.open-bio.org>


gss
Thu Jun 10 19:09:39 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv18051/ref-impl

Added Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl build.xml,NONE,1.1
From gss at pub.open-bio.org  Thu Jun 10 19:10:02 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 18:54:55 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102310.i5ANA2ta018104@pub.open-bio.org>


gss
Thu Jun 10 19:10:02 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv18083/ref-impl

Added Files:
	common.example.properties 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl common.example.properties,NONE,1.1
From gss at pub.open-bio.org  Thu Jun 10 19:10:31 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 18:55:23 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102310.i5ANAVTl018142@pub.open-bio.org>


gss
Thu Jun 10 19:10:31 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv18117/ref-impl

Modified Files:
	index.html 
Log Message:
Reference installation/deployment document

moby-live/S-MOBY/ref-impl index.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/index.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/index.html	2004/03/12 17:48:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/index.html	2004/06/10 23:10:30	1.2
@@ -65,7 +65,8 @@
 </div>
 <br>
 The above links provide more information about each part of the
-reference implementation.<br>
+reference implementation. See the file <a href="INSTALL.html">INSTALL.html</a>
+for information on building and installing the reference implementation.<br>
 <div style="margin-left: 40px;">
 <div style="margin-left: 40px;"></div>
 </div>

From gss at pub.open-bio.org  Thu Jun 10 19:10:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 18:55:37 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102310.i5ANAiop018168@pub.open-bio.org>


gss
Thu Jun 10 19:10:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv18147/ref-impl

Added Files:
	servlet.xml common.xml INSTALL.html 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl servlet.xml,NONE,1.1 common.xml,NONE,1.1 INSTALL.html,NONE,1.1
From gss at pub.open-bio.org  Thu Jun 10 19:11:02 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 18:55:55 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102311.i5ANB25b018206@pub.open-bio.org>


gss
Thu Jun 10 19:11:02 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv18181/ref-impl/core

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/core build.xml,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/05/27 15:54:44	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/06/10 23:11:02	1.4
@@ -3,24 +3,42 @@
 <project name="smoby-core" default="jar" basedir=".">
 
     <!-- Import shared stuff -->
-    <import file="../library.xml"/>
+    <import file="../common.xml"/>
 
-    <!-- Package the compiled source files into the main jar file -->
-    <target name="jar" depends="compile">
-        <jar destfile="${core-jar-file}" basedir="${classes-dir}"/>
-    </target>
+    <!-- Relative path for where to put stuff that gets built -->
+    <property name="build-dir" value="build"/>
     
+    <!-- Relative path for where javac should output class files -->
+    <property name="classes-dir" value="${build-dir}/classes"/>
+
     <!-- Compile all the source files that go into the library -->
     <target name="compile">
         <mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="core.classpath"/>
         </javac>
     </target>
     
+    <!-- Package the compiled source files into the main jar file -->
+    <target name="jar" depends="compile">
+        <jar destfile="${core-jar-file}" basedir="${classes-dir}"/>
+    </target>
+
     <!-- Deploy the jar file to the Tomcat shared library directory -->
     <target name="deploy-to-tomcat" depends="jar">
-        <copy file="${core-jar-file}" todir="${tomcat-shared-lib-dir}"/>
+        <copy file="${core-jar-file}"
+              todir="${tomcat-shared-lib-dir}"/>
+    </target>
+    
+	<!-- Remove the build directory and its contents -->
+	<target name="clean">
+		<delete dir="${build-dir}" includeEmptyDirs="true"/>
+        <delete file="${core-jar-file}"/>
+	</target>
+    
+    <!-- Un-deploy the jar file from the Tomcat shared library directory -->
+    <target name="undeploy-from-tomcat">
+        <delete file="${tomcat-shared-lib-dir}/${core-jar-file}"/>
     </target>
     
 </project>

From gss at pub.open-bio.org  Thu Jun 10 19:13:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 18:58:39 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDi92018265@pub.open-bio.org>


gss
Thu Jun 10 19:13:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF web.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/web.xml	2004/03/27 01:34:51	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.2
@@ -1,4 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE web-app PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN" "http://java.sun.com/dtd/web-app_2_3.dtd">
 <web-app>
+  <display-name>Example MOBY provider pubs.org</display-name>
 </web-app>

From gss at pub.open-bio.org  Thu Jun 10 19:13:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 18:58:40 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDiBN018284@pub.open-bio.org>


gss
Thu Jun 10 19:13:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF web.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml	2004/03/27 01:17:58	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.3
@@ -2,6 +2,8 @@
 <!DOCTYPE web-app PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN" "http://java.sun.com/dtd/web-app_2_3.dtd">
 <web-app>
   
+  <display-name>Example MOBY provider megapubs.com</display-name>
+
   <servlet>
     <servlet-name>CitationSearchServlet</servlet-name>
     <display-name>Publication Search</display-name>

From gss at pub.open-bio.org  Thu Jun 10 19:13:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 18:58:40 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDiOa018303@pub.open-bio.org>


gss
Thu Jun 10 19:13:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/server/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF web.xml,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml	2004/03/27 01:23:21	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.4
@@ -3,6 +3,8 @@
 
 <web-app>
 
+  <display-name>Semantic MOBY Server</display-name>
+
   <servlet>
     <servlet-name>GraphConversionServlet</servlet-name>
     <display-name>Graph Converter</display-name>

From gss at pub.open-bio.org  Thu Jun 10 19:13:45 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 18:58:40 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDjAt018322@pub.open-bio.org>


gss
Thu Jun 10 19:13:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF web.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml	2004/03/19 00:37:48	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.2
@@ -1,6 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE web-app PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN" "http://java.sun.com/dtd/web-app_2_3.dtd">
 <web-app>
+
+  <display-name>Example MOBY provider acmepubs.com</display-name>
   
   <servlet>
     <servlet-name>CitationSearchServlet</servlet-name>

From gss at pub.open-bio.org  Thu Jun 10 19:13:45 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 18:58:41 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDjKv018344@pub.open-bio.org>


gss
Thu Jun 10 19:13:45 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/example-providers/go.org/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF web.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/web.xml	2004/04/01 00:30:50	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.2
@@ -1,4 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE web-app PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN" "http://java.sun.com/dtd/web-app_2_3.dtd">
 <web-app>
+  <display-name>Example MOBY provider go.org</display-name>
 </web-app>

From gss at pub.open-bio.org  Thu Jun 10 19:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:00:32 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbSC018409@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-clients

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-clients build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/build.xml	2004/03/12 17:48:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/build.xml	2004/06/10 23:15:37	1.2
@@ -1,2 +1,11 @@
-<project name="example-clients" basedir=".">
+<project name="example-clients" default="all" basedir=".">
+
+    <target name="all">
+        <ant dir="SimpleEngager"/>
+    </target>
+
+    <target name="clean">
+        <ant dir="SimpleEngager" target="clean"/>
+    </target>
+
 </project>

From gss at pub.open-bio.org  Thu Jun 10 19:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:00:33 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbBK018428@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/server

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/server build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/05/27 15:54:12	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/06/10 23:15:37	1.3
@@ -1,29 +1,42 @@
-<!-- Apache Ant format build file for s-moby.org example provider -->
+<!-- Apache Ant format build file for s-moby.org server -->
 
-<project name="s-moby.org" default="war" basedir=".">
+<project name="s-moby.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="s-moby.org.war"/>
+    <!-- The web application name -->
+    <property name="webapp-name" value="s-moby.org"/>
 	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
-	
-	<!-- Compile all the source files that go into the library -->
+    <!-- Compile all the source files that go into the library, and copy any
+         properties files (i.e. smoby.properties and log4j.properties) into
+         the classes directory -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
+        <copy toDir="${classes-dir}">
+            <fileset dir="WebRoot">
+                <include name="*.properties"/>
+            </fileset>
+        </copy>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>

From gss at pub.open-bio.org  Thu Jun 10 19:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:00:34 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbfV018512@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-providers/megapubs.com

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml	2004/05/27 15:54:28	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml	2004/06/10 23:15:37	1.3
@@ -1,29 +1,35 @@
-<!-- Apache Ant format build file for acmepubs.com example provider -->
+<!-- Apache Ant format build file for megapubs.com server -->
 
-<project name="megapubs.com" default="war" basedir=".">
+<project name="s-moby.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="megapubs.com.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="megapubs.com"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>

From gss at pub.open-bio.org  Thu Jun 10 19:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:00:34 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbjJ018489@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-clients/SimpleEngager

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml	2004/05/28 21:35:17	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml	2004/06/10 23:15:37	1.3
@@ -3,22 +3,34 @@
 <project name="simple-engager" default="jar" basedir=".">
 
     <!-- Import shared stuff -->
-    <import file="../../library.xml"/>
+    <import file="../../common.xml"/>
+
+    <!-- Relative path for where to put stuff that gets built -->
+    <property name="build-dir" value="build"/>
+    
+    <!-- Relative path for where javac should output class files -->
+    <property name="classes-dir" value="${build-dir}/classes"/>
 
     <!-- The main jar file -->
-    <property name="jar-file" value="${build-dir}/engager.jar"/>
+    <property name="jar-file" value="simple-engager.jar"/>
 
-    <!-- Package the compiled source files into the main jar file -->
-    <target name="jar" depends="compile">
-        <jar destfile="${jar-file}" basedir="${classes-dir}"/>
-    </target>
-    
     <!-- Compile all the source files that go into the library -->
     <target name="compile">
         <mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
     </target>
     
+    <!-- Package the compiled source files into the main jar file -->
+    <target name="jar" depends="compile">
+        <jar destfile="${jar-file}" basedir="${classes-dir}"/>
+    </target>
+    
+	<!-- Remove the build directory and its contents -->
+	<target name="clean">
+		<delete dir="${build-dir}" includeEmptyDirs="true"/>
+        <delete file="${jar-file}"/>
+	</target>
+    
 </project>

From gss at pub.open-bio.org  Thu Jun 10 19:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:00:39 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbtN018470@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-providers/go.org

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/go.org build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/build.xml	2004/05/27 16:23:59	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/build.xml	2004/06/10 23:15:37	1.2
@@ -1,29 +1,35 @@
 <!-- Apache Ant format build file for go.org example provider -->
 
-<project name="go.org" default="war" basedir=".">
+<project name="go.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="go.org.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="go.org"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>

From gss at pub.open-bio.org  Thu Jun 10 19:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:00:39 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbSU018534@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-providers/pubs.org

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/pubs.org build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/build.xml	2004/05/27 15:54:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/build.xml	2004/06/10 23:15:37	1.2
@@ -1,29 +1,35 @@
 <!-- Apache Ant format build file for pubs.org example provider -->
 
-<project name="pubs.org" default="war" basedir=".">
+<project name="s-moby.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="pubs.org.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="pubs.org"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>

From gss at pub.open-bio.org  Thu Jun 10 19:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:00:39 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFb1V018448@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-providers/acmepubs.com

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml	2004/05/27 15:54:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml	2004/06/10 23:15:37	1.3
@@ -1,29 +1,35 @@
 <!-- Apache Ant format build file for acmepubs.com example provider -->
 
-<project name="acmepubs.com" default="war" basedir=".">
+<project name="acmepubs.com" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="acmepubs.com.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="acmepubs.com"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>

From gss at pub.open-bio.org  Thu Jun 10 19:16:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:01:45 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102316.i5ANGmJn018573@pub.open-bio.org>


gss
Thu Jun 10 19:16:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data
In directory pub.open-bio.org:/tmp/cvs-serv18549/ref-impl/test-data

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data added to the repository

moby-live/S-MOBY/ref-impl/test-data - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Thu Jun 10 19:16:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:01:45 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102316.i5ANGmfG018591@pub.open-bio.org>


gss
Thu Jun 10 19:16:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser
In directory pub.open-bio.org:/tmp/cvs-serv18549/ref-impl/test-data/parser

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser added to the repository

moby-live/S-MOBY/ref-impl/test-data/parser - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Thu Jun 10 19:16:51 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:01:46 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102316.i5ANGpqR018636@pub.open-bio.org>


gss
Thu Jun 10 19:16:51 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser
In directory pub.open-bio.org:/tmp/cvs-serv18615/ref-impl/test-data/parser

Added Files:
	unparsable.n3 minimal.n3 three-providers.n3 README.txt 
Log Message:
Began writing JUnit test cases (feel free to help out, everyone :-)

moby-live/S-MOBY/ref-impl/test-data/parser unparsable.n3,NONE,1.1 minimal.n3,NONE,1.1 three-providers.n3,NONE,1.1 README.txt,NONE,1.1
From gss at pub.open-bio.org  Thu Jun 10 19:24:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:09:11 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102324.i5ANOGLl018745@pub.open-bio.org>


gss
Thu Jun 10 19:24:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv18720/ref-impl/server/src/org/smoby/ref/tools

Modified Files:
	DiscoveryQuery.java 
Log Message:
Commented out most functionality until I figure out the new
ResultBindingIterator protocol...

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/05/19 18:26:40	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/06/10 23:24:16	1.5
@@ -4,11 +4,10 @@
 import java.text.*;
 import java.util.*;
 
-import org.smoby.parser.Parser;
+import org.smoby.parser.*;
 import org.smoby.ref.tools.db.*;
 import org.smoby.graph.*;
-import org.smoby.graph.impl.MOBYObjectFactory;
-import org.smoby.graph.impl.MOBYProviderImpl;
+import org.smoby.graph.impl.*;
 import org.smoby.vocabulary.*;
 
 import com.hp.hpl.jena.db.*;
@@ -257,22 +256,23 @@
 		if (! node.asNode().isBlank()) {
 			return node;
 		}
-		
-		ResultBinding.ResultBindingIterator results = binding.iterator();
+		//ResultBinding
+		ResultBindingIterator results = binding.iterator();
 		
 		while (results.hasNext())
 		{
-			results.next();
+			Object object = results.next();
+			Value value = (Value) object;
 			String varName = results.varName();
-			Value value = results.value();
+//			Value value = results.value();
 			Object cachedName = varNames.get(node.toString());
 			if (varName.equals(cachedName))
 			{
-				if (value.isRDFLiteral()) {
-					return value.getRDFLiteral();
-				} else if (value.isRDFResource()) {
-					return value.getRDFResource();
-				}
+//				if (value.isRDFLiteral()) {
+//					return value.getRDFLiteral();
+//				} else if (value.isRDFResource()) {
+//					return value.getRDFResource();
+//				}
 			}
 		}
 		return node;

From gss at pub.open-bio.org  Thu Jun 10 19:25:49 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:10:43 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102325.i5ANPnGe018783@pub.open-bio.org>


gss
Thu Jun 10 19:25:49 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src
In directory pub.open-bio.org:/tmp/cvs-serv18760/ref-impl/server/src

Removed Files:
	log4j.properties smoby.properties 
Log Message:
Moved from src/ to WebRoot/

moby-live/S-MOBY/ref-impl/server/src log4j.properties,1.1,NONE smoby.properties,1.4,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/log4j.properties,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/smoby.properties,v: No such file or directory

From gss at pub.open-bio.org  Thu Jun 10 19:25:49 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:10:43 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102325.i5ANPn6V018798@pub.open-bio.org>


gss
Thu Jun 10 19:25:49 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv18760/ref-impl/server/WebRoot

Added Files:
	smoby.properties 
Log Message:
Moved from src/ to WebRoot/

moby-live/S-MOBY/ref-impl/server/WebRoot smoby.properties,NONE,1.1
From gss at pub.open-bio.org  Thu Jun 10 19:26:31 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:11:24 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102326.i5ANQV5p018845@pub.open-bio.org>


gss
Thu Jun 10 19:26:31 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage
In directory pub.open-bio.org:/tmp/cvs-serv18822/ref-impl/queries/engage

Removed Files:
	engage-megapubs-citationSearch.rdf 
	engage-megapubs-citationSearch.n3 
Log Message:
No longer needed

moby-live/S-MOBY/ref-impl/queries/engage engage-megapubs-citationSearch.rdf,1.1,NONE engage-megapubs-citationSearch.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/RCS/engage-megapubs-citationSearch.rdf,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/RCS/engage-megapubs-citationSearch.n3,v: No such file or directory

From gss at pub.open-bio.org  Thu Jun 10 19:27:12 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:12:05 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102327.i5ANRCR3018875@pub.open-bio.org>


gss
Thu Jun 10 19:27:12 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage
In directory pub.open-bio.org:/tmp/cvs-serv18850/ref-impl/queries/engage

Modified Files:
	engage-acmepubs-citationSearch.n3 
Log Message:
Simplified N3 by using un-named blank nodes

moby-live/S-MOBY/ref-impl/queries/engage engage-acmepubs-citationSearch.n3,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3	2004/04/02 00:05:16	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3	2004/06/10 23:27:12	1.2
@@ -10,28 +10,44 @@
 
 acmepubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
-    rdfs:comment "Industry standard search" ;
-    moby:operatesOn _:bnode1 .
-
-_:bnode1
-    a moby:Graph, rdf:Bag ;
-    moby:hasMapping _:bnode2 .
-
-_:bnode2
-    a moby:Subject, go:GeneSymbol ;
-    moby:mapsTo _:bnode3 ;
-    acmepubs:geneSymbol "REV7" .
-
-_:bnode3
-    a moby:Object, sgd:LiteratureGuide ;
-    acmepubs:literatureGuideURL _:bnode6 .
+    moby:name "AcmePubs Citation Search" ;
+    moby:oneLineDescription "Industry standard search" ;
+    moby:aboutURI "http://www.acmepubs.com/about/citationSearch" ;
+    moby:operatesOn [
+        a rdf:Bag ;
+        rdf:_1 [
+            a moby:Graph ;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                acmepubs:geneSymbol "REV5" ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide ;
+                    acmepubs:literatureGuideURL _:bnode1
+                ]
+            ]
+        ] ;
+        rdf:_2 [
+            a moby:Graph ;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                acmepubs:geneSymbol "REV7" ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide ;
+                    acmepubs:literatureGuideURL _:bnode2
+                ]
+            ]
+        ] ;
+    ] .
 
 acmepubs:geneSymbol
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain go:GeneSymbol ;
     rdfs:range xsd:string .
 
 acmepubs:literatureGuideURL
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain sgd:LiteratureGuide ;
     rdfs:range xsd:anyURI .
+

From gss at pub.open-bio.org  Thu Jun 10 19:27:41 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:12:51 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102327.i5ANRfwJ018915@pub.open-bio.org>


gss
Thu Jun 10 19:27:41 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage
In directory pub.open-bio.org:/tmp/cvs-serv18890/ref-impl/queries/engage

Modified Files:
	engage-acmepubs-citationSearch.rdf 
Log Message:
Use un-named blank nodes

moby-live/S-MOBY/ref-impl/queries/engage engage-acmepubs-citationSearch.rdf,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf	2004/04/02 00:05:16	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf	2004/06/10 23:27:41	1.2
@@ -12,31 +12,54 @@
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A0">
     <moby:hasMapping rdf:nodeID="A1"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A1">
-    <moby:mapsTo rdf:nodeID="A2"/>
+  <rdf:Description rdf:nodeID="A2">
+    <moby:mapsTo rdf:nodeID="A3"/>
     <acmepubs:geneSymbol>REV7</acmepubs:geneSymbol>
     <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
   </rdf:Description>
+  <rdf:Description rdf:nodeID="A4">
+    <acmepubs:literatureGuideURL rdf:nodeID="A5"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A6">
+    <moby:hasMapping rdf:nodeID="A2"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <acmepubs:literatureGuideURL rdf:nodeID="A7"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A8">
+    <rdf:_2 rdf:nodeID="A6"/>
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A0"/>
+  </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <moby:oneLineDescription>Industry standard search</moby:oneLineDescription>
+    <moby:operatesOn rdf:nodeID="A8"/>
+    <moby:aboutURI>http://www.acmepubs.com/about/citationSearch</moby:aboutURI>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <rdfs:comment>Industry standard search</rdfs:comment>
-    <moby:operatesOn rdf:nodeID="A0"/>
+    <moby:name>AcmePubs Citation Search</moby:name>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <acmepubs:literatureGuideURL rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  <rdf:Description rdf:nodeID="A1">
+    <acmepubs:geneSymbol>REV5</acmepubs:geneSymbol>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <moby:mapsTo rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/literatureGuideURL">
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>

From gss at pub.open-bio.org  Thu Jun 10 19:27:58 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:12:53 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102327.i5ANRwYw018953@pub.open-bio.org>


gss
Thu Jun 10 19:27:58 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery
In directory pub.open-bio.org:/tmp/cvs-serv18928/ref-impl/queries/discovery

Modified Files:
	query.n3 
Log Message:
Simplified N3 by using un-named blank nodes

moby-live/S-MOBY/ref-impl/queries/discovery query.n3,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3	2004/04/02 00:05:16	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3	2004/06/10 23:27:58	1.2
@@ -5,15 +5,15 @@
 
 _:provider
     a moby:Provider ;
-    moby:operatesOn _:bnode1 .
-
-_:bnode1
-    a moby:Graph, rdf:Bag ;
-    moby:hasMapping _:bnode2 .
-
-_:bnode2
-    a moby:Subject, go:GeneSymbol ;
-    moby:mapsTo _:bnode3 .
-
-_:bnode3
-    a moby:Object, sgd:LiteratureGuide .
+    moby:operatesOn [
+        a rdf:Bag ;
+        rdf:_1 [
+            a moby:Graph;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide
+                ]
+            ]
+        ]
+    ] .

From gss at pub.open-bio.org  Thu Jun 10 19:28:06 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:13:00 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102328.i5ANS68x018983@pub.open-bio.org>


gss
Thu Jun 10 19:28:06 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery
In directory pub.open-bio.org:/tmp/cvs-serv18958/ref-impl/queries/discovery

Modified Files:
	query.rdf 
Log Message:
Use un-named blank nodes

moby-live/S-MOBY/ref-impl/queries/discovery query.rdf,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf	2004/04/02 00:05:16	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf	2004/06/10 23:28:06	1.2
@@ -4,21 +4,24 @@
     xmlns:moby="http://www.s-moby.org:8080/terms#"
     xmlns:sgd="http://www.sgd.org:8080/terms#" >
   <rdf:Description rdf:nodeID="A0">
-    <moby:mapsTo rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+    <moby:hasMapping rdf:nodeID="A1"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A2">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <moby:operatesOn rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A0"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A1">
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <moby:mapsTo rdf:nodeID="A3"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
     <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A3">
-    <moby:hasMapping rdf:nodeID="A0"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+  <rdf:Description rdf:nodeID="A4">
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
+    <moby:operatesOn rdf:nodeID="A2"/>
   </rdf:Description>
 </rdf:RDF>

From gss at pub.open-bio.org  Thu Jun 10 19:30:53 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:15:46 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102330.i5ANUr5l019096@pub.open-bio.org>


gss
Thu Jun 10 19:30:53 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv19071/ref-impl/example-providers/sgd.org

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/sgd.org build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/build.xml	2004/05/27 15:54:20	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/build.xml	2004/06/10 23:30:53	1.2
@@ -1,29 +1,35 @@
 <!-- Apache Ant format build file for sgd.org example provider -->
 
-<project name="sgd.org" default="war" basedir=".">
+<project name="sgd.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="sgd.org.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="sgd.org"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>

From gss at pub.open-bio.org  Thu Jun 10 19:31:51 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:16:44 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102331.i5ANVp4D019169@pub.open-bio.org>


gss
Thu Jun 10 19:31:51 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv19144/ref-impl/example-providers/sgd.org

Modified Files:
	.cvsignore 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-providers/sgd.org .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore	2004/05/27 15:54:20	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore	2004/06/10 23:31:50	1.2
@@ -1 +1,5 @@
 *.war
+.classpath
+.encoding
+.mymetadata
+.project

From gss at pub.open-bio.org  Thu Jun 10 19:32:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 10 19:17:01 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102332.i5ANW9GK019207@pub.open-bio.org>


gss
Thu Jun 10 19:32:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers
In directory pub.open-bio.org:/tmp/cvs-serv19182/ref-impl/example-providers

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/build.xml	2004/03/12 17:48:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/build.xml	2004/06/10 23:32:09	1.2
@@ -1,2 +1,39 @@
-<project name="example-providers" basedir=".">
+<project name="example-providers" basedir="." default="all">
+
+    <!-- Build all the example providers -->
+    <target name="all">
+        <ant dir="acmepubs.com"/>
+        <ant dir="go.org"/>
+        <ant dir="megapubs.com"/>
+        <ant dir="pubs.org"/>
+        <ant dir="sgd.org"/>
+    </target>
+
+    <!-- Clean all the example providers -->
+    <target name="clean">
+        <ant dir="acmepubs.com" target="clean"/>
+        <ant dir="go.org" target="clean"/>
+        <ant dir="megapubs.com" target="clean"/>
+        <ant dir="pubs.org" target="clean"/>
+        <ant dir="sgd.org" target="clean"/>
+    </target>
+
+    <!-- Deploy all the example providers to Tomcat -->
+    <target name="deploy-to-tomcat">
+        <ant dir="acmepubs.com" target="deploy-to-tomcat"/>
+        <ant dir="go.org" target="deploy-to-tomcat"/>
+        <ant dir="megapubs.com" target="deploy-to-tomcat"/>
+        <ant dir="pubs.org" target="deploy-to-tomcat"/>
+        <ant dir="sgd.org" target="deploy-to-tomcat"/>
+    </target>
+
+    <!-- Un-deploy all the example providers from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <ant dir="acmepubs.com" target="undeploy-from-tomcat"/>
+        <ant dir="go.org" target="undeploy-from-tomcat"/>
+        <ant dir="megapubs.com" target="undeploy-from-tomcat"/>
+        <ant dir="pubs.org" target="undeploy-from-tomcat"/>
+        <ant dir="sgd.org" target="undeploy-from-tomcat"/>
+    </target>
+
 </project>

From gss at pub.open-bio.org  Fri Jun 11 14:26:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 11 14:11:16 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111826.i5BIQQnt022787@pub.open-bio.org>


gss
Fri Jun 11 14:26:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv22758/S-MOBY/ref-impl

Modified Files:
	build.xml common.xml 
Log Message:
Needed to copy another jar file to Tomcat in deploy-to-tomcat target

moby-live/S-MOBY/ref-impl build.xml,1.1,1.2 common.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/build.xml	2004/06/10 23:09:39	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/build.xml	2004/06/11 18:26:25	1.2
@@ -72,9 +72,11 @@
         <!-- Copy jar files to the Tomcat shared library directory -->
         <copy toDir="${tomcat-shared-lib-dir}">
             <!-- Copy the HTTPClient jar files -->
+            <fileset dir="${http-client-lib-dir}">
+                <include name="*.jar"/>
+            </fileset>
             <fileset dir="${http-client-dist-dir}">
                 <include name="commons-httpclient.jar"/>
-                <include name="lib/*.jar"/>
             </fileset>
             <!-- Copy the jena jar files -->
             <fileset dir="${jena-lib-dir}">

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/common.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/common.xml	2004/06/10 23:10:44	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/common.xml	2004/06/11 18:26:25	1.2
@@ -25,6 +25,8 @@
         <property name="http-client-package" value="jakarta-commons/httpclient"/>
         <!-- Top level directory of the package -->
         <property name="http-client-top-dir" value="${third-party-dir}/${http-client-package}"/>
+        <!-- Library directory -->
+        <property name="http-client-lib-dir" value="${http-client-top-dir}/lib"/>
         <!-- Distribution directory -->
         <property name="http-client-dist-dir" value="${http-client-top-dir}/dist"/>
 

From gss at pub.open-bio.org  Fri Jun 11 14:43:15 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 11 14:28:03 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111843.i5BIhFkb022876@pub.open-bio.org>


gss
Fri Jun 11 14:43:15 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv22851/S-MOBY/ref-impl/core

Modified Files:
	.cvsignore 
Log Message:
Don't include smoby.jar in CVS

moby-live/S-MOBY/ref-impl/core .cvsignore,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/05/27 15:30:40	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/06/11 18:43:15	1.5
@@ -1,2 +1,2 @@
-classes
-build
\ No newline at end of file
+build
+smoby.jar
\ No newline at end of file

From gss at pub.open-bio.org  Fri Jun 11 14:44:07 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 11 14:28:55 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111844.i5BIi7jR022915@pub.open-bio.org>


gss
Fri Jun 11 14:44:07 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv22890/S-MOBY/ref-impl/example-clients/SimpleEngager

Modified Files:
	.cvsignore 
Log Message:
Don't include simple-engager.jar in CVS

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .cvsignore,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/05/27 19:37:10	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/11 18:44:07	1.3
@@ -1,2 +1,2 @@
-classes
 build
+simple-engager.jar
\ No newline at end of file

From gss at pub.open-bio.org  Fri Jun 11 14:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 11 14:30:04 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGtV022950@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-providers/acmepubs.com

Removed Files:
	.mymetadata .project .xdoclet .classpath 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .mymetadata,1.5,NONE .project,1.6,NONE .xdoclet,1.3,NONE .classpath,1.4,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.mymetadata,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.xdoclet,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.classpath,v: No such file or directory

From gss at pub.open-bio.org  Fri Jun 11 14:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 11 14:30:05 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGHd022967@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/core

Removed Files:
	.classpath .project 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/core .classpath,1.4,NONE .project,1.4,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/.project,v: No such file or directory

From gss at pub.open-bio.org  Fri Jun 11 14:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 11 14:30:06 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGfc022986@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-providers/pubs.org

Removed Files:
	.mymetadata .classpath .project 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-providers/pubs.org .mymetadata,1.1,NONE .classpath,1.2,NONE .project,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/.mymetadata,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/.project,v: No such file or directory

From gss at pub.open-bio.org  Fri Jun 11 14:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 11 14:30:06 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGex023009@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/server

Removed Files:
	.project .classpath xdoclet-build.xml .xdoclet .mymetadata 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/server .project,1.2,NONE .classpath,1.4,NONE xdoclet-build.xml,1.1,NONE .xdoclet,1.1,NONE .mymetadata,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/xdoclet-build.xml,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/.xdoclet,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/.mymetadata,v: No such file or directory

From gss at pub.open-bio.org  Fri Jun 11 14:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 11 14:30:09 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGmj023028@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY

Removed Files:
	.project 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY .project,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/RCS/.project,v: No such file or directory

From gss at pub.open-bio.org  Fri Jun 11 14:45:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 11 14:30:10 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjHcq023069@pub.open-bio.org>


gss
Fri Jun 11 14:45:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-clients/SimpleEngager

Removed Files:
	.classpath .project 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .classpath,1.2,NONE .project,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/.project,v: No such file or directory

From gss at pub.open-bio.org  Fri Jun 11 14:45:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 11 14:30:10 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjHnQ023049@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-providers/go.org

Removed Files:
	.mymetadata .project .classpath 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-providers/go.org .mymetadata,1.1,NONE .project,1.1,NONE .classpath,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/.mymetadata,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/.classpath,v: No such file or directory

From gss at pub.open-bio.org  Fri Jun 11 14:45:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 11 14:30:11 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjHCS023090@pub.open-bio.org>


gss
Fri Jun 11 14:45:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-providers/megapubs.com

Removed Files:
	.project .classpath .mymetadata 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .project,1.2,NONE .classpath,1.2,NONE .mymetadata,1.3,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/.mymetadata,v: No such file or directory

From gss at pub.open-bio.org  Fri Jun 11 14:45:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 11 14:30:11 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjH6W023108@pub.open-bio.org>


gss
Fri Jun 11 14:45:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/server/.externalToolBuilders

Removed Files:
	XDoclet Builder.launch 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/server/.externalToolBuilders XDoclet Builder.launch,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/XDoclet,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/Builder.launch,v: No such file or directory

From ambrose at pub.open-bio.org  Fri Jun 11 18:06:56 2004
From: ambrose at pub.open-bio.org (Ambrose Ng)
Date: Fri Jun 11 17:51:42 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406112206.i5BM6uPZ023829@pub.open-bio.org>


ambrose
Fri Jun 11 18:06:56 EDT 2004
Update of /home/repository/moby/moby-live/Perl/Accessories
In directory pub.open-bio.org:/tmp/cvs-serv23807

Added Files:
	SearchDatabase.cgi 
Log Message:
adding Namespace Database search page

moby-live/Perl/Accessories SearchDatabase.cgi,NONE,1.1
From gss at pub.open-bio.org  Mon Jun 14 12:24:12 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 12:08:51 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141624.i5EGOCrf009597@pub.open-bio.org>


gss
Mon Jun 14 12:24:12 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv9572

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/core .cvsignore,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/06/11 18:43:15	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/06/14 16:24:12	1.6
@@ -1,2 +1,4 @@
 build
-smoby.jar
\ No newline at end of file
+smoby.jar
+.classpath
+.project

From gss at pub.open-bio.org  Mon Jun 14 12:30:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 12:15:28 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141630.i5EGUxLx009701@pub.open-bio.org>


gss
Mon Jun 14 12:30:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com
In directory pub.open-bio.org:/tmp/cvs-serv9676

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.cvsignore	2004/05/27 15:54:40	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.cvsignore	2004/06/14 16:30:58	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project

From gss at pub.open-bio.org  Mon Jun 14 12:35:27 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 12:19:55 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141635.i5EGZRma009780@pub.open-bio.org>


gss
Mon Jun 14 12:35:26 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com
In directory pub.open-bio.org:/tmp/cvs-serv9755

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.cvsignore	2004/05/27 15:54:28	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.cvsignore	2004/06/14 16:35:26	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project

From gss at pub.open-bio.org  Mon Jun 14 12:44:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 12:29:14 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141644.i5EGiiFa010077@pub.open-bio.org>


gss
Mon Jun 14 12:44:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org
In directory pub.open-bio.org:/tmp/cvs-serv10052

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/pubs.org .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.cvsignore	2004/05/27 15:54:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.cvsignore	2004/06/14 16:44:44	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project

From gss at pub.open-bio.org  Mon Jun 14 12:44:45 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 12:29:14 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141644.i5EGijjL010107@pub.open-bio.org>


gss
Mon Jun 14 12:44:45 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv10082

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .cvsignore,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/11 18:44:07	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/14 16:44:45	1.4
@@ -1,2 +1,4 @@
 build
-simple-engager.jar
\ No newline at end of file
+simple-engager.jar
+.classpath
+.project

From gss at pub.open-bio.org  Mon Jun 14 12:44:46 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 12:29:16 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141644.i5EGikoR010137@pub.open-bio.org>


gss
Mon Jun 14 12:44:46 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org
In directory pub.open-bio.org:/tmp/cvs-serv10112

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/go.org .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.cvsignore	2004/05/27 16:23:59	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.cvsignore	2004/06/14 16:44:46	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project

From gss at pub.open-bio.org  Mon Jun 14 12:45:53 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 12:30:23 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141645.i5EGjrJs010177@pub.open-bio.org>


gss
Mon Jun 14 12:45:53 EDT 2004
Update of /home/repository/moby/moby-live
In directory pub.open-bio.org:/tmp/cvs-serv10156

Added Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live .cvsignore,NONE,1.1
From gss at pub.open-bio.org  Mon Jun 14 12:49:24 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 12:33:51 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141649.i5EGnOhi010210@pub.open-bio.org>


gss
Mon Jun 14 12:49:23 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv10185/S-MOBY/ref-impl/example-clients/SimpleEngager

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .cvsignore,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/14 16:44:45	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/14 16:49:23	1.5
@@ -2,3 +2,4 @@
 simple-engager.jar
 .classpath
 .project
+classes

From gss at pub.open-bio.org  Mon Jun 14 12:52:32 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 12:37:01 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141652.i5EGqWqV010289@pub.open-bio.org>


gss
Mon Jun 14 12:52:32 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv10265/S-MOBY/ref-impl/example-providers/sgd.org

Removed Files:
	.project .mymetadata .classpath 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/sgd.org .project,1.1,NONE .mymetadata,1.1,NONE .classpath,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/.mymetadata,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/.classpath,v: No such file or directory

From gss at pub.open-bio.org  Mon Jun 14 13:17:57 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 13:02:27 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141717.i5EHHvJx010453@pub.open-bio.org>


gss
Mon Jun 14 13:17:56 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv10428

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/server .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore	2004/05/27 18:31:46	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore	2004/06/14 17:17:56	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project

From gss at pub.open-bio.org  Mon Jun 14 16:58:13 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 16:42:43 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142058.i5EKwD3K010951@pub.open-bio.org>


gss
Mon Jun 14 16:58:12 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv10926/src/org/smoby/ref/tools

Modified Files:
	MOBYProperties.java 
Log Message:
Use servlet context to find properties file

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools MOBYProperties.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/MOBYProperties.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/MOBYProperties.java	2004/03/20 00:36:48	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/MOBYProperties.java	2004/06/14 20:58:12	1.2
@@ -3,6 +3,8 @@
 import java.io.*;
 import java.util.*;
 
+import javax.servlet.ServletContext;
+
 
 /**
  * This abstract class contains a set of static methods for retrieving
@@ -32,25 +34,12 @@
     public static String getProperty(String propName, boolean required)
         throws MissingPropertyException
     {
-        try {
-            String value = getProps().getProperty(propName);
-            if (required && (value == null)) {
-                throw new MissingPropertyException(propName,
-                    "Property " + propName + " not found in " + PROP_FILE_NAME);
-            }
-            return value;
-        } catch (FileNotFoundException e) {
-            if (required) {
-                throw new MissingPropertyException(propName,
-                    "Properties file " + PROP_FILE_NAME + " not found on classpath", e);
-            }
-        } catch (IOException e) {
-            if (required) {
-            	throw new MissingPropertyException(propName,
-                    "Error while reading " + PROP_FILE_NAME, e);
-            }
+        String value = props.getProperty(propName);
+        if (required && (value == null)) {
+            throw new MissingPropertyException(propName,
+                "Property " + propName + " not found in " + PROP_FILE_NAME);
         }
-        return null;
+        return value;
     }
 
     /**
@@ -68,21 +57,22 @@
     }
     
     /**
-     * Use lazy evaluation to create a Properties object and load the
-     * properties file into it.
-     * @return the Properties object.
-     * @throws FileNotFoundException
-     * @throws IOException
+     * Read the properties file
+     * @throws FileNotFoundException if the file cannot be located
+     * @throws IOException if the file cannot be read
      */
-    private static Properties getProps()
-        throws FileNotFoundException, IOException
+    public static void initProps(ServletContext context)
+    	throws FileNotFoundException, IOException
     {
-        if (props == null) {
+        if (props == null) // Only try to read it once
+        {
         	props = new Properties();
-            InputStream is = MOBYProperties.class.getClassLoader().
-                getResourceAsStream(PROP_FILE_NAME);
-            props.load(is);
+            InputStream is = context.getResourceAsStream(PROP_FILE_NAME);
+            if (is == null) {
+            	throw new FileNotFoundException(
+            		"Properties file \"" + PROP_FILE_NAME + "\" not found");
+            }
+        	props.load(is);
         }
-        return props;
     }
 }

From gss at pub.open-bio.org  Mon Jun 14 16:58:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 16:43:27 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142058.i5EKwxLf010977@pub.open-bio.org>


gss
Mon Jun 14 16:58:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets
In directory pub.open-bio.org:/tmp/cvs-serv10956/src/org/smoby/ref/servlets

Added Files:
	BaseServlet.java 
Log Message:
Base class that does common initialization tasks

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets BaseServlet.java,NONE,1.1
From gss at pub.open-bio.org  Mon Jun 14 16:59:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 16:44:04 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142059.i5EKxae0011019@pub.open-bio.org>


gss
Mon Jun 14 16:59:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets
In directory pub.open-bio.org:/tmp/cvs-serv10990/src/org/smoby/ref/servlets

Modified Files:
	ProviderInvestigationServlet.java DiscoveryServlet.java 
Log Message:
Make subclass of new common superclass BaseServlet

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets ProviderInvestigationServlet.java,1.3,1.4 DiscoveryServlet.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java	2004/05/19 18:26:40	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java	2004/06/14 20:59:36	1.4
@@ -7,7 +7,7 @@
 import org.apache.commons.logging.*;
 import org.smoby.ref.tools.db.*;
 import org.smoby.graph.*;
-import org.smoby.ref.tools.URIInvestigator;
+import org.smoby.ref.tools.*;
 import org.smoby.servlet.*;
 
 /**
@@ -17,7 +17,7 @@
  * The only feedback given is that if the provider-url is missing, the response
  * status is set to 406 NOT ACCEPTABLE; otherwise, the status is set to 200 OK.
  */
-public class ProviderInvestigationServlet extends HttpServlet
+public class ProviderInvestigationServlet extends BaseServlet
 {
     private final static Log syncLog = LogFactory.getLog("SYNC");
     

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/06/14 20:59:36	1.3
@@ -25,7 +25,7 @@
  * into an array of ProviderDescriptionGraph objects, by calling the
  * GraphListTransceiverFactory.newReceiver() factory method.
  */
-public class DiscoveryServlet extends HttpServlet
+public class DiscoveryServlet extends BaseServlet
 {
 	public void doPost(HttpServletRequest request, HttpServletResponse response)
 		throws ServletException, IOException

From gss at pub.open-bio.org  Mon Jun 14 16:59:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 16:44:04 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142059.i5EKxaxO011055@pub.open-bio.org>


gss
Mon Jun 14 16:59:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev
In directory pub.open-bio.org:/tmp/cvs-serv10990/src/org/smoby/ref/servlets/dev

Modified Files:
	OWLValidationServlet.java MOBYGraphValidationServlet.java 
	GraphConversionServlet.java RepositoryPrintServlet.java 
	ProviderListServlet.java 
Log Message:
Make subclass of new common superclass BaseServlet

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev OWLValidationServlet.java,1.2,1.3 MOBYGraphValidationServlet.java,1.2,1.3 GraphConversionServlet.java,1.2,1.3 RepositoryPrintServlet.java,1.1,1.2 ProviderListServlet.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java	2004/06/14 20:59:36	1.3
@@ -1,5 +1,6 @@
 package org.smoby.ref.servlets.dev;
 
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.servlet.ParamReader;
 import org.smoby.servlet.ParameterException;
 
@@ -13,7 +14,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class OWLValidationServlet extends HttpServlet
+public class OWLValidationServlet extends BaseServlet
 {
 	public void doPost(HttpServletRequest request, HttpServletResponse response)
 		throws ServletException, IOException

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java	2004/06/14 20:59:36	1.3
@@ -1,6 +1,7 @@
 package org.smoby.ref.servlets.dev;
 
 import org.smoby.parser.Parser;
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.servlet.*;
 import org.smoby.graph.*;
 
@@ -11,7 +12,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class MOBYGraphValidationServlet extends HttpServlet
+public class MOBYGraphValidationServlet extends BaseServlet
 {
 	public void doPost(HttpServletRequest request, HttpServletResponse response)
 		throws ServletException, IOException

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java	2004/06/14 20:59:36	1.3
@@ -1,5 +1,6 @@
 package org.smoby.ref.servlets.dev;
 
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.servlet.ParamReader;
 import org.smoby.servlet.ParameterException;
 
@@ -9,7 +10,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class GraphConversionServlet extends HttpServlet
+public class GraphConversionServlet extends BaseServlet
 {
 	public void doPost(HttpServletRequest request, HttpServletResponse response)
 		throws ServletException, IOException

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java	2004/06/14 20:59:36	1.2
@@ -1,5 +1,6 @@
 package org.smoby.ref.servlets.dev;
 
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.ref.tools.db.*;
 
 import com.hp.hpl.jena.rdf.model.*;
@@ -8,7 +9,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class RepositoryPrintServlet extends HttpServlet
+public class RepositoryPrintServlet extends BaseServlet
 {
     public void doGet(HttpServletRequest request, HttpServletResponse response)
         throws ServletException, IOException

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/06/14 20:59:36	1.3
@@ -2,6 +2,7 @@
 
 import org.smoby.servlet.*;
 import org.smoby.tools.*;
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.ref.tools.db.*;
 import org.smoby.ref.tools.*;
 
@@ -11,7 +12,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class ProviderListServlet extends HttpServlet
+public class ProviderListServlet extends BaseServlet
 {
     public void doGet(HttpServletRequest request, HttpServletResponse response)
         throws ServletException, IOException

From gss at pub.open-bio.org  Mon Jun 14 17:07:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 16:52:02 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142107.i5EL7ZId011109@pub.open-bio.org>


gss
Mon Jun 14 17:07:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv11084

Modified Files:
	build.xml 
Log Message:
No longer need to copy properties files to WEB-INF/classes

moby-live/S-MOBY/ref-impl/server build.xml,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/06/10 23:15:37	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/06/14 21:07:35	1.4
@@ -16,11 +16,6 @@
         <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
-        <copy toDir="${classes-dir}">
-            <fileset dir="WebRoot">
-                <include name="*.properties"/>
-            </fileset>
-        </copy>
 	</target>
 
     <!-- Deploy the application to Tomcat -->

From gss at pub.open-bio.org  Mon Jun 14 18:04:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon Jun 14 17:48:52 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142204.i5EM4KjS011316@pub.open-bio.org>


gss
Mon Jun 14 18:04:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools
In directory pub.open-bio.org:/tmp/cvs-serv11291/WebRoot/tools

Modified Files:
	client.html 
Log Message:
Added radio buttons on Discover form

moby-live/S-MOBY/ref-impl/server/WebRoot/tools client.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html	2004/03/30 22:25:51	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html	2004/06/14 22:04:20	1.2
@@ -24,8 +24,14 @@
 
 <h4><u>Discover matching graphs in the S-MOBY metadata repository</u></h4>
 <form action="http://www.s-moby.org:8080/find-providers" method="post">
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Paste a graph in RDF/XML format
-  and press "Discover" to find matching graphs. &nbsp;&nbsp;
+  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Paste a graph in RDF/XML format, select
+  statements to return, and press "Discover" to find matching graphs. &nbsp;&nbsp;
+  <p>
+  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+  Statements to return:&nbsp;&nbsp;
+  <input type="radio" name="statements" value="minimal">Minimal&nbsp;&nbsp;
+  <input type="radio" name="statements" value="query" CHECKED>Query only&nbsp;&nbsp;
+  <input type="radio" name="statements" value="cached">Cached&nbsp;&nbsp;
   <input value="Discover" type="submit">
   <p>
   &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

From mwilkinson at pub.open-bio.org  Mon Jun 14 20:08:14 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Jun 14 19:52:41 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150008.i5F08EAc011629@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:08:14 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11614

Added Files:
	Config.pm 
Log Message:
added a configuration module.  MOBY Central will no longer use environment variables to get the database connection information

moby-live/Perl/MOBY Config.pm,NONE,1.1
From mwilkinson at pub.open-bio.org  Mon Jun 14 20:09:37 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Jun 14 19:54:04 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150009.i5F09bw9011701@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:09:36 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11678

Modified Files:
	Central.pm Central.html 
Log Message:
modified the way Central gets its configuration.  Also fixed a bug that allowed object names to be registered with spaces

moby-live/Perl/MOBY Central.pm,1.127,1.128 Central.html,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.127
retrieving revision 1.128
diff -u -r1.127 -r1.128
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/04/20 23:24:25	1.127
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/15 00:09:36	1.128
@@ -18,6 +18,7 @@
 use MOBY::authority;
 use MOBY::service_instance;
 use MOBY::central_db_connection;
+use MOBY::Config;
 
 my $debug = 0;
 
@@ -72,6 +73,43 @@
 Servers/Services, or queryiong for available services given certain input/output
 or service type constraints.
 
+=cut
+
+
+=head1 CONFIGURATION
+
+This depends on a config file to get its database connection information.  At a minimum
+this config file must have the following clause:
+
+ [mobycentral]
+ url = some.url 
+ username = foo
+ password = bar
+ port = portnumber
+ dbname = mobycentral
+
+
+The space before and after the '=' is critical.
+
+The end of a clause is indicated by a blank line.
+
+Additional identically formatted clauses may be added for each of:
+
+  [mobyobject]
+  [mobynamespace]
+  [mobyservice]
+  [mobyrelationship]
+
+if these ontologies are being served from a local database (via the
+OntologyServer module).  These clauses will be read by the OntologyServer
+module if they are present, otherwise default connections will be made
+to the MOBY Central ontology server.
+
+The config file must be readable by the webserver, and the webserver
+environment should include the following ENV variable:
+
+$ENV{MOBY_CENTRAL_CONFIG} = /path/to/config/file.name
+
 
 =head1 AUTHORS
 
@@ -141,21 +179,20 @@
 }
 
 sub _dbAccess {
-	
-# this configuration system was stoopid and is now defunkt.
-	
-#    my $filename = "./MOBY/central.cfg";# $self->config;
-#	$debug && &_LOG("trying to open file $filename\n");
-#	open (IN, $filename) || die "can't open configuration file $filename:  $!";
-#	my $url = <IN>; chomp $url;
-#	my $dbname = <IN>; chomp $dbname;
-#	my $username = <IN>; chomp $username;
-#	my $password = <IN>; chomp $password;
-	my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
-	my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
-	my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
-	my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
-	my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
+
+    my $conf = MOBY::Config->new;
+
+    $username = $conf->{mobycentral}->{username};
+    $password = $conf->{mobycentral}->{password};
+    $port = $conf->{mobycentral}->{port};
+    $dbname = $conf->{mobycentral}->{dbname};
+    $url = $conf->{mobycentral}->{url};
+    
+	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
+	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
+	#my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
+	#my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
+	#my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
 	
 	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
 	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
@@ -237,6 +274,10 @@
 	return &_error("Malformed authURI - must not have an http:// prefix","") if $auth =~ '[/:]';
 	return &_error("Malformed authURI - must take the form NNN.NNN.NNN","") unless $auth =~ /\./;
 	return &_error("Malformed email - must be a valid email address of the form name\@organization.foo","") unless $email =~ /\S\@\S+\.\S+/;
+	return &_error("Object name may not contain spaces or other characters invalid in a URN","") if $term =~ /\s\"\&\<\>\[\]\^\`\{\|\}\~/;
+	if ($term =~ m"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?"){  # matches a URI
+        return &_error("Object name may not be an URN or URI","") if $1;
+    }
 
 	# validate that the final ontology will be valid by testing against existing relationships and such
 	while (my ($reltype, $obj) = each %{$relationships}){

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.html,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOBY/Central.html	2004/04/15 14:38:22	1.13
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.html	2004/06/15 00:09:36	1.14
@@ -15,6 +15,7 @@
 	<li><a href="#name">NAME</a></li>
 	<li><a href="#synopsis">SYNOPSIS</a></li>
 	<li><a href="#description">DESCRIPTION</a></li>
+	<li><a href="#configuration">CONFIGURATION</a></li>
 	<li><a href="#authors">AUTHORS</a></li>
 	<li><a href="#registration_xml_object">Registration XML Object</a></li>
 	<li><a href="#methods">METHODS</a></li>
@@ -107,6 +108,34 @@
 <p>
 </p>
 <hr />
+<h1><a name="configuration">CONFIGURATION</a></h1>
+<p>This depends on a config file to get its database connection information.  At a minimum
+this config file must have the following clause:</p>
+<pre>
+ [mobycentral]
+ url = some.url 
+ username = foo
+ password = bar
+ port = portnumber
+ dbname = mobycentral</pre>
+<p>The space before and after the '=' is critical.</p>
+<p>The end of a clause is indicated by a blank line.</p>
+<p>Additional identically formatted clauses may be added for each of:</p>
+<pre>
+  [mobyobject]
+  [mobynamespace]
+  [mobyservice]
+  [mobyrelationship]</pre>
+<p>if these ontologies are being served from a local database (via the
+OntologyServer module).  These clauses will be read by the OntologyServer
+module if they are present, otherwise default connections will be made
+to the MOBY Central ontology server.</p>
+<p>The config file must be readable by the webserver, and the webserver
+environment should include the following ENV variable:</p>
+<p>$ENV{MOBY_CENTRAL_CONFIG} = /path/to/config/file.name</p>
+<p>
+</p>
+<hr />
 <h1><a name="authors">AUTHORS</a></h1>
 <p>Mark Wilkinson (<a href="mailto:markw@illuminae.com">markw@illuminae.com</a>)</p>
 <p>BioMOBY Project:  <a href="http://www.biomoby.org">http://www.biomoby.org</a></p>

From mwilkinson at pub.open-bio.org  Mon Jun 14 20:22:05 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Jun 14 20:06:38 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150022.i5F0M5db011857@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:22:05 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11838

Modified Files:
	OntologyServer.pm 
Log Message:
OntologyServer now reads the config file as well

moby-live/Perl/MOBY OntologyServer.pm,1.41,1.42
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.41
retrieving revision 1.42
diff -u -r1.41 -r1.42
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/05/11 15:48:45	1.41
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 00:22:05	1.42
@@ -74,6 +74,7 @@
 use vars qw($AUTOLOAD);
 use DBI;
 use DBD::mysql;
+use MOBY::Config;
 
 my $debug = 0;
 
@@ -139,6 +140,14 @@
     $self->ontology eq 'service' && $self->database('mobyservice');
     $self->ontology eq 'relationship' && $self->database('mobyrelationship');
 
+	
+	my $conf = MOBY::Config->new;
+	$self->username = $conf->{$self->database}->{username} unless $self->username;
+    $self->password = $conf->{$self->database}->{password} unless $self->password;
+    $self->port = $conf->{$self->database}->{port} unless $self->port;
+    $self->dbname = $self->database unless $self->dbname;
+    $self->host = $conf->{$self->database}->{url} unless $self->host;
+ 
 	my $host = $self->host?$self->host:$ENV{MOBY_CENTRAL_URL}; chomp $host;
 	my $username = $self->username?$self->username:$ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
 	my $password = $self->password?$self->password:$ENV{MOBY_CENTRAL_DBPASS}; chomp $password if $password; $password =~ s/\s//g if $password;

From mwilkinson at pub.open-bio.org  Mon Jun 14 20:37:55 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Jun 14 20:22:22 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150037.i5F0btA2011994@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:37:55 EDT 2004
Update of /home/repository/moby/moby-live/Perl
In directory pub.open-bio.org:/tmp/cvs-serv11975

Modified Files:
	MANIFEST 
Log Message:
using config file here too

moby-live/Perl MANIFEST,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MANIFEST,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MANIFEST	2004/03/18 23:10:34	1.9
+++ /home/repository/moby/moby-live/Perl/MANIFEST	2004/06/15 00:37:55	1.10
@@ -6,6 +6,7 @@
 MOBY/central_db_connection.pm
 MOBY/mysql.pm
 MOBY/OntologyServer.pm
+MOBY/Config.pm
 MOBY/CommonSubs.pm
 MOBY/CrossReference.pm
 MOBY/service_instance.pm

From mwilkinson at pub.open-bio.org  Mon Jun 14 20:37:55 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Jun 14 20:22:23 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150037.i5F0btjl012018@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:37:55 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11975/MOBY

Modified Files:
	CommonSubs.pm central_db_connection.pm 
Log Message:
using config file here too

moby-live/Perl/MOBY CommonSubs.pm,1.51,1.52 central_db_connection.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.51
retrieving revision 1.52
diff -u -r1.51 -r1.52
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/04 23:54:16	1.51
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/06/15 00:37:55	1.52
@@ -200,6 +200,7 @@
     getResponseArticles
     getCrossReferences
     genericServiceInputParser
+    genericServiceInputParserAsObject
     complexServiceInputParser
     whichDeepestParentObject
     getServiceNotes
@@ -233,6 +234,7 @@
     getResponseArticles
     getCrossReferences
     genericServiceInputParser
+    genericServiceInputParserAsObject
     complexServiceInputParser
     whichDeepestParentObject
     getServiceNotes
@@ -327,6 +329,48 @@
 
 
 
+=head2 serviceInputParser
+
+ name     : DO NOT USE!!
+ function : to take a MOBY message and break the objects out of it.  This is identical
+            to the genericServiceInputParser method above, except that it returns the data as
+            Objects rather than XML::DOM nodes.  This is an improvement!
+ usage    : my @inputs = serviceInputParser($MOBY_mssage));
+ args     : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message
+ returns  : @inputs - the structure of @inputs is a list of listrefs.
+            Each listref has three components:
+                1. COLLECTION|SIMPLE|SECONDARY (i.e. constants 1, 2, 3)
+                2. queryID (undef for Secondary parameters)
+                3. $data - either MOBY::Client::SimpleArticle, CollectionArticle, or SecondaryArticle
+
+=cut
+
+
+sub serviceInputParser {
+    my ($message) = @_;  # get the incoming MOBY query XML
+    my @inputs;           # set empty response
+    my @queries = getInputs($message);  # returns XML::DOM nodes <mobyData>...</mobyData>
+
+
+# mark, this doesn't work for complex services.  We need to allow more than one input per invocation
+    foreach my $query(@queries){
+        my $queryID = getInputID($query);  # get the queryID attribute of the mobyData
+        my @input_articles = getArticlesAsObjects($query); # get the Simple/Collection articles making up this query <Simple>...</Simple> or <Collection>...</Collection> or <Parameter>...</Parameter
+        foreach my $article(@input_articles){       # input is a listref
+            if ($article->isCollection){
+                my @simples = getCollectedSimples($article->XML);
+                push @inputs, [COLLECTION,$queryID, \@simples];
+            } elsif ($article->isSimple){
+                push @inputs, [SIMPLE,$queryID,$article];
+            } elsif ($article->isSecondary){
+                push @inputs, [SECONDARY,$queryID,$article];
+            }
+        }
+    }
+    return @inputs;
+}
+
+
 =head2 complexServiceInputParser
 
  name     : complexServiceInputParser
@@ -487,46 +531,6 @@
 
 
 
-=head2 genericServiceInputParserAsObject
-
- name     : DO NOT USE!
- function : to take a MOBY message and break the objects out of it.  This is identical
-            to the subroutine above, except that it returns the data as
-            Objects rather than XML::DOM nodes
- usage    : my @inputs = genericServiceInputParser($MOBY_mssage));
- args     : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message
- returns  : @inputs - the structure of @inputs is a list of listrefs.
-            Each listref has three components:
-                1. COLLECTION|SIMPLE|SECONDARY (i.e. constants 1, 2, 3)
-                2. queryID (undef for Secondary parameters)
-                3. $data - either MOBY::Client::SimpleArticle, CollectionArticle, or SecondaryArticle
-
-=cut
-
-
-sub genericServiceInputParserAsObject {
-    my ($message) = @_;  # get the incoming MOBY query XML
-    my @inputs;           # set empty response
-    my @queries = getInputs($message);  # returns XML::DOM nodes <mobyData>...</mobyData>
-
-    foreach my $query(@queries){
-        my $queryID = getInputID($query);  # get the queryID attribute of the mobyData
-        my @input_articles = getArticlesAsObjects($query); # get the Simple/Collection articles making up this query <Simple>...</Simple> or <Collection>...</Collection> or <Parameter>...</Parameter
-        foreach my $article(@input_articles){       # input is a listref
-            if ($article->isCollection){
-                my @simples = getCollectedSimples($article->XML);
-                push @inputs, [COLLECTION,$queryID, \@simples];
-            } elsif ($article->isSimple){
-                push @inputs, [SIMPLE,$queryID,$article];
-            } elsif ($article->isSecondary){
-                push @inputs, [SECONDARY,$queryID,$article];
-            }
-        }
-    }
-    return @inputs;
-}
-
-
 #################################################
 					 ##################################
 					 ##################################

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2003/06/10 17:12:52	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/15 00:37:55	1.3
@@ -3,7 +3,7 @@
 use Carp;
 use XML::DOM;
 use vars qw($AUTOLOAD @ISA);
-
+use MOBY::Config;
 
 =head1 NAME
 
@@ -116,6 +116,26 @@
     #    $self->host,
     #    $self->port);
 
+
+    my $conf = MOBY::Config->new;
+
+    $username = $conf->{mobycentral}->{username};
+    $password = $conf->{mobycentral}->{password};
+    $port = $conf->{mobycentral}->{port};
+    $dbname = $conf->{mobycentral}->{dbname};
+    $url = $conf->{mobycentral}->{url};
+    
+	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
+	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
+	#my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
+	#my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
+	#my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
+	
+	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
+	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
+	
+	return ($dbh);
+
 	my $host = $ENV{MOBY_CENTRAL_URL}; chomp $host;
 	my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
 	my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;

From mwilkinson at pub.open-bio.org  Mon Jun 14 20:37:55 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Jun 14 20:22:24 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150037.i5F0btFP012043@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:37:55 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv11975/MOBY/Client

Modified Files:
	CollectionArticle.pm SimpleArticle.pm 
Log Message:
using config file here too

moby-live/Perl/MOBY/Client CollectionArticle.pm,1.7,1.8 SimpleArticle.pm,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm	2004/04/14 19:56:59	1.7
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm	2004/06/15 00:37:55	1.8
@@ -9,12 +9,39 @@
 
 =head1 NAME
 
-MOBY::Client::CollectionArticle - a small object describing the Collection articles from the findService Response message of MOBY Central
+MOBY::Client::CollectionArticle - a small object describing the Collection articles from the findService Response message of MOBY Central or representing the collection part of a MOBY invocation or response block
 
 =head1 SYNOPSIS
 
-experimental - please do not use in your code
+This module can be used in two ways.  One is to represent the Collection
+portion of a findService response.  The other is to represent the Collecion
+portion of a MOBY service invocation or response message.
+
+Parsing a MOBY Service Invocation
+
+ use MOBY::CommonSubs qw(:all);
+ 
+ sub myService {
+    my ($caller, $data) = @_;
+	
+    my (@inputs)= serviceInputParser($data);
+
+    foreach (@inputs){
+        my ($articleType, $qID, $OBJECT) = @{$_};
+        if ($articleType == COLLECTION){
+            $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;  # send back a blank response for this queryID
+            next;
+        } elsif ($articleType == SIMPLE) {
+        
+        } elsif ($articleType == SECONDARY){
+        
+        }
+    }
+ }
 
+ 
+ 
+ 
 =cut
 
 =head1 DESCRIPTION

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm	2004/04/14 19:56:59	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm	2004/06/15 00:37:55	1.5
@@ -328,6 +328,11 @@
     return $self;
 }
 
+sub value {
+    my ($self) = @_;
+    # ?????  what to do here ????
+    
+}
 sub AUTOLOAD {
     no strict "refs";
     my ($self, $newval) = @_;

From mwilkinson at pub.open-bio.org  Mon Jun 14 21:00:26 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Jun 14 20:44:53 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150100.i5F10QMf012399@pub.open-bio.org>


mwilkinson
Mon Jun 14 21:00:26 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv12372/MOBY

Modified Files:
	Central.pm OntologyServer.pm central_db_connection.pm 
Log Message:
a few bugfixes for undeclared variables etc

moby-live/Perl/MOBY Central.pm,1.128,1.129 OntologyServer.pm,1.42,1.43 central_db_connection.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.128
retrieving revision 1.129
diff -u -r1.128 -r1.129
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/15 00:09:36	1.128
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/15 01:00:26	1.129
@@ -182,11 +182,11 @@
 
     my $conf = MOBY::Config->new;
 
-    $username = $conf->{mobycentral}->{username};
-    $password = $conf->{mobycentral}->{password};
-    $port = $conf->{mobycentral}->{port};
-    $dbname = $conf->{mobycentral}->{dbname};
-    $url = $conf->{mobycentral}->{url};
+    my $username = $conf->{mobycentral}->{username};
+    my $password = $conf->{mobycentral}->{password};
+    my $port = $conf->{mobycentral}->{port};
+    my $dbname = $conf->{mobycentral}->{dbname};
+    my $url = $conf->{mobycentral}->{url};
     
 	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
 	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.42
retrieving revision 1.43
diff -u -r1.42 -r1.43
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 00:22:05	1.42
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 01:00:26	1.43
@@ -142,11 +142,10 @@
 
 	
 	my $conf = MOBY::Config->new;
-	$self->username = $conf->{$self->database}->{username} unless $self->username;
-    $self->password = $conf->{$self->database}->{password} unless $self->password;
-    $self->port = $conf->{$self->database}->{port} unless $self->port;
-    $self->dbname = $self->database unless $self->dbname;
-    $self->host = $conf->{$self->database}->{url} unless $self->host;
+	$self->username($conf->{$self->database}->{username}) unless $self->username;
+    $self->password($conf->{$self->database}->{password}) unless $self->password;
+    $self->port($conf->{$self->database}->{port}) unless $self->port;
+    $self->host($conf->{$self->database}->{url}) unless $self->host;
  
 	my $host = $self->host?$self->host:$ENV{MOBY_CENTRAL_URL}; chomp $host;
 	my $username = $self->username?$self->username:$ENV{MOBY_CENTRAL_DBUSER}; chomp $username;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/15 00:37:55	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/15 01:00:26	1.4
@@ -119,40 +119,17 @@
 
     my $conf = MOBY::Config->new;
 
-    $username = $conf->{mobycentral}->{username};
-    $password = $conf->{mobycentral}->{password};
-    $port = $conf->{mobycentral}->{port};
-    $dbname = $conf->{mobycentral}->{dbname};
-    $url = $conf->{mobycentral}->{url};
-    
-	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
-	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
-	#my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
-	#my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
-	#my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
-	
+    my $username = $conf->{mobycentral}->{username};
+    my $password = $conf->{mobycentral}->{password};
+    my $port = $conf->{mobycentral}->{port};
+    my $dbname = $conf->{mobycentral}->{dbname};
+    my $url = $conf->{mobycentral}->{url};
+    	
 	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
 	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
 	
-	return ($dbh);
-
-	my $host = $ENV{MOBY_CENTRAL_URL}; chomp $host;
-	my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
-	my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
-	my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
-    my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
-    
-    #my $dbname = $self->dbname;
-    #my $host = $self->host;
-    #my $port = $self->port;
-    #my $username = $self->username;
-    #my $password = $self->password;
-    my ($dsn) = "DBI:mysql:$dbname:$host:$port";
-
-    my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
-
     $self->dbh($dbh);
-    return $self;
+	return $self;
 
 }
 

From mwilkinson at pub.open-bio.org  Mon Jun 14 21:15:16 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Jun 14 20:59:43 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150115.i5F1FGWS012533@pub.open-bio.org>


mwilkinson
Mon Jun 14 21:15:16 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv12514/MOBY

Modified Files:
	Config.pm 
Log Message:
Doh.  I hard-coded a testing path in there.

moby-live/Perl/MOBY Config.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Config.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/Config.pm	2004/06/15 00:08:14	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/Config.pm	2004/06/15 01:15:16	1.2
@@ -65,7 +65,6 @@
     }
 
     my $file = $ENV{MOBY_CENTRAL_CONFIG};
-    $file = "/home/markw/conf.conf";
     chomp $file;
     if ((-e $file) && (!(-d $file))){
         open IN, $file || die "can't open MOBY Configuration file $!\n";

From mwilkinson at pub.open-bio.org  Tue Jun 15 10:55:17 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Jun 15 10:39:40 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406151455.i5FEtHJL014835@pub.open-bio.org>


mwilkinson
Tue Jun 15 10:55:17 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv14816/MOBY

Modified Files:
	OntologyServer.pm 
Log Message:
be sure to extract the database name from the config file in the case of a non-standard installation of the registry

moby-live/Perl/MOBY OntologyServer.pm,1.43,1.44
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.43
retrieving revision 1.44
diff -u -r1.43 -r1.44
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 01:00:26	1.43
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 14:55:17	1.44
@@ -152,7 +152,7 @@
 	my $password = $self->password?$self->password:$ENV{MOBY_CENTRAL_DBPASS}; chomp $password if $password; $password =~ s/\s//g if $password;
     my $port = $self->port?$self->port:$ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
     
-    my ($dsn) = "DBI:mysql:".($self->database).":".($host).":".($port);
+    my ($dsn) = "DBI:mysql:".($conf->{$self->database}->{dbname}).":".($host).":".($port);
 
     my $dbh;
 #	$debug && &_LOG("connecting to db with params ",$self->database, $self->username, $self->password,"\n");

From mwilkinson at pub.open-bio.org  Tue Jun 15 21:15:30 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Jun 15 20:59:52 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406160115.i5G1FU0T016502@pub.open-bio.org>


mwilkinson
Tue Jun 15 21:15:30 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv16447/MOBY/Client

Modified Files:
	Central.pm SecondaryArticle.pm 
Added Files:
	SimpleInput.pm 
Log Message:
all sorts of additions and changes.  Secondary parameters now work for me on two systems, so that problem should now be solved.  I am starting to rip out the SQL that is in MOBY Central into other modules, and it will eventually end up in a single mysql-specific module with an API to make it easier to code MOBY onto other data back-ends.  Various bug fixes here and there as well.

moby-live/Perl/MOBY/Client SimpleInput.pm,NONE,1.1 Central.pm,1.75,1.76 SecondaryArticle.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.75
retrieving revision 1.76
diff -u -r1.75 -r1.76
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/05/03 19:49:18	1.75
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/06/16 01:15:30	1.76
@@ -10,6 +10,7 @@
 use MOBY::Client::Registration;
 use MOBY::Client::SimpleArticle;
 use MOBY::Client::CollectionArticle;
+use MOBY::Client::SecondaryArticle;
 use MOBY::Client::OntologyServer;
 
 use vars qw($AUTOLOAD @ISA $MOBY_server $MOBY_uri);
@@ -722,8 +723,8 @@
 
 	if ($Category eq "moby" || $Category eq 'soap') {
 		my %SEC;
-		if ($a{'secondary'} && ref($a{'secondary'} =~ /hash/i)){
-			%SEC = %{$a{secondary}}
+		if ($a{'secondary'} && (ref($a{'secondary'}) =~ /hash/i)){
+			%SEC = %{$a{secondary}};
 		} elsif ($a{'secondary'} && !(ref($a{'secondary'}) =~ /hash/i)){
 			return $self->errorRegXML("invalid structure of secondary parameters.  Expected hashref.")
 		}
@@ -799,13 +800,14 @@
 			my $min = $data{min};
 			my $datatype = $data{datatype};
 			unless ($datatype){return $self->errorRegXML("a secondaryArticle must contain at least a datatype value in secondary article $param");}
+			unless (($datatype =~ /Integer/) || ($datatype =~ /Float/) || ($datatype =~ /String/) || ($datatype =~ /DateTime/)){return $self->errorRegXML("a secondaryArticle must have a datatype of Integer, Float, String, or DateTime");}
 			unless ((ref($data{enum})) =~ /array/i){return $self->errorRegXML("invalid structure of enum limits in secondary article $param; expected arrayref")}
 			my @enums = @{$data{enum}};
 			$message .="<Parameter articleName='$param'>\n";
 			$message .="<default>$default</default>\n";
 			$message .="<datatype>$datatype</datatype>\n";
-			$message .="<max></max>\n";
-			$message .="<min></min>\n";
+			$message .="<max>$max</max>\n";
+			$message .="<min>$min</min>\n";
 			foreach (@enums){
 				$message .="<enum>$_</enum>\n";
 			}

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm	2004/05/03 19:49:18	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm	2004/06/16 01:15:30	1.2
@@ -185,7 +185,7 @@
 
     sub addEnum {
         my ($self, $enum) = @_;
-        return $self->{enum} unless $enum;
+        return $self->{enum} unless defined($enum);
         push @{$self->{enum}}, $enum;
         return $self->{enum};
     }
@@ -265,36 +265,46 @@
 
     my $objects = $dom->getElementsByTagName("datatype");
     if ($objects->item(0)){
+        my $data;
         foreach my $child($objects->item(0)->getChildNodes){ 
             next unless $child->getNodeType == TEXT_NODE;
-            $self->datatype($self->datatype . $child->toString);
+            $data .= $child->toString;
+            $data =~ s/\s//g;
         }
+        $self->datatype($data);
     }
-    $self->datatype($self->datatype =~ s/^\s//);
-    $self->datatype($self->datatype =~ s/\s$//);
     
     $objects = $dom->getElementsByTagName("default");
     if ($objects->item(0)){
+        my $def;
         foreach my $child($objects->item(0)->getChildNodes){ 
             next unless $child->getNodeType == TEXT_NODE;
-            $self->default($self->default . $child->toString);
+            $def .= $child->toString;
+            $def =~ s/\s//g;
         }
+        $self->default($def);
     }
     
     $objects = $dom->getElementsByTagName("max");
     if ($objects->item(0)){
+        my $max;
         foreach my $child($objects->item(0)->getChildNodes){ 
             next unless $child->getNodeType == TEXT_NODE;
-            $self->max($self->max . $child->toString);
+            $max .= $child->toString;
+            $max =~ s/\s//g;
         }
+        $self->max($max);
     }
     
     $objects = $dom->getElementsByTagName("min");
     if ($objects->item(0)){
+        my $min;
         foreach my $child($objects->item(0)->getChildNodes){ 
             next unless $child->getNodeType == TEXT_NODE;
-            $self->min($self->min . $child->toString);
+            $min .= $child->toString;
+            $min =~ s/\s//g;
         }
+        $self->min($min);
     }
     
     $objects = $dom->getElementsByTagName("enum");
@@ -303,7 +313,8 @@
             foreach my $child($objects->item($_)->getChildNodes){
                 my $val;
                 next unless $child->getNodeType == TEXT_NODE;
-                next unless $val = $child->toString;
+                $val = $child->toString;
+                next unless defined($val);
                 $val =~ s/^\s//; $val =~ s/\s$//;
                 $self->addEnum($val);
             }

From mwilkinson at pub.open-bio.org  Tue Jun 15 21:15:30 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Jun 15 20:59:53 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406160115.i5G1FURZ016478@pub.open-bio.org>


mwilkinson
Tue Jun 15 21:15:30 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv16447/MOBY

Modified Files:
	Central.pm service_instance.pm simple_input.pm 
	simple_output.pm 
Added Files:
	collection_input.pm collection_output.pm secondary_input.pm 
Log Message:
all sorts of additions and changes.  Secondary parameters now work for me on two systems, so that problem should now be solved.  I am starting to rip out the SQL that is in MOBY Central into other modules, and it will eventually end up in a single mysql-specific module with an API to make it easier to code MOBY onto other data back-ends.  Various bug fixes here and there as well.

moby-live/Perl/MOBY collection_input.pm,NONE,1.1 collection_output.pm,NONE,1.1 secondary_input.pm,NONE,1.1 Central.pm,1.129,1.130 service_instance.pm,1.3,1.4 simple_input.pm,1.2,1.3 simple_output.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.129
retrieving revision 1.130
diff -u -r1.129 -r1.130
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/15 01:00:26	1.129
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/16 01:15:30	1.130
@@ -17,6 +17,11 @@
 use MOBY::service_type;
 use MOBY::authority;
 use MOBY::service_instance;
+use MOBY::simple_input;
+use MOBY::simple_output;
+use MOBY::collection_input;
+use MOBY::collection_output;
+use MOBY::secondary_input;
 use MOBY::central_db_connection;
 use MOBY::Config;
 
@@ -1150,7 +1155,7 @@
 	return &_error("Service with this authority/servicename already exists","") if ($SVC == -1);
 
 	$debug && &_LOG("new service instance created\n");
-	
+    
 	foreach my $IN(@IN){
 		my ($success,$msg) = &_registerArticles($SVC, "input", $IN, undef); 
 		return &_error("Registration Failed During INPUT Article Registration: $msg","") unless ($success==1);
@@ -1160,7 +1165,7 @@
 		return &_error("Registration Failed During OUTPUT Article Registration: $msg","") unless ($success==1);
 	}
 	foreach my $SEC(@SECS){
-		my ($success,$msg) = &_registerArticles($SVC, "secondary", $SEC, undef); 
+    	my ($success,$msg) = &_registerArticles($SVC, "secondary", $SEC, undef); 
 		return &_error("Registration Failed During SECONDARY Article Registration: $msg","") unless ($success==1);
 	}
 	
@@ -1172,7 +1177,7 @@
     my $dbh = $SVC->dbh;
     return  (-1,'Bad node') unless $node->getNodeType == ELEMENT_NODE;
 
-    # this is a Simple or a Collection object
+    # this is a Simple, Collection, or Parameter object
     my $simp_coll = $node->getTagName;
 	$debug && &_LOG("TAGNAME in $inout _registerArticle is $simp_coll");
 	
@@ -1183,9 +1188,20 @@
     my ($object_type, @namespaces);
 
     if ($simp_coll eq "Collection"){
-		$debug && &_LOG("Collection!\n");  # the following SQl belongs in the service_instance object, but screw it, I'm running out of time!
-		$dbh->do("insert into collection_$inout (service_instance_id, article_name) values (?,?)", undef, ($SVC->service_instance_id, $article));
-		my $collection_id=$dbh->{mysql_insertid};
+		$debug && &_LOG("Collection!\n");
+        my $collection_id;
+        if ($inout eq 'input'){
+            $collection_id = $SVC->add_collection_input(article_name => $article);
+        } elsif ($inout eq 'output') {
+            $collection_id = $SVC->add_collection_output(article_name => $article);            
+        } else {
+            $SVC->DELETE_THYSELF; return (-1,"found article that was neither input nor output");
+        }
+        
+        # the following SQl belongs in the service_instance object, but screw it, I'm running out of time!
+		#$dbh->do("insert into collection_$inout (service_instance_id, article_name) values (?,?)", undef, ($SVC->service_instance_id, $article));
+		#my $collection_id=$dbh->{mysql_insertid};
+        
 		my $Simples = $node->getElementsByTagName('Simple');
 		my $length = $Simples->getLength;
 		for (my $x=0; $x<$length; ++$x){
@@ -1227,67 +1243,88 @@
 		chop($namespace_string);  # remove trailing comma
 		my $dbh = $SVC->dbh;
 		my $service_instance_id;
-		unless ($collid) {
+		unless ($collid) {  # this SIMPLE is either alone, or is part of a COLLECTION ($collid > 0)
+                            # therefore we want either its service instance ID, or its Collection ID.
 			$service_instance_id = $SVC->service_instance_id;
 		}				# one or the other, but not both
-		$dbh->do("insert into simple_".$inout."
-				 (object_type_uri,
-				  namespace_type_uris,
-				  article_name,
-				  service_instance_id,
-				  collection_".$inout."_id)
-				 values (?,?,?,?,?)",
-		undef,
-		($typeURI,
-		$namespace_string,
-		$article,
-		$service_instance_id,
-		$collid));
-
+        
+        if ($inout eq 'input'){
+            my $sinput = $SVC->add_simple_input(
+                    object_type_uri	=> $typeURI,
+                    namespace_type_uris	=> $namespace_string,
+                    article_name 	=> $article,
+                    collection_input_id 	=> 	$collid,
+                    );
+            unless ($sinput){
+       			$SVC->DELETE_THYSELF; return (-1,"registration failed during registration of input object $typeURI.  Unknown reasons.");
+            }
+
+        } elsif ($inout eq 'output'){
+            my $soutput = $SVC->add_simple_output(
+                    object_type_uri	=> $typeURI,
+                    namespace_type_uris	=> $namespace_string,
+                    article_name 	=> $article,
+                    collection_input_id 	=> 	$collid,
+                    );
+            unless ($soutput){
+       			$SVC->DELETE_THYSELF; return (-1,"registration failed during registration of output object $typeURI.  Unknown reasons.");
+            }
+        }
+        
     } elsif ($simp_coll eq "Parameter"){
-	    my $article = $node->getAttributeNode("articleName");
-		$article = $article->getValue() if $article;
-        my $types =  $node->getElementsByTagName('datatype');
-	    my ($datatype, $def, $max, $min, @enums);
+        my $parameter = $node;
+        my $article = $parameter->getAttributeNode("articleName");
+        $article = $article->getValue() if $article;
+        my ($datatype, $def, $max, $min, @enums);
+        my $types =  $parameter->getElementsByTagName('datatype');
         if ($types->item(0)){
-			foreach ($types->item(0)->getChildNodes){ # should only ever be one!
+            foreach ($types->item(0)->getChildNodes){ # should only ever be one!
             ($_->getNodeType == TEXT_NODE) && ($datatype = $_->toString);
-	        }
-		}
-        my $defs =  $node->getElementsByTagName('default');
+            }
+        }
+        my $defs =  $parameter->getElementsByTagName('default');
         if ($defs->item(0)){
-			foreach ($defs->item(0)->getChildNodes){ # should only ever be one!
-				($_->getNodeType == TEXT_NODE) && ($def = $_->toString);
-			}
-		}
-        my $maxs =  $node->getElementsByTagName('max');
+            foreach ($defs->item(0)->getChildNodes){ # should only ever be one!
+                ($_->getNodeType == TEXT_NODE) && ($def = $_->toString);
+            }
+        }
+        my $maxs =  $parameter->getElementsByTagName('max');
         if ($maxs->item(0)){
-			foreach ($maxs->item(0)->getChildNodes){ # should only ever be one!
-				($_->getNodeType == TEXT_NODE) && ($max = $_->toString);
-			}
-		}
-        my $mins =  $node->getElementsByTagName('min');
+            foreach ($maxs->item(0)->getChildNodes){ # should only ever be one!
+                ($_->getNodeType == TEXT_NODE) && ($max = $_->toString);
+            }
+        }
+        my $mins =  $parameter->getElementsByTagName('min');
         if ($mins->item(0)){
-			foreach ($mins->item(0)->getChildNodes){ # should only ever be one!
-				($_->getNodeType == TEXT_NODE) && ($min = $_->toString);
-			}
-		}
-        my $enums =  $node->getElementsByTagName('enum');
-		my $numenums = $enums->getLength;
-		for (my $n=0;$n<$numenums;++$n){
-			foreach ($enums->item($n)->getChildNodes){ # should only ever be one!
-				($_->getNodeType == TEXT_NODE) && (push @enums, $_->toString);
-			}
-		}
-		my $enum_string = join "",(map {$_.","} @enums);
-		chop $enum_string; # get rid of trailing comma
-		my $dbh = $SVC->dbh;
-		$dbh->do(q{insert into secondary_input (default_value,maximum_value,minimum_value,enum_value,datatype,article_name,service_instance_id) values (?,?,?,?,?,?,?)},
-				 undef,
-				 ($def, $max, $min, $enum_string, $datatype, $article, $SVC->service_instance_id));		
+            foreach ($mins->item(0)->getChildNodes){ # should only ever be one!
+                ($_->getNodeType == TEXT_NODE) && ($min = $_->toString);
+            }
+        }
+        my $enums =  $parameter->getElementsByTagName('enum');
+        my $numenums = $enums->getLength;
+        for (my $n=0;$n<$numenums;++$n){
+            foreach ($enums->item($n)->getChildNodes){ # should only ever be one!
+                ($_->getNodeType == TEXT_NODE) && (push @enums, $_->toString);
+            }
+        }
+        my $enum_string = join "",(map {$_.","} @enums);
+        chop $enum_string; # get rid of trailing comma
+        my $sec = $SVC->add_secondary_input(
+                    default_value => $def,
+                    maximum_value => $max,
+                    minimum_value => $min,
+                    enum_value   => $enum_string,
+                    datatype     => $datatype,
+                    article_name => $article,
+                                            );
+        unless ($sec){
+            $SVC->DELETE_THYSELF; return (-1,"registration failed during registration of parameter $article.  Must be of type Integer, String, DateTime, or Float.");
+        }       
 	}
 	return 1;
 }
+
+
 sub _registerServicePayload {
 	my ($payload) = @_;
 	my $Parser = new XML::DOM::Parser;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm	2003/12/02 00:23:23	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm	2004/06/16 01:15:30	1.4
@@ -43,7 +43,7 @@
 
 =head1 AUTHORS
 
-Mark Wilkinson (mwilkinson@gene.pbi.nrc.ca)
+Mark Wilkinson (mwilkinson@mrl.ubc.ca)
 
 
 =cut
@@ -321,6 +321,94 @@
     return $authority;
 }
 
+sub add_simple_input {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $simple = MOBY::simple_input->new(
+				object_type_uri	=> $a{'object_type_uri'},
+				namespace_type_uris	=> $a{'namespace_type_uris'},
+				article_name 	=> $a{'article_name'},
+				service_instance_id	=> 	$self->service_instance_id,
+				collection_input_id 	=> 	$a{'collection_input_id'}
+					   );
+
+	push @{$self->{inputs}}, $simple;
+	return $simple->simple_input_id;
+}
+
+
+sub add_simple_output {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $simple = MOBY::simple_output->new(
+				object_type_uri	=> $a{'object_type_uri'},
+				namespace_type_uris	=> $a{'namespace_type_uris'},
+				article_name 	=> $a{'article_name'},
+				service_instance_id	=> 	$self->service_instance_id,
+				collection_input_id 	=> 	$a{'collection_output_id'}
+					   );
+
+	push @{$self->{outputs}}, $simple;
+	return $simple->simple_output_id;
+}
+
+
+sub add_collection_input {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $coll = MOBY::collection_input->new(
+				article_name 	=> $a{'article_name'},
+				service_instance_id	=> 	$self->service_instance_id,
+					   );
+
+	push @{$self->{inputs}}, $coll;
+	return $coll->collection_input_id;
+}
+
+
+sub add_collection_output {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $coll = MOBY::collection_output->new(
+				article_name 	=> $a{'article_name'},
+				service_instance_id	=> 	$self->service_instance_id,
+					   );
+
+	push @{$self->{outputs}}, $coll;
+	return $coll->collection_output_id;
+}
+
+
+sub add_secondary_input {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $sec = MOBY::secondary_input->new(
+		default_value => $a{'default_value'},
+		maximum_value => $a{'maximum_value'},
+		minimum_value => $a{'minimum_value'},
+		enum_value   => $a{'enum_value'},
+		datatype     => $a{'datatype'},
+		article_name => $a{'article_name'},
+		service_instance_id => $self->service_instance_id,
+					   );
+
+	push @{$self->{inputs}}, $sec;
+	return $sec->secondary_input_id;	
+
+}
+
+
+
 sub AUTOLOAD {
     no strict "refs";
     my ($self, $newval) = @_;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm	2003/12/28 20:41:59	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm	2004/06/16 01:15:30	1.3
@@ -9,11 +9,13 @@
 
 =head1 NAME
 
-MOBY::authority - a lightweight connection to the
+MOBY::simple_input - a lightweight connection to the
 simple_input table in the database
 
 =head1 SYNOPSIS
 
+NON FUNCTIONAL AT THIS TIME
+
  use MOBY::simple_input;
  my $Instance = MOBY::simple_input->new(
           object_type => "Sequence",
@@ -28,7 +30,7 @@
 
 =head1 DESCRIPTION
 
-representation of the authority table.  Can write to the database
+representation of the simple_input table.  Can write to the database
 
 =head1 AUTHORS
 
@@ -46,11 +48,13 @@
 	#ATTRIBUTES
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
-                    object_type          => [undef,        'read/write'],
-                    namespaces => [undef,        'read/write'],
-                    article_name         => [undef,       'read/write'],
-                    simple_input_id         => [undef,       'read/write'],
-                    service_instance_id         => [undef,       'read/write'],
+				simple_input_id	=> 	[undef, 		'read/write'],
+				object_type_uri	=> 	[undef, 		'read/write'],
+				namespace_type_uris	=> 	[undef, 		'read/write'],
+				article_name 	=> 	[undef, 		'read/write'],
+				service_instance_id	=> 	[undef, 		'read/write'],
+				collection_input_id 	=> 	[undef, 		'read/write'],
+				dbh 	=> 	[undef, 		'read/write'],
 				);
 
    #_____________________________________________________________
@@ -76,6 +80,17 @@
 
 }
 
+
+sub _dbh {
+    my ($self) = @_;
+    
+    my $central_connect = MOBY::central_db_connection->new();
+	$self->dbh($central_connect->dbh);
+	return $central_connect->dbh;
+	
+}
+
+
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -95,10 +110,33 @@
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
 
+	my $id = $self->WRITE;
+	$self->simple_input_id($id) if defined $id;
     return $self;
 
 }
 
+sub WRITE {
+	my ($self) = @_;	
+	my $dbh = $self->_dbh;
+	
+	$dbh->do("insert into simple_input
+				 (object_type_uri,
+				  namespace_type_uris,
+				  article_name,
+				  service_instance_id,
+				  collection_input_id)
+				 values (?,?,?,?,?)",
+		undef,
+		($self->object_type_uri,
+		$self->namespace_type_uris,
+		$self->article_name,
+		$self->service_instance_id,
+		$self->collection_input_id));
+	my $id=$dbh->{mysql_insertid};
+	return $id;
+}
+
 
 sub AUTOLOAD {
     no strict "refs";

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm	2003/05/07 19:20:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm	2004/06/16 01:15:30	1.2
@@ -14,6 +14,7 @@
 
 =head1 SYNOPSIS
 
+NON FUNCTIONAL AT THIS TIME
  use MOBY::simple_output;
  my $Instance = MOBY::simple_output->new(
           object_type => "Sequence",
@@ -28,7 +29,7 @@
 
 =head1 DESCRIPTION
 
-representation of the authority table.  Can write to the database
+representation of the simple_output table.  Can write to the database
 
 =head1 AUTHORS
 
@@ -46,11 +47,13 @@
 	#ATTRIBUTES
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
-                    object_type          => [undef,        'read/write'],
-                    namespaces => [undef,        'read/write'],
-                    article_name         => [undef,       'read/write'],
-                    simple_output_id         => [undef,       'read/write'],
-                    service_instance_id         => [undef,       'read/write'],
+				simple_output_id	=> 	[undef, 		'read/write'],
+				object_type_uri	=> 	[undef, 		'read/write'],
+				namespace_type_uris	=> 	[undef, 		'read/write'],
+				article_name 	=> 	[undef, 		'read/write'],
+				service_instance_id	=> 	[undef, 		'read/write'],
+				collection_output_id 	=> 	[undef, 		'read/write'],
+				dbh 	=> 	[undef, 		'read/write'],
 				);
 
    #_____________________________________________________________
@@ -76,6 +79,18 @@
 
 }
 
+
+
+sub _dbh {
+    my ($self) = @_;
+    
+    my $central_connect = MOBY::central_db_connection->new();
+	$self->dbh($central_connect->dbh);
+	return $central_connect->dbh;
+	
+}
+
+
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -95,15 +110,31 @@
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
 
+	my $id = $self->WRITE;
+	$self->simple_output_id($id) if defined $id;
     return $self;
 
 }
 
-sub object_type
 sub WRITE {
-    my ($caller, $dbh) = @_;
-    my $sth = $dbh->prepare("insert into simple_input (object_type_id, namespace_type_ids, article_name, service_instance_id) values (?,?,?,?)");
-    
+	my ($self) = @_;
+	my $dbh = $self->_dbh;	
+	$dbh->do("insert into simple_output
+				 (object_type_uri,
+				  namespace_type_uris,
+				  article_name,
+				  service_instance_id,
+				  collection_output_id)
+				 values (?,?,?,?,?)",
+		undef,
+		($self->object_type_uri,
+		$self->namespace_type_uris,
+		$self->article_name,
+		$self->service_instance_id,
+		$self->collection_output_id));
+	my $id=$dbh->{mysql_insertid};
+	return $id;		
+
 }
 
 sub AUTOLOAD {

From mwilkinson at pub.open-bio.org  Tue Jun 15 21:15:30 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Jun 15 20:59:54 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406160115.i5G1FUai016521@pub.open-bio.org>


mwilkinson
Tue Jun 15 21:15:30 EDT 2004
Update of /home/repository/moby/moby-live/Perl/scripts
In directory pub.open-bio.org:/tmp/cvs-serv16447/scripts

Modified Files:
	testMOBYClientCentral_v05.pl 
Log Message:
all sorts of additions and changes.  Secondary parameters now work for me on two systems, so that problem should now be solved.  I am starting to rip out the SQL that is in MOBY Central into other modules, and it will eventually end up in a single mysql-specific module with an API to make it easier to code MOBY onto other data back-ends.  Various bug fixes here and there as well.

moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.15,1.16
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl	2004/04/20 23:24:25	1.15
+++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl	2004/06/16 01:15:30	1.16
@@ -24,10 +24,10 @@
 }
 
 my $C = MOBY::Client::Central->new(
-#Registries => {
-#	mobycentral => {URL => 'http://localhost/cgi-bin/MOBY-Central.pl',
-#                       URI => 'http://localhost/MOBY/Central'}
-#		}
+Registries => {
+  mobycentral => {URL => $ENV{MOBY_SERVER}?$ENV{MOBY_SERVER}:'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl',
+		  URI => $ENV{MOBY_URI}?$ENV{MOBY_URI}:'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'}
+						}
 );
 
 

From mwilkinson at pub.open-bio.org  Tue Jun 15 21:15:30 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Jun 15 20:59:55 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406160115.i5G1FU7Y016541@pub.open-bio.org>


mwilkinson
Tue Jun 15 21:15:30 EDT 2004
Update of /home/repository/moby/moby-live/Perl/t
In directory pub.open-bio.org:/tmp/cvs-serv16447/t

Modified Files:
	Client-Central.t 
Log Message:
all sorts of additions and changes.  Secondary parameters now work for me on two systems, so that problem should now be solved.  I am starting to rip out the SQL that is in MOBY Central into other modules, and it will eventually end up in a single mysql-specific module with an API to make it easier to code MOBY onto other data back-ends.  Various bug fixes here and there as well.

moby-live/Perl/t Client-Central.t,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/t/Client-Central.t,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/t/Client-Central.t	2004/01/08 19:05:58	1.3
+++ /home/repository/moby/moby-live/Perl/t/Client-Central.t	2004/06/16 01:15:30	1.4
@@ -12,9 +12,11 @@
 
 # Test 2
 my $C = MOBY::Client::Central->new(
-    #MOBY_server => "http://localhost/cgi-bin/MOBY-Central.pl",
-    #MOBY_uri  => "http://localhost/MOBY/Central"
-    );
+		Registries => {
+						mobycentral => {	URL => 'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl',
+											URI => 'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'}
+						}
+                                  );
 
 isa_ok( $C,'MOBY::Client::Central',"Connected to test MOBY Central") or
     die("Cannot Connect to MOBY Central... cannot continue?");

From gss at pub.open-bio.org  Wed Jun 16 14:37:19 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 14:21:35 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161837.i5GIbJHC020447@pub.open-bio.org>


gss
Wed Jun 16 14:37:19 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20422/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed Jun 16 14:49:45 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 14:34:01 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161849.i5GInjsF020496@pub.open-bio.org>


gss
Wed Jun 16 14:49:45 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20472/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed Jun 16 14:50:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 14:35:13 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161850.i5GIoxcl020538@pub.open-bio.org>


gss
Wed Jun 16 14:50:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20517/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms

Added Files:
	literatureGuideURI.n3 literatureGuideURI geneSymbol 
	geneSymbol.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms literatureGuideURI.n3,NONE,1.1 literatureGuideURI,NONE,1.1 geneSymbol,NONE,1.1 geneSymbol.n3,NONE,1.1
From gss at pub.open-bio.org  Wed Jun 16 14:50:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 14:35:16 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161850.i5GIox5V020562@pub.open-bio.org>


gss
Wed Jun 16 14:50:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv20517/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot

Modified Files:
	citationSearch.rdf citationSearch.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.6,1.7 citationSearch.n3,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/05/19 20:42:37	1.6
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/06/16 18:50:59	1.7
@@ -1,50 +1,37 @@
 <rdf:RDF
-    xmlns:go="http://www.go.org:8080/terms#"
+    xmlns:sgd="http://www.sgd.org:8080/terms/"
     xmlns:acmepubs="http://www.acmepubs.com:8080/"
+    xmlns:pubs="http://www.pubs.org:8080/terms/"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+    xmlns:acmeterms="http://www.acmepubs.com:8080/terms/"
+    xmlns:go="http://www.go.org:8080/terms/"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
-    xmlns:pubs="http://www.pubs.org:8081/terms#"
-    xmlns:moby="http://www.s-moby.org:8080/terms#"
-    xmlns:sgd="http://www.sgd.org:8080/terms#" >
-  <rdf:Description rdf:about="http://www.acmepubs.com:8080/geneSymbol">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
-  </rdf:Description>
+    xmlns:moby="http://www.s-moby.org:8080/terms/" >
   <rdf:Description rdf:nodeID="A0">
-    <moby:hasMapping rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A1">
-    <acmepubs:geneSymbol rdf:nodeID="A2"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <moby:mapsTo rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms/GeneSymbol"/>
+    <acmeterms:geneSymbol rdf:nodeID="A1"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Subject"/>
+    <moby:mapsTo rdf:nodeID="A2"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A2">
+    <acmeterms:literatureGuideURI rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms/LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Object"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A4">
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-    <rdf:_1 rdf:nodeID="A0"/>
+    <moby:hasMapping rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Graph"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/citationSearch">
-    <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
-    <moby:operatesOn rdf:nodeID="A4"/>
-    <moby:oneLineDescription>Industry standard search</moby:oneLineDescription>
-    <moby:aboutURI>http://www.acmepubs.com/about/citationSearch</moby:aboutURI>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
     <moby:name>AcmePubs Citation Search</moby:name>
+    <moby:oneLineDescription>Industry standard search</moby:oneLineDescription>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Provider"/>
+    <moby:operatesOn rdf:nodeID="A5"/>
+    <rdf:type rdf:resource="http://www.pubs.org:8080/terms/citationSearch"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A3">
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <acmepubs:literatureGuideURL rdf:nodeID="A5"/>
-  </rdf:Description>
-  <rdf:Description rdf:about="http://www.acmepubs.com:8080/literatureGuideURL">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
-    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  <rdf:Description rdf:nodeID="A5">
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A4"/>
   </rdf:Description>
 </rdf:RDF>
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3	2004/05/19 20:42:37	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3	2004/06/16 18:50:59	1.6
@@ -1,41 +1,28 @@
-@prefix pubs:     <http://www.pubs.org:8081/terms#> .
-@prefix xsd:      <http://www.w3.org/2001/XMLSchema#> .
-@prefix acmepubs: <http://www.acmepubs.com:8080/> .
-@prefix go:       <http://www.go.org:8080/terms#> .
-@prefix sgd:      <http://www.sgd.org:8080/terms#> .
-@prefix moby:     <http://www.s-moby.org:8080/terms#> .
-@prefix rdfs:     <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix rdf:      <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-@prefix owl:      <http://www.w3.org/2002/07/owl#> .
+@prefix acmepubs:   <http://www.acmepubs.com:8080/> .
+@prefix acmeterms:  <http://www.acmepubs.com:8080/terms/> .
+@prefix pubs:       <http://www.pubs.org:8080/terms/> .
+@prefix go:         <http://www.go.org:8080/terms/> .
+@prefix sgd:        <http://www.sgd.org:8080/terms/> .
+@prefix moby:       <http://www.s-moby.org:8080/terms/> .
+@prefix rdfs:       <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix rdf:        <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix owl:        <http://www.w3.org/2002/07/owl#> .
 
 acmepubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
     moby:name "AcmePubs Citation Search" ;
     moby:oneLineDescription "Industry standard search" ;
-    moby:aboutURI "http://www.acmepubs.com/about/citationSearch" ;
     moby:operatesOn [
         a rdf:Bag ;
         rdf:_1 [
             a moby:Graph ;
             moby:hasMapping [
                 a moby:Subject, go:GeneSymbol ;
-                acmepubs:geneSymbol _:bnode1 ;
+                acmeterms:geneSymbol _:bnode1 ;
                 moby:mapsTo [
                     a moby:Object, sgd:LiteratureGuide ;
-                    acmepubs:literatureGuideURL _:bnode2
+                    acmeterms:literatureGuideURI _:bnode2
                 ]
             ]
         ]
-    ] .
-
-acmepubs:geneSymbol
-    a owl:DataTypeProperty ;
-    rdfs:subPropertyOf moby:Property ;
-    rdfs:domain go:GeneSymbol ;
-    rdfs:range xsd:string .
-
-acmepubs:literatureGuideURL
-    a owl:DataTypeProperty ;
-    rdfs:subPropertyOf moby:Property ;
-    rdfs:domain sgd:LiteratureGuide ;
-    rdfs:range xsd:anyURI .
\ No newline at end of file
+    ] .
\ No newline at end of file

From gss at pub.open-bio.org  Wed Jun 16 14:51:13 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 14:35:30 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161851.i5GIpDk0020600@pub.open-bio.org>


gss
Wed Jun 16 14:51:13 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20579/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms

Added Files:
	literatureGuideURI.n3 geneSymbol geneSymbol.n3 
	literatureGuideURI 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms literatureGuideURI.n3,NONE,1.1 geneSymbol,NONE,1.1 geneSymbol.n3,NONE,1.1 literatureGuideURI,NONE,1.1
From gss at pub.open-bio.org  Wed Jun 16 14:51:13 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 14:35:31 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161851.i5GIpDCp020624@pub.open-bio.org>


gss
Wed Jun 16 14:51:13 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv20579/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot

Modified Files:
	citationSearch.n3 citationSearch.rdf 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.5,1.6 citationSearch.rdf,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3	2004/05/19 20:42:33	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3	2004/06/16 18:51:13	1.6
@@ -1,41 +1,28 @@
-@prefix pubs:     <http://www.pubs.org:8081/terms#> .
-@prefix xsd:      <http://www.w3.org/2001/XMLSchema#> .
-@prefix megapubs: <http://www.megapubs.com:8080/> .
-@prefix go:       <http://www.go.org:8080/terms#> .
-@prefix sgd:      <http://www.sgd.org:8080/terms#> .
-@prefix moby:     <http://www.s-moby.org:8080/terms#> .
-@prefix rdfs:     <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix rdf:      <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-@prefix owl:      <http://www.w3.org/2002/07/owl#> .
+@prefix megapubs:   <http://www.megapubs.com:8080/> .
+@prefix megaterms:  <http://www.megapubs.com:8080/terms/> .
+@prefix pubs:       <http://www.pubs.org:8080/terms/> .
+@prefix go:         <http://www.go.org:8080/terms/> .
+@prefix sgd:        <http://www.sgd.org:8080/terms/> .
+@prefix moby:       <http://www.s-moby.org:8080/terms/> .
+@prefix rdfs:       <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix rdf:        <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix owl:        <http://www.w3.org/2002/07/owl#> .
 
 megapubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
     moby:name "MegaPubs Citation Search" ;
     moby:oneLineDescription "Cool new search" ;
-    moby:aboutURI "http://www.megapubs.com/about/citationSearch" ;
     moby:operatesOn [
         a rdf:Bag ;
         rdf:_1 [
             a moby:Graph ;
             moby:hasMapping [
                 a moby:Subject, go:GeneSymbol ;
-                megapubs:geneSymbol _:bnode1 ;
+                megaterms:geneSymbol _:bnode1 ;
                 moby:mapsTo [
                     a moby:Object, sgd:LiteratureGuide ;
-                    megapubs:literatureGuideURL _:bnode2
+                    megaterms:literatureGuideURI _:bnode2
                 ]
             ]
         ]
-    ] .
-
-megapubs:geneSymbol
-    a owl:DataTypeProperty ;
-    rdfs:subPropertyOf moby:Property ;
-    rdfs:domain go:GeneSymbol ;
-    rdfs:range xsd:string .
-
-megapubs:literatureGuideURL
-    a owl:DataTypeProperty ;
-    rdfs:subPropertyOf moby:Property ;
-    rdfs:domain sgd:LiteratureGuide ;
-    rdfs:range xsd:anyURI .
\ No newline at end of file
+    ] .
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/05/19 20:42:34	1.6
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/06/16 18:51:13	1.7
@@ -1,50 +1,37 @@
 <rdf:RDF
-    xmlns:go="http://www.go.org:8080/terms#"
+    xmlns:sgd="http://www.sgd.org:8080/terms/"
+    xmlns:pubs="http://www.pubs.org:8080/terms/"
     xmlns:megapubs="http://www.megapubs.com:8080/"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+    xmlns:go="http://www.go.org:8080/terms/"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
-    xmlns:pubs="http://www.pubs.org:8081/terms#"
-    xmlns:moby="http://www.s-moby.org:8080/terms#"
-    xmlns:sgd="http://www.sgd.org:8080/terms#" >
+    xmlns:moby="http://www.s-moby.org:8080/terms/"
+    xmlns:megaterms="http://www.megapubs.com:8080/terms/" >
   <rdf:Description rdf:nodeID="A0">
-    <moby:hasMapping rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-  </rdf:Description>
-  <rdf:Description rdf:about="http://www.megapubs.com:8080/literatureGuideURL">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
-    <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <megaterms:geneSymbol rdf:nodeID="A1"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Subject"/>
+    <moby:mapsTo rdf:nodeID="A2"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms/GeneSymbol"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/citationSearch">
-    <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Provider"/>
+    <moby:operatesOn rdf:nodeID="A3"/>
     <moby:oneLineDescription>Cool new search</moby:oneLineDescription>
-    <moby:operatesOn rdf:nodeID="A2"/>
-    <moby:aboutURI>http://www.megapubs.com/about/citationSearch</moby:aboutURI>
+    <rdf:type rdf:resource="http://www.pubs.org:8080/terms/citationSearch"/>
     <moby:name>MegaPubs Citation Search</moby:name>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <rdf:_1 rdf:nodeID="A0"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A1">
-    <moby:mapsTo rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <megapubs:geneSymbol rdf:nodeID="A4"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A3">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <megapubs:literatureGuideURL rdf:nodeID="A5"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:_1 rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
-  <rdf:Description rdf:about="http://www.megapubs.com:8080/geneSymbol">
-    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
-    <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
+  <rdf:Description rdf:nodeID="A2">
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms/LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Object"/>
+    <megaterms:literatureGuideURI rdf:nodeID="A5"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A4">
+    <moby:hasMapping rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Graph"/>
   </rdf:Description>
 </rdf:RDF>

From gss at pub.open-bio.org  Wed Jun 16 14:52:04 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 14:36:18 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161852.i5GIq4QV020656@pub.open-bio.org>


gss
Wed Jun 16 14:52:04 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv20631/S-MOBY/ref-impl/example-providers/sgd.org

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/sgd.org .cvsignore,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore	2004/06/10 23:31:50	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore	2004/06/16 18:52:04	1.3
@@ -3,3 +3,4 @@
 .encoding
 .mymetadata
 .project
+.settings

From gss at pub.open-bio.org  Wed Jun 16 14:55:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 14:39:52 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161855.i5GItaBd020712@pub.open-bio.org>


gss
Wed Jun 16 14:55:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv20690/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot

Removed Files:
	terms 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot terms,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/RCS/terms,v: No such file or directory

From gss at pub.open-bio.org  Wed Jun 16 14:57:56 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 14:42:11 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161857.i5GIvutQ020758@pub.open-bio.org>


gss
Wed Jun 16 14:57:56 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv20736/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot

Removed Files:
	terms.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot terms.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/RCS/terms.n3,v: No such file or directory

From gss at pub.open-bio.org  Wed Jun 16 15:00:29 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 14:44:44 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161900.i5GJ0Tdc020857@pub.open-bio.org>


gss
Wed Jun 16 15:00:29 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20833/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed Jun 16 15:00:31 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 14:44:47 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161900.i5GJ0VRJ020891@pub.open-bio.org>


gss
Wed Jun 16 15:00:31 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20870/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms

Added Files:
	LiteratureGuide LiteratureGuide.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms LiteratureGuide,NONE,1.1 LiteratureGuide.n3,NONE,1.1
From gss at pub.open-bio.org  Wed Jun 16 15:01:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 14:45:34 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161901.i5GJ1K3b020933@pub.open-bio.org>


gss
Wed Jun 16 15:01:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv20908/S-MOBY/ref-impl/server

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/server .cvsignore,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore	2004/06/14 17:17:56	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore	2004/06/16 19:01:20	1.3
@@ -2,3 +2,4 @@
 .classpath
 .mymetadata
 .project
+.settings

From mwilkinson at pub.open-bio.org  Wed Jun 16 15:07:34 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed Jun 16 14:51:49 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161907.i5GJ7Y7o021017@pub.open-bio.org>


mwilkinson
Wed Jun 16 15:07:34 EDT 2004
Update of /home/repository/moby/moby-live/Perl/scripts
In directory pub.open-bio.org:/tmp/cvs-serv20998/scripts

Modified Files:
	testMOBYClientCentral_v05.pl 
Log Message:
fixed test script

moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.16,1.17
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl	2004/06/16 01:15:30	1.16
+++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl	2004/06/16 19:07:34	1.17
@@ -148,7 +148,7 @@
 	         ],
 	secondary => {
         parametername1 => {
-            datatype => 'Int',
+            datatype => 'Integer',
     		default => 0,
 			max => 10,
 			min => -10,

From mwilkinson at pub.open-bio.org  Wed Jun 16 15:08:05 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed Jun 16 14:52:20 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161908.i5GJ85Qi021064@pub.open-bio.org>


mwilkinson
Wed Jun 16 15:08:05 EDT 2004
Update of /home/repository/moby/moby-live/Perl/t
In directory pub.open-bio.org:/tmp/cvs-serv21045/t

Modified Files:
	Client-Central.t 
Log Message:
fixing an incorrect test in the test suite

moby-live/Perl/t Client-Central.t,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/t/Client-Central.t,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/t/Client-Central.t	2004/06/16 01:15:30	1.4
+++ /home/repository/moby/moby-live/Perl/t/Client-Central.t	2004/06/16 19:08:05	1.5
@@ -100,7 +100,7 @@
 	         ],
 	secondary => {
         parametername1 => {
-            datatype => 'Int',
+            datatype => 'Integer',
     		default => 0,
 			max => 10,
 			min => -10,

From gss at pub.open-bio.org  Wed Jun 16 15:19:54 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 15:04:10 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161919.i5GJJsei021114@pub.open-bio.org>


gss
Wed Jun 16 15:19:54 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv21093/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms

Added Files:
	index.html 
Log Message:
Index of OWL terms

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms index.html,NONE,1.1
From gss at pub.open-bio.org  Wed Jun 16 15:21:57 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 15:06:45 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161921.i5GJLvAF021170@pub.open-bio.org>


gss
Wed Jun 16 15:21:57 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv21149/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms

Added Files:
	index.html 
Log Message:
Index of OWL terms

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms index.html,NONE,1.1
From gss at pub.open-bio.org  Wed Jun 16 18:07:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 17:51:16 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162207.i5GM70mA021799@pub.open-bio.org>


gss
Wed Jun 16 18:07:00 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir
In directory pub.open-bio.org:/tmp/cvs-serv21775/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir added to the repository

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed Jun 16 18:07:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 17:51:19 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162207.i5GM73iE021841@pub.open-bio.org>


gss
Wed Jun 16 18:07:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir
In directory pub.open-bio.org:/tmp/cvs-serv21820/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir

Added Files:
	CitationSearch CitationSearch.n3 index.html PubAbstract 
	PubAbstract.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir CitationSearch,NONE,1.1 CitationSearch.n3,NONE,1.1 index.html,NONE,1.1 PubAbstract,NONE,1.1 PubAbstract.n3,NONE,1.1
From gss at pub.open-bio.org  Wed Jun 16 18:08:53 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 17:53:08 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162208.i5GM8rkW021880@pub.open-bio.org>


gss
Wed Jun 16 18:08:53 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv21857/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot

Removed Files:
	terms terms.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot terms,1.1,NONE terms.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/terms,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/terms.n3,v: No such file or directory

From gss at pub.open-bio.org  Wed Jun 16 18:11:54 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 17:56:07 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162211.i5GMBsNP021939@pub.open-bio.org>


gss
Wed Jun 16 18:11:54 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv21915/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed Jun 16 18:13:13 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 17:57:26 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162213.i5GMDDUL021984@pub.open-bio.org>


gss
Wed Jun 16 18:13:13 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv21963/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms

Added Files:
	index.html PubAbstract CitationSearch PubAbstract.n3 
	CitationSearch.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms index.html,NONE,1.1 PubAbstract,NONE,1.1 CitationSearch,NONE,1.1 PubAbstract.n3,NONE,1.1 CitationSearch.n3,NONE,1.1
From gss at pub.open-bio.org  Wed Jun 16 18:14:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 17:58:31 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162214.i5GMEIpb022021@pub.open-bio.org>


gss
Wed Jun 16 18:14:18 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir
In directory pub.open-bio.org:/tmp/cvs-serv21995/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir

Removed Files:
	CitationSearch CitationSearch.n3 index.html PubAbstract 
	PubAbstract.n3 
Log Message:
Moved to terms/ directory

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir CitationSearch,1.1,NONE CitationSearch.n3,1.1,NONE index.html,1.1,NONE PubAbstract,1.1,NONE PubAbstract.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/CitationSearch,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/CitationSearch.n3,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/index.html,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/PubAbstract,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/PubAbstract.n3,v: No such file or directory

From gss at pub.open-bio.org  Wed Jun 16 18:18:50 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 18:03:05 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162218.i5GMIoag022108@pub.open-bio.org>


gss
Wed Jun 16 18:18:50 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22079/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms

Modified Files:
	LiteratureGuide LiteratureGuide.n3 
Added Files:
	index.html 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms index.html,NONE,1.1 LiteratureGuide,1.1,1.2 LiteratureGuide.n3,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide	2004/06/16 19:00:30	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide	2004/06/16 22:18:50	1.2
@@ -1,8 +1,8 @@
 <rdf:RDF
+    xmlns:sgd="http://www.sgd.org:8080/terms/"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:owl="http://www.w3.org/2002/07/owl#"
-    xmlns:sgd="http://www.sgd.org:8080/terms#" >
-  <rdf:Description rdf:about="http://www.sgd.org:8080/terms#LiteratureGuide">
+    xmlns:owl="http://www.w3.org/2002/07/owl#" >
+  <rdf:Description rdf:about="http://www.sgd.org:8080/terms/LiteratureGuide">
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
   </rdf:Description>
 </rdf:RDF>
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide.n3,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide.n3	2004/06/16 19:00:30	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide.n3	2004/06/16 22:18:50	1.2
@@ -1,4 +1,4 @@
-@prefix sgd: <http://www.sgd.org:8080/terms#> .
+@prefix sgd: <http://www.sgd.org:8080/terms/> .
 @prefix owl: <http://www.w3.org/2002/07/owl#> .
 
 sgd:LiteratureGuide

From gss at pub.open-bio.org  Wed Jun 16 18:23:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 18:08:16 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162223.i5GMNxai022173@pub.open-bio.org>


gss
Wed Jun 16 18:23:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv22150/S-MOBY/ref-impl/example-providers/go.org/WebRoot

Removed Files:
	terms terms.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot terms,1.1,NONE terms.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/RCS/terms,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/RCS/terms.n3,v: No such file or directory

From gss at pub.open-bio.org  Wed Jun 16 18:25:14 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 18:09:28 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162225.i5GMPEj3022216@pub.open-bio.org>


gss
Wed Jun 16 18:25:14 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22192/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed Jun 16 18:25:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 18:09:31 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162225.i5GMPGCH022258@pub.open-bio.org>


gss
Wed Jun 16 18:25:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22237/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms

Added Files:
	index.html GeneSymbol GeneSymbol.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms index.html,NONE,1.1 GeneSymbol,NONE,1.1 GeneSymbol.n3,NONE,1.1
From gss at pub.open-bio.org  Wed Jun 16 18:27:14 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 18:11:27 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162227.i5GMRExb022299@pub.open-bio.org>


gss
Wed Jun 16 18:27:14 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools
In directory pub.open-bio.org:/tmp/cvs-serv22274/S-MOBY/ref-impl/server/WebRoot/tools

Modified Files:
	developer.html 
Log Message:
Added developer tool to list statements in metadata repository

moby-live/S-MOBY/ref-impl/server/WebRoot/tools developer.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html	2004/03/30 23:54:34	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html	2004/06/16 22:27:14	1.3
@@ -1,67 +1,112 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
 <html>
-<head>
-  <title>Semantic MOBY Developer Tools</title>
-</head>
-<body>
-	<table style="text-align: center; width: 100%;" border="1"
+  <head>
+    <meta name="generator" content="HTML Tidy, see www.w3.org">
+
+    <title>Semantic MOBY Developer Tools</title>
+  </head>
+
+  <body>
+    <table style="WIDTH: 100%; TEXT-ALIGN: center" border="1"
     cellspacing="0" cellpadding="0">
-    <tbody>
-      <tr>
-        <td style="vertical-align: top; background-color: rgb(204, 204, 204);">
-      	  <b>Semantic MOBY Developer Tools</b>
-        </td>
-      </tr>
-    </tbody>
-  </table>
-  <br>
-  <h4><u>Convert a graph to a different format</u></h4>
-<form method="POST" action="http://www.s-moby.org:8080/convert-graph">
-  Paste a graph, select its input format,
-  and press "Convert Graph" to convert to the other format
-  <p>
-  Input format:&nbsp;&nbsp;&nbsp;
-  <input type="radio" name="input-format" value="N3" CHECKED>N3&nbsp;&nbsp;
-  <input type="radio" name="input-format" value="RDF/XML">RDF/XML
-  <input type="radio" name="input-format" value="N-TRIPLE">N-Triples&nbsp;&nbsp;
-  <br>
-  Output format:
-  <input type="radio" name="output-format" value="N3">N3&nbsp;&nbsp;
-  <input type="radio" name="output-format" value="RDF/XML" CHECKED>RDF/XML
-  <input type="radio" name="output-format" value="N-TRIPLE">N-Triples&nbsp;&nbsp;
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-  <input type="submit" value="Convert Graph">
-  <p>
-  <textarea name="graph" rows="15" cols="80"></textarea>
-  &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;
-
-</form>
-<H4><U>List the providers in the S-MOBY metadata repository</U></H4>
-<FORM method="GET" action="http://www.s-moby.org:8080/list-providers">
-  &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;
-  <INPUT type="submit" value="List Providers">&nbsp;&nbsp;
-  <INPUT type="checkbox" name="show-contents" value=true>
-  Show provider description graphs
-</FORM>
-<h4><u>Validate an OWL Graph using Jena</u></h4>
-<form method="POST" action="http://www.s-moby.org:8080/validate-owl-graph">
-  Paste a graph in RDF/XML format and press "Validate" to see what type of
-  OWL the graph represents
-  <p>
-  <input type="submit" value="Validate">
-  <p>
-  <textarea name="graph" rows="15" cols="80"></textarea>
-</form>
-
-<h4><u>Validate that a graph is MOBY canonical form</u></h4>
-<form method="POST" action="http://www.s-moby.org:8080/validate-canonical-graph">
-  Paste a graph in RDF/XML format and press "Validate" to see if it is
-  MOBY canonical form
-  <p>
-  <input type="submit" value="Validate">
-  <p>
-  <textarea name="graph" rows="15" cols="80"></textarea>
-</form>
-  
-</body>
+      <tbody>
+        <tr>
+          <td style=
+          "VERTICAL-ALIGN: top; BACKGROUND-COLOR: rgb(204,204,204)">
+          <b>Semantic MOBY Developer Tools</b></td>
+        </tr>
+      </tbody>
+    </table><br>
+     
+
+    <h4><u>Convert a graph to a different format</u></h4>
+
+    <form method="post" action=
+    "http://www.s-moby.org:8080/convert-graph">
+      Paste a graph, select its input format, and press "Convert Graph"
+      to convert to the other format 
+
+      <p>Input format:&nbsp;&nbsp;&nbsp; <input type="radio" name=
+      "input-format" value="N3" checked>N3&nbsp;&nbsp; <input type=
+      "radio" name="input-format" value="RDF/XML">RDF/XML <input type=
+      "radio" name="input-format" value=
+      "N-TRIPLE">N-Triples&nbsp;&nbsp;<br>
+       Output format: <input type="radio" name="output-format" value=
+      "N3">N3&nbsp;&nbsp; <input type="radio" name="output-format"
+      value="RDF/XML" checked>RDF/XML <input type="radio" name=
+      "output-format" value="N-TRIPLE">N-Triples&nbsp;&nbsp;
+      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <input type="submit" value=
+      "Convert Graph"></p>
+
+      <p><textarea name="graph" rows="15" cols="80">
+                                              
+                                               
+                                       
+                                 
+                         
+                   
+           
+      </textarea> &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;</p>
+    </form>
+
+    <h4><u>List the providers in the S-MOBY metadata
+    repository</u></h4>
+
+    <form method="get" action=
+    "http://www.s-moby.org:8080/list-providers">
+      &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; <input type="submit"
+      value="List Providers">&nbsp;&nbsp; <input type="checkbox" name=
+      "show-contents" value="true"> Show provider description graphs
+    </form>
+
+    <h4><u>List&nbsp;all statements&nbsp;in the S-MOBY metadata
+    repository</u></h4>
+
+    <form name="List statements" action=
+    "http://www.s-moby.org:8080/print-repository" method="get">
+      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;<input type=
+      "submit" value="List Statements in Repository">
+    </form>
+
+    <h4><u>Validate an OWL Graph using Jena</u></h4>
+
+    <form method="post" action=
+    "http://www.s-moby.org:8080/validate-owl-graph">
+      Paste a graph in RDF/XML format and press "Validate" to see what
+      type of OWL the graph represents 
+
+      <p><input type="submit" value="Validate"></p>
+
+      <p><textarea name="graph" rows="15" cols="80">
+                                              
+                                               
+                                       
+                                 
+                         
+                   
+           
+      </textarea></p>
+    </form>
+
+    <h4><u>Validate that a graph is MOBY canonical form</u></h4>
+
+    <form method="post" action=
+    "http://www.s-moby.org:8080/validate-canonical-graph">
+      Paste a graph in RDF/XML format and press "Validate" to see if it
+      is MOBY canonical form 
+
+      <p><input type="submit" value="Validate"></p>
+
+      <p><textarea name="graph" rows="15" cols="80">
+                                              
+                                               
+                                       
+                                 
+                         
+                   
+           
+      </textarea></p>
+    </form>
+  </body>
 </html>

From gss at pub.open-bio.org  Wed Jun 16 18:27:47 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 18:12:01 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162227.i5GMRln5022326@pub.open-bio.org>


gss
Wed Jun 16 18:27:47 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv22304/S-MOBY/ref-impl/server/WebRoot

Removed Files:
	terms 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/server/WebRoot terms,1.2,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/terms,v: No such file or directory

From gss at pub.open-bio.org  Wed Jun 16 19:27:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 19:11:42 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162327.i5GNRQwk022472@pub.open-bio.org>


gss
Wed Jun 16 19:27:26 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22448/S-MOBY/ref-impl/server/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/server/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed Jun 16 19:27:29 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 19:11:44 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162327.i5GNRTDB022514@pub.open-bio.org>


gss
Wed Jun 16 19:27:29 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22493/S-MOBY/ref-impl/server/WebRoot/terms

Added Files:
	operatesOn oneLineDescription objectProperty.n3 __Seq.n3 
	__NonCollection.n3 providerAboutURI.n3 index.html Provider 
	Subject mapsTo __Collection.n3 __List.n3 Object.n3 hasMapping 
	providerAboutURI Graph.n3 subjectProperty mapsTo.n3 __List 
	name.n3 oneLineDescription.n3 __Alt __Bag.n3 __Bag Graph __Seq 
	objectProperty name operatesOn.n3 Provider.n3 hasMapping.n3 
	subjectProperty.n3 __NonCollection __Collection __Alt.n3 
	Subject.n3 Object 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/server/WebRoot/terms operatesOn,NONE,1.1 oneLineDescription,NONE,1.1 objectProperty.n3,NONE,1.1 __Seq.n3,NONE,1.1 __NonCollection.n3,NONE,1.1 providerAboutURI.n3,NONE,1.1 index.html,NONE,1.1 Provider,NONE,1.1 Subject,NONE,1.1 mapsTo,NONE,1.1 __Collection.n3,NONE,1.1 __List.n3,NONE,1.1 Object.n3,NONE,1.1 hasMapping,NONE,1.1 providerAboutURI,NONE,1.1 Graph.n3,NONE,1.1 subjectProperty,NONE,1.1 mapsTo.n3,NONE,1.1 __List,NONE,1.1 name.n3,NONE,1.1 oneLineDescription.n3,NONE,1.1 __Alt,NONE,1.1 __Bag.n3,NONE,1.1 __Bag,NONE,1.1 Graph,NONE,1.1 __Seq,NONE,1.1 objectProperty,NONE,1.1 name,NONE,1.1 operatesOn.n3,NONE,1.1 Provider.n3,NONE,1.1 hasMapping.n3,NONE,1.1 subjectProperty.n3,NONE,1.1 __NonCollection,NONE,1.1 __Collection,NONE,1.1 __Alt.n3,NONE,1.1 Subject.n3,NONE,1.1 Object,NONE,1.1
From gss at pub.open-bio.org  Wed Jun 16 19:28:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 19:12:14 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162328.i5GNS0EK022541@pub.open-bio.org>


gss
Wed Jun 16 19:28:00 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv22519/S-MOBY/ref-impl/server/WebRoot

Removed Files:
	terms.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/server/WebRoot terms.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/terms.n3,v: No such file or directory

From gss at pub.open-bio.org  Wed Jun 16 19:29:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 19:13:35 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162329.i5GNTK4q022587@pub.open-bio.org>


gss
Wed Jun 16 19:29:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv22562/S-MOBY/ref-impl/core/src/org/smoby/parser

Modified Files:
	Parser.java 
Log Message:
Documentation

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/05/24 22:05:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/16 23:29:20	1.2
@@ -3,15 +3,17 @@
 import java.io.*;
 import java.net.*;
 import java.util.*;
-
 import org.smoby.graph.*;
 import org.smoby.graph.impl.*;
 import org.smoby.parser.*;
 import org.smoby.vocabulary.*;
-
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.vocabulary.*;
 
+/**
+ * This class is used to parse OWL models, stored as Jena2 models, into
+ * objects that implement interfaces from the org.smoby.graph package.
+ */
 public class Parser
 {
     /**
@@ -25,15 +27,17 @@
     public final static String LANGUAGE_N3 = "N3";
     
     /**
-     * The underlying Jena model on which the parsed graph is based
+     * Inference models containing inferred statements derived using
+     * rdfs:subClassOf relationships.
      */
-    private Model model;
+    private Map inferenceModels = new HashMap();
     
     /**
-     * An inference model containing inferred statements derived using
-     * rdfs:subClassOf relationships.
+     * Return the inference model associated with a given plain model
      */
-    private InfModel inferenceModel;
+    private InfModel getInferenceModel(Model model) {
+    	return (InfModel) inferenceModels.get(model);
+    }
 
     /**
      * Create and return a parser for parsing an N3 file
@@ -86,8 +90,8 @@
 	}
 
     /**
-     * Create and return a parser for parsing an input stream having
-     * the given format
+     * Create and return a parser for parsing an input stream containing
+     * the given language
      * @return a new instance of Parser
      * @throws IOException if reading the stream 
      * @throws UnparsableGraphException if the file doesn't contain a
@@ -105,6 +109,11 @@
         return new Parser(model);
     }
     
+    /**
+     * Create and return a parser for parsing a string in a given language
+     * @param graphString the string containing the graph
+     * @param language the language the model is expressed in
+     */
     public static Parser forString(String graphString, String language)
     	throws UnparsableGraphException
 	{
@@ -114,28 +123,71 @@
 	}
     
     /**
-     * Create an instance for parsing from the given model
+     * Create an instance for parsing the given model.
      */
     public Parser(Model model)
     {
-        this.model = model;
-        this.inferenceModel = ModelFactory.createRDFSModel(model);
-    }
-    
-    /**
-     * Return the underlying model
-     */
-    public Model getModel()
-    {
-        return model;
+    	
+        StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
+        while (it.hasNext())
+        {
+        	Statement stmt = it.nextStatement();
+        	Model subModel = ModelFactory.createDefaultModel();
+        	subModel.setNsPrefixes(model.getNsPrefixMap());
+        	Resource subject = stmt.getSubject();
+        	addReachableStmts(subModel, subject, subject.getURI());
+        	inferenceModels.put(subModel,
+        		ModelFactory.createRDFSModel(subModel));
+        }
     }
     
+	private void addReachableStmts(Model model, Resource subject, String uri)
+	{
+		// For each statement whose subject is the given resource
+		//
+		StmtIterator it = subject.getModel().listStatements(
+			subject, null, (RDFNode) null);
+		
+		while (it.hasNext())
+		{
+			Statement stmt = it.nextStatement();
+			
+			// The statement itself should be added
+			//
+			model.add(model.createStatement(
+				stmt.getSubject(), stmt.getPredicate(), stmt.getObject()));
+			
+			// If the object of the statement is a blank node or a
+			// resource whose URI starts with the provider URI, then
+			// recursively add the statements that are reachable
+			// from the object
+			//
+			if (stmt.getObject().canAs(Resource.class))
+			{
+				Resource object = (Resource) stmt.getObject().as(Resource.class);
+				if (object.isAnon() || object.getURI().startsWith(uri)) {
+					addReachableStmts(model, object, uri);
+				}
+			}
+		}
+	}
+
     /**
-     * Return the inference model
+     * Parse a provider from the model. If the model contains
+     * multiple providers, only one will be returned (at random). If
+     * the model is expected to contain multiple providers, then call
+     * parseProviders() instead to get all the providers in a
+     * MOBYCollection.
      */
-    public InfModel getInferenceModel()
+    public MOBYProvider parseProvider()
     {
-        return inferenceModel;
+    	MOBYUnorderedCollection providers = parseProviders();
+    	
+    	if (providers.size() == 0) {
+    		return null;
+    	} else {
+    		return (MOBYProvider) providers.iterator().next();
+    	}
     }
     
     /**
@@ -147,38 +199,28 @@
         
         // Find the statements that say something is of type Provider
         //
-        StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
+//        StmtIterator it = underlying.listStatements(null, RDF.type, MOBY.Provider);
+        
+        Iterator it = inferenceModels.keySet().iterator();
         
         // Parse each provider
         //
         while (it.hasNext())
         {
-            Statement stmt = it.nextStatement();
-            Resource provider = stmt.getSubject();
-            providers.add(parseProvider(provider));
+        	Model model = (Model) it.next();
+        	StmtIterator it2 = model.listStatements(null, RDF.type, MOBY.Provider);
+        	
+        	if (it2 != null)
+        	{
+        		Statement stmt = it2.nextStatement();
+	            Resource provider = stmt.getSubject();
+	            providers.add(parseProvider(provider));
+        	}
         }
         
         // Create and return an unordered collection of the parsed providers
         //
-        return MOBYObjectFactory.newUnorderedCollection(null, providers, model);
-    }
-
-    /**
-     * Parse a provider from the model. If the model contains
-     * multiple providers, only one will be parsed (at random). If
-     * the model is expected to contain multiple providers, then call
-     * parseProviders() instead to get all the providers in a
-     * MOBYCollection.
-     */
-    public MOBYProvider parseProvider()
-    {
-        StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
-        
-        if (it.hasNext()) {
-            return parseProvider(it.nextStatement().getSubject());
-        } else {
-            return null;
-        }
+        return MOBYObjectFactory.newUnorderedCollection(null, providers, null);
     }
     
     /**
@@ -187,6 +229,8 @@
      */
     public MOBYProvider parseProvider(Resource provider)
     {
+    	Model model = provider.getModel();
+    	
         // First parse the scalar properties name, oneLineDescription, and aboutURI
         //
         String name 	= getDataPropertyValue(provider, MOBY.name);
@@ -223,6 +267,8 @@
      */
     private MOBYGraphNode parseOperatesOn(Resource res)
     {
+    	Model model = res.getModel();
+    	
         if (isGraph(res))
         {
             // The resource is a MOBY Graph, so should have exactly one
@@ -263,6 +309,8 @@
      */
     private MOBYSubject parseHasMapping(Resource res)
     {
+    	Model model = res.getModel();
+    	
         // Collect the properties of this subject resource that are
         // subproperties of moby:Property, and create MOBY statements
         // for each.
@@ -354,6 +402,7 @@
         
         // Create and return a new MOBYObject
         //
+        Model model = res.getModel();
         return MOBYObjectFactory.newObject(res.getURI(),
             MOBYObjectFactory.newFixedCollection(null, statements, model),
             collectionFor(res, nested), model);
@@ -375,6 +424,9 @@
             Property p = stmt.getPredicate();
             RDFNode pval = stmt.getObject();
             
+            Model model = res.getModel();
+            Model inferenceModel = getInferenceModel(model);
+            
             if (model.contains(res, p, pval) &&
                 inferenceModel.contains(p, RDFS.subPropertyOf, MOBY.Property))
             {
@@ -409,13 +461,13 @@
     
     private String getDataPropertyValue(Resource subject, Property property)
     {
-        Statement s = model.getProperty(subject, property);
+        Statement s = subject.getModel().getProperty(subject, property);
         return (s == null) ? null : s.getObject().toString();
     }
     
     private Resource getResourcePropertyValue(Resource subject, Property property)
     {
-        Statement s = model.getProperty(subject, property);
+        Statement s = subject.getModel().getProperty(subject, property);
         return (s == null) ? null : (Resource) s.getObject();
     }
     
@@ -445,185 +497,100 @@
     private MOBYCollection collectionFor(Resource res, List elements)
     {
         if (isList(res)) {
-            return MOBYObjectFactory.newFixedCollection(null, elements, model);
+            return MOBYObjectFactory.newFixedCollection(null, elements, res.getModel());
         } else if (isBag(res)) {
-            return MOBYObjectFactory.newUnorderedCollection(null, elements, model);
+            return MOBYObjectFactory.newUnorderedCollection(null, elements, res.getModel());
         } else if (isSeq(res)) {
-            return MOBYObjectFactory.newOrderedCollection(null, elements, model);
+            return MOBYObjectFactory.newOrderedCollection(null, elements, res.getModel());
         } else if (isAlt(res)) {
-            return MOBYObjectFactory.newEnumeration(null, elements, model);
+            return MOBYObjectFactory.newEnumeration(null, elements, res.getModel());
         } else {
             return null;
         }
     }
     
-    private boolean isList(Resource res) { return res.canAs(RDFList.class); }
-    private boolean isBag (Resource res) { return isType(res, RDF.Bag);  }
-    private boolean isSeq (Resource res) { return isType(res, RDF.Seq);  }
-    private boolean isAlt (Resource res) { return isType(res, RDF.Alt);  }
-    
-    private boolean isDataStructure(Resource r) {
-        return isList(r) || isBag(r) || isSeq(r) || isAlt(r);
+    /**
+     * Return whether or not the given resource is an RDF List
+     */
+    private boolean isList(Resource res)
+    {
+    	return res.canAs(RDFList.class);
     }
-    
-    private boolean isGraph(Resource r) {
-        return isType(r, MOBY.Graph);
+
+    /**
+     * Return whether or not the given resource is an RDF Bag
+     */
+    private boolean isBag (Resource res)
+    {
+    	return isType(res, RDF.Bag);
     }
-    
-    private boolean isSubject(Resource res) {
-        return isType(res, MOBY.Subject);
+
+    /**
+     * Return whether or not the given resource is an RDF Seq
+     */
+    private boolean isSeq (Resource res)
+    {
+    	return isType(res, RDF.Seq);
     }
-    
-    private boolean isObject(Resource res) {
-        return isType(res, MOBY.Object);
+
+    /**
+     * Return whether or not the given resource is an RDF Alt
+     */
+    private boolean isAlt (Resource res)
+    {
+    	return isType(res, RDF.Alt);
     }
     
-    private boolean isType(Resource res, Resource type) {
-        return model.contains(res, RDF.type, type);
+    /**
+     * Return whether or not the given resource is an RDF data structure,
+     * i.e. a List, Bag, Seq, or Alt
+     */
+    private boolean isDataStructure(Resource r)
+    {
+        return isList(r) || isBag(r) || isSeq(r) || isAlt(r);
     }
     
-    public static String unparse(MOBYProvider provider) {
-        return Unparser.unparse(provider, 0);
+    /**
+     * Return whether or not the given resource is a MOBY Graph,
+     * i.e. the model contains a statement with the given resource
+     * as its subject, a predicate of rdf:type, and an object of
+     * moby:Graph
+     */
+    private boolean isGraph(Resource r)
+    {
+        return isType(r, MOBY.Graph);
     }
-    
-    public static String unparse(MOBYGraph graph) {
-        return Unparser.unparse(graph, 0);
+
+    /**
+     * Return whether or not the given resource is a MOBY Subject,
+     * i.e. the model contains a statement with the given resource
+     * as its subject, a predicate of rdf:type, and an object of
+     * moby:Subject
+     */
+    private boolean isSubject(Resource res)
+    {
+        return isType(res, MOBY.Subject);
     }
-    
-    public static String unparse(MOBYCollection collection) {
-        return Unparser.unparse(collection, 0);
+
+    /**
+     * Return whether or not the given resource is a MOBY Object,
+     * i.e. the model contains a statement with the given resource
+     * as its subject, a predicate of rdf:type, and an object of
+     * moby:Object
+     */
+    private boolean isObject(Resource res)
+    {
+        return isType(res, MOBY.Object);
     }
-    
-    private static class Unparser
+
+    /**
+     * Return whether or not the given resource is of the given type,
+     * i.e. the model contains a statement with the given resource
+     * as its subject, a predicate of rdf:type, and an object of the
+     * given type
+     */
+    private boolean isType(Resource res, Resource type)
     {
-        private static String unparse(MOBYProvider provider, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            
-            indent(sb, indent);
-            sb.append("Provider {");
-            newline(sb);
-            indent(sb, indent+4);
-            sb.append("name=\""); sb.append(provider.getName()); sb.append("\"");
-            newline(sb);
-            indent(sb, indent+4);
-            sb.append("oneLineDescription=\"");
-            sb.append(provider.getOneLineDescription()); sb.append("\"");
-            newline(sb);
-            indent(sb, indent+4);
-            sb.append("moreInfoURI=\"");
-            sb.append(provider.getMoreInfoURI().toString()); sb.append("\"");
-            
-            for (Iterator it = provider.getOperatesOn().iterator(); it.hasNext();)
-            {
-                MOBYGraphNode node = (MOBYGraphNode) it.next();
-                newline(sb);
-                indent(sb, indent+4);
-                sb.append("Operates on:");
-                newline(sb);
-                if (node.isSingular()) {
-                    sb.append(unparse((MOBYGraph) node, indent+8));
-                } else {
-                    sb.append(unparse((MOBYCollection) node, indent+8));
-                }
-            }
-            newline(sb);
-            indent(sb, indent);
-            sb.append("}");
-            
-            return sb.toString();
-        }
-        
-        private static String unparse(MOBYGraph graph, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            
-            indent(sb, indent);
-            sb.append("Graph {");
-            newline(sb);
-            MOBYGraphNode node = graph.gethasMapping();
-            if (node.isSingular()) {
-                sb.append(unparse((MOBYSubject) node, indent+4));
-            } else {
-                sb.append(unparse((MOBYCollection) node, indent+4));
-            }
-            indent(sb, indent);
-            sb.append("}");
-            
-            return sb.toString();
-        }
-        
-        private static String unparse(MOBYSubject subject, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            indent(sb, indent);
-            if (subject.isBlank()) {
-                sb.append("<bnode>");
-            } else {
-                sb.append("<"); sb.append(subject.getURI()); sb.append(">");
-            }
-            newline(sb);
-            
-            return sb.toString();
-        }
-        
-        private static String unparse(MOBYObject object, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            
-            return sb.toString();
-        }
-        
-        private static String unparse(MOBYCollection c, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            indent(sb, indent);
-            sb.append(descriptionOf(c));
-            sb.append(" {");
-            for (Iterator it = c.iterator(); it.hasNext();)
-            {
-                newline(sb);
-                Object element = it.next();
-                if (element instanceof MOBYProvider) {
-                    sb.append(unparse((MOBYProvider) element, indent+4));
-                } else if (element instanceof MOBYCollection) {
-                    sb.append(unparse((MOBYCollection) element, indent+4));
-                } else if (element instanceof MOBYGraph) {
-                    sb.append(unparse((MOBYGraph) element, indent+4));
-                } else if (element instanceof MOBYSubject) {
-                    sb.append(unparse((MOBYSubject) element, indent+4));
-                } else if (element instanceof MOBYObject) {
-                    sb.append(unparse((MOBYObject) element, indent+4));
-                } else {
-                    indent(sb, indent+4);
-                    sb.append(element.toString());
-                }
-            }
-            newline(sb);
-            indent(sb, indent);
-            sb.append("}");
-            return sb.toString();
-        }
-        
-        private static void newline(StringBuffer sb) {
-            sb.append("\n");
-        }
-        
-        private static void indent(StringBuffer sb, int count) {
-            for (int i = 0; i < count; i++) {
-                sb.append(' ');
-            }
-        }
-        
-        private static String descriptionOf(MOBYCollection c) {
-            
-            String name = "Collection";
-                 if (c instanceof MOBYFixedCollection)     name = "Fixed collection";
-            else if (c instanceof MOBYEnumeration)         name = "Choice collection";
-            else if (c instanceof MOBYOrderedCollection)   name = "Ordered collection";
-            else if (c instanceof MOBYUnorderedCollection) name = "Unordered collection";
-            
-            return name + " of " + c.size() + " elements";
-        }
+        return res.getModel().contains(res, RDF.type, type);
     }
 }
\ No newline at end of file

From gss at pub.open-bio.org  Wed Jun 16 19:29:32 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 19:13:48 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162329.i5GNTWJc022617@pub.open-bio.org>


gss
Wed Jun 16 19:29:32 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv22592/S-MOBY/ref-impl/core/src/org/smoby/parser/test

Modified Files:
	Test.java 
Log Message:
Documentation

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test Test.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java	2004/05/24 22:05:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java	2004/06/16 23:29:32	1.2
@@ -17,7 +17,5 @@
             "C|//Documents and Settings/gss/Desktop/citationSearch.n3");
         Parser parser = Parser.forN3File(inputFile);
         MOBYCollection coll = parser.parseProviders();
-        System.out.println("Providers:");
-        System.out.println(Parser.unparse(coll));
     }
 }

From gss at pub.open-bio.org  Wed Jun 16 19:30:14 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 19:14:27 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162330.i5GNUEaO022676@pub.open-bio.org>


gss
Wed Jun 16 19:30:13 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv22651/S-MOBY/ref-impl/core/src/org/smoby/vocabulary

Modified Files:
	MOBY.java 
Log Message:
No longer need registeredBy property

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/05/24 22:05:34	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/16 23:30:13	1.2
@@ -24,7 +24,6 @@
     public static final Property operatesOn			= property(getURI(), "operatesOn");
     public static final Property hasMapping			= property(getURI(), "hasMapping");
     public static final Property mapsTo				= property(getURI(), "mapsTo");
-    public static final Property registeredBy		= property(getURI(), "registeredBy");
     public static final Property lastModifiedDate	= property(getURI(), "lastModifiedDate");
     public static final Property Property			= property(getURI(), "Property");
 }
\ No newline at end of file

From gss at pub.open-bio.org  Wed Jun 16 19:30:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 19:14:58 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162330.i5GNUir3022714@pub.open-bio.org>


gss
Wed Jun 16 19:30:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev
In directory pub.open-bio.org:/tmp/cvs-serv22689/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev

Modified Files:
	RepositoryPrintServlet.java 
Log Message:
Print individual statements as N-triples

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev RepositoryPrintServlet.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java	2004/06/14 20:59:36	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java	2004/06/16 23:30:44	1.3
@@ -22,7 +22,10 @@
             if (model.isEmpty()) {
             	out.println("The repository is empty");
             } else {
-            	model.write(out, "RDF/XML-ABBREV");
+            	StmtIterator it = model.listStatements();
+            	while (it.hasNext()) {
+            		out.println(it.nextStatement());
+            	}
             }
             model.close();
         } catch (StorageException e) {

From gss at pub.open-bio.org  Wed Jun 16 19:31:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 19:15:51 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162331.i5GNVbrM022756@pub.open-bio.org>


gss
Wed Jun 16 19:31:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv22735/S-MOBY/ref-impl/server/src/org/smoby/ref/tools

Added Files:
	ProviderRemover.java 
Log Message:
Utility class to remove a provider's statements from a model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools ProviderRemover.java,NONE,1.1
From gss at pub.open-bio.org  Wed Jun 16 19:33:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 19:17:14 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162333.i5GNX02f022802@pub.open-bio.org>


gss
Wed Jun 16 19:33:00 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db
In directory pub.open-bio.org:/tmp/cvs-serv22777/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db

Modified Files:
	StorageManager.java 
Log Message:
No longer cache separate model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/05/19 18:26:41	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/06/16 23:33:00	1.4
@@ -1,7 +1,7 @@
 package org.smoby.ref.tools.db;
 
 import org.smoby.graph.*;
-import org.smoby.graph.impl.MOBYProviderImpl;
+import org.smoby.graph.impl.*;
 import org.smoby.ref.tools.*;
 import org.smoby.vocabulary.*;
 import com.hp.hpl.jena.db.*;
@@ -17,19 +17,6 @@
 public class StorageManager
 {
     /**
-     * Return whether or not the database contains a provider with a
-     * given URI.
-     * @param providerURI URI of the provider in question
-     * @return boolean flag indicating if the database contains the provider in question
-     * @throws StorageException if unable to access the model in the database
-     */
-    public boolean containsProvider(String providerURI)
-        throws StorageException
-    {
-        return getModelMaker().hasModel(providerURI);
-    }
-    
-    /**
      * Return the date when a given provider was registered
      * @param providerURL URI of the provider
      * @return the registration date if the provider has been registered in
@@ -41,20 +28,19 @@
     {
         Date registrationDate = null;
         
-        ModelMaker maker = getModelMaker();
+        Model dbModel = openDBModel();
         
-        Model model = maker.openModel(providerURI);
+        Resource provider = dbModel.createResource(providerURI);
         
-        Resource provider = model.createResource(providerURI);
-        
-        NodeIterator it = model.listObjectsOfProperty(provider, MOBY.lastModifiedDate);
+        NodeIterator it = dbModel.listObjectsOfProperty(
+        	provider, MOBY.lastModifiedDate);
         
         if (it.hasNext()) {
             Literal lit = (Literal) it.nextNode().as(Literal.class);
             registrationDate = new Date(lit.getLong());
         }
         
-        model.close();
+        dbModel.close();
         
         return registrationDate;
     }
@@ -73,7 +59,8 @@
 	{
 	    Model model = ((MOBYProviderImpl) provider).getUnderlying();
         Model dbModel = null;
-        Resource uri = model.createResource(provider.getURI());
+        String uriString = provider.getURI();
+        Resource uri = model.createResource(uriString);
         
         try
         {
@@ -84,50 +71,32 @@
             // Open the database model
             //
             dbModel = openDBModel(maker);
-            
-            // First check if the database already has a graph registered under
-            // the URI of the new graph. If so, then throw an exception
-            //
-            if (dbModel.contains(null, MOBY.registeredBy, uri)) {
-                throw new StorageException("Graph already exists for " + uri);
-            }
 
             // Start a transaction on the database model
             //
             dbModel.begin();
             
-            // Add to the database the statements from providerGraph whose
-            // subjects are in the same namespace as the provider
+            // Add to the database all statements whose subjects are
+            // at the URI or deeper
             //
-            String providerNameSpace = uri.getNameSpace();
+            StmtIterator it = model.listStatements();
+            while (it.hasNext()) {
+            	Statement stmt = it.nextStatement();
+            	Resource subject = stmt.getSubject();
+            	if (subject.isAnon() || subject.getURI().startsWith(uriString)) {
+            		dbModel.add(stmt);
+            	}
+            }
             
-            for (StmtIterator it = model.listStatements(); it.hasNext();)
-            {
-                Statement stmt = it.nextStatement();
-                Resource subject = stmt.getSubject();
-                String nameSpace = subject.getNameSpace();
-                
-                if (subject.isAnon() || providerNameSpace.equals(nameSpace)) {
-                    dbModel.add(stmt);
-                }
+            // Add a statement asserting when the model was added
+            //
+            if (lastModifiedDate != null) {
+            	dbModel.add(uri, MOBY.lastModifiedDate, lastModifiedDate.getTime());
             }
             
             // Commit the transaction on the database model
             //
             dbModel.commit();
-            
-            // Add to the database another model, with the provider URL as its name
-            //
-            Model providerModel = maker.createModel(uri.getURI());
-            providerModel.add(model);
-            providerModel.setNsPrefixes(model.getNsPrefixMap());
-            
-            // Add a statement asserting when the model was added to the database
-            //
-            if (lastModifiedDate != null) {
-                providerModel.add(uri, MOBY.lastModifiedDate, lastModifiedDate.getTime());
-            }
-            providerModel.close();
         }
         catch (StorageException se) {
             throw se;
@@ -160,21 +129,16 @@
             Resource provider = dbModel.createResource(providerURI);
             String providerNameSpace = provider.getNameSpace();
             
-            Model modelToRemove = maker.openModel(providerURI);
-            
+            // Start a transaction on the database
+            //
             dbModel.begin();
-            for (StmtIterator it = modelToRemove.listStatements(); it.hasNext();)
-            {
-                Statement stmt = it.nextStatement();
-                Resource subject = stmt.getSubject();
-                String nameSpace = subject.getNameSpace();
-                
-                if (subject.isAnon() || providerNameSpace.equals(nameSpace)) {
-                	dbModel.remove(stmt);
-                }
-            }
-            modelToRemove.close();
-            maker.removeModel(providerURI);
+            
+            // Remove all statements that are reachable from the provider URI
+            //
+            ProviderRemover.remove(dbModel, providerURI);
+            
+            // Commit the transaction on the database
+            //
             dbModel.commit();
         }
         catch (StorageException se) {

From gss at pub.open-bio.org  Wed Jun 16 19:33:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 16 19:17:38 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162333.i5GNXPOW022832@pub.open-bio.org>


gss
Wed Jun 16 19:33:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv22807/S-MOBY/ref-impl/server/src/org/smoby/ref/tools

Modified Files:
	URIInvestigator.java 
Log Message:
Use new StorageManager protocol

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/05/19 18:26:40	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/06/16 23:33:25	1.4
@@ -131,33 +131,21 @@
         StorageManager manager = new StorageManager();
     
         // Find out if the provider is already registered, and if so, when
-        // was its graph last modified. If either operation fail, log a
-        // message and return.
+        // was its graph last modified.
         //
-        boolean alreadyRegistered = false;
         Date lastModifiedDate = null;
+        boolean alreadyRegistered = false;
         
         try {
-            alreadyRegistered = manager.containsProvider(providerURI);
+        	lastModifiedDate = manager.getLastModifiedDate(providerURI);
+            alreadyRegistered = (lastModifiedDate != null);
         }
         catch (StorageException e)
         {
-        	syncLog.error("Couldn't check if provider URL " + providerURI + " exists", e);
+        	syncLog.error("Couldn't check for last modified date of provider URL " + providerURI, e);
             return;
         }
         
-        if (alreadyRegistered)
-        {
-            try {
-            	lastModifiedDate = manager.getLastModifiedDate(providerURI);
-            }
-            catch (StorageException e)
-            {
-            	syncLog.error("Couldn't check for last modified date of provider URL " + providerURI, e);
-                return;
-            }
-        }
-        
         // Helper class for making the HTTP GET call
         //
         HTTPRequest request = HTTPRequest.newGetRequest(providerURI);

From gss at pub.open-bio.org  Thu Jun 17 13:34:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 17 13:18:27 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171734.i5HHYHoV025365@pub.open-bio.org>


gss
Thu Jun 17 13:34:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25340/S-MOBY/ref-impl/core/src/org/smoby/vocabulary

Modified Files:
	MOBY.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/16 23:30:13	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/17 17:34:17	1.3
@@ -10,7 +10,7 @@
 
     public static String getURI()
     {
-        return "http://www.s-moby.org:8080/terms#";
+        return "http://www.s-moby.org:8080/terms/";
     }
     
     public static final Resource Provider   		= resource(getURI(), "Provider");

From gss at pub.open-bio.org  Thu Jun 17 13:35:01 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 17 13:19:11 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171735.i5HHZ1eA025407@pub.open-bio.org>


gss
Thu Jun 17 13:35:01 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv25380/S-MOBY/ref-impl/core/src/org/smoby/parser

Modified Files:
	Parser.java 
Log Message:
Fixed typo

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/16 23:29:20	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/17 17:35:01	1.3
@@ -127,8 +127,7 @@
      */
     public Parser(Model model)
     {
-    	
-        StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
+    	StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
         while (it.hasNext())
         {
         	Statement stmt = it.nextStatement();

From gss at pub.open-bio.org  Thu Jun 17 13:35:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 17 13:20:02 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171735.i5HHZqHf025445@pub.open-bio.org>


gss
Thu Jun 17 13:35:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools
In directory pub.open-bio.org:/tmp/cvs-serv25420/S-MOBY/ref-impl/server/WebRoot/tools

Modified Files:
	developer.html 
Log Message:
Minor fixes

moby-live/S-MOBY/ref-impl/server/WebRoot/tools developer.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html	2004/06/16 22:27:14	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html	2004/06/17 17:35:52	1.4
@@ -40,7 +40,9 @@
       "Convert Graph"></p>
 
       <p><textarea name="graph" rows="15" cols="80">
-                                              
+                                                          
+                                                             
+                                                     
                                                
                                        
                                  
@@ -56,8 +58,7 @@
     <form method="get" action=
     "http://www.s-moby.org:8080/list-providers">
       &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; <input type="submit"
-      value="List Providers">&nbsp;&nbsp; <input type="checkbox" name=
-      "show-contents" value="true"> Show provider description graphs
+      value="List Providers">
     </form>
 
     <h4><u>List&nbsp;all statements&nbsp;in the S-MOBY metadata
@@ -79,7 +80,9 @@
       <p><input type="submit" value="Validate"></p>
 
       <p><textarea name="graph" rows="15" cols="80">
-                                              
+                                                          
+                                                             
+                                                     
                                                
                                        
                                  
@@ -99,7 +102,9 @@
       <p><input type="submit" value="Validate"></p>
 
       <p><textarea name="graph" rows="15" cols="80">
-                                              
+                                                          
+                                                             
+                                                     
                                                
                                        
                                  

From gss at pub.open-bio.org  Thu Jun 17 13:35:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 17 13:20:03 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171735.i5HHZqgT025464@pub.open-bio.org>


gss
Thu Jun 17 13:35:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv25420/S-MOBY/ref-impl/server/WebRoot

Modified Files:
	domains.html 
Log Message:
Minor fixes

moby-live/S-MOBY/ref-impl/server/WebRoot domains.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html	2004/04/01 00:34:23	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html	2004/06/17 17:35:52	1.4
@@ -1,178 +1,176 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
 <html>
-<head>
-  <title>Semantic MOBY Server - Hosted Pages</title>
-</head>
-<body>
-<table style="text-align: center; width: 100%;" border="1"
- cellpadding="0" cellspacing="0">
-  <tbody>
-    <tr>
-      <td
- style="vertical-align: top; background-color: rgb(204, 204, 204);"> <b>Semantic
-MOBY Server - Hosted Pages</b> </td>
-    </tr>
-  </tbody>
-</table>
-<p>
-The Semantic MOBY reference implementation server hosts the following
-pages:<br>
-<br>
-<table style="text-align: left; width: 100%;" border="1" cellpadding="2"
- cellspacing="0">
-  <tbody>
-    <tr>
-      <td style="vertical-align: top;"><span style="font-weight: bold;">Page</span><br>
-      </td>
-      <td style="vertical-align: top;"><span style="font-weight: bold;">Description</span><br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.acmepubs.com:8080">www.acmepubs.com</a></td>
-      <td style="vertical-align: top;">Home page of an
-acmepubs.com, a hypothetical citation search provider.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.acmepubs.com:8080/citationSearch">www.acmepubs.com/citationSearch</a></td>
-      <td style="vertical-align: top;">Provider description
-graph for acmepubs.com. Note that doing an HTTP GET on this URI (e.g.
-by clicking on the link at the left), by definition returns an RDF
-graph that describes the provider. Also note that in this reference
-implementation, the URI is implemented as a Java Servlet.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.megapubs.com:8080">www.megapubs.com</a></td>
-      <td style="vertical-align: top;">Home page of an
-megapubs.com, another example citation search provider.</td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.megapubs.com:8080/citationSearch">www.megapubs.com/citationSearch</a></td>
-      <td style="vertical-align: top;">Provider description
-graph for megapubs.com. The notes regarding the
-www.acmepubs.com/citationSearch also apply to this URI.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.pubs.org:8080">www.pubs.org</a></td>
-      <td style="vertical-align: top;">Home page of a
-hypothetical vocabulary provider, pubs.org.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.pubs.org:8080/terms">www.pubs.org/terms</a></td>
-      <td style="vertical-align: top;">The vocabulary of terms
-defined by pubs.org. Note that in this reference implementation, unlike
-the two citation search providers, this vocabulary is provided in a
-resource file (terms) delivered as is by the web server - no servlets
-are involved.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a href="http://www.go.org:8080">www.go.org</a></td>
-      <td style="vertical-align: top;">Home page of a
-hypothetical vocabulary provider, go.org. This provider is meant to be
-representative of the type of vocabulary information that the real Gene
-Ontology (GO) Consortium would need to provide in order to be a
-Semantic MOBY vocabulary provider.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.go.org:8080/terms">www.go.org/terms</a></td>
-      <td style="vertical-align: top;">The vocabulary of terms
-defined by go.org. The notes regarding www.pubs.org/terms apply
-here as well.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.sgd.org:8080/">www.sgd.org</a></td>
-      <td style="vertical-align: top;">Home page of a
-hypothetical vocabulary provider, sgd.org. This provider is meant to be
-representative of the type of vocabulary
-information that the real <i>Saccharomyces Gene Database </i>would
-need to
-provide in order to be a Semantic MOBY vocabulary provider.</td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.sgd.org:8080/terms">www.sgd.org/terms</a></td>
-      <td style="vertical-align: top;">The vocabulary of terms
-defined by go.org. The notes regarding www.pubs.org/terms apply
-here as well.</td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;">www.s-moby.org</td>
-      <td style="vertical-align: top;">This page you're
-currently viewing.</td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.s-moby.org:8080/terms">www.s-moby.org/terms</a></td>
-      <td style="vertical-align: top;">The Semantic MOBY
-vocabulary terms. The notes regarding www.pubs.org/terms
-apply here as well.</td>
-    </tr>
-  </tbody>
-</table>
-<span style="font-weight: bold;"></span><br>
-</p>
-<div style="margin-left: 40px;">
-<div style="margin-left: 40px;"></div>
-</div>
-Since these hosts are virtual, in order to access their pages by name,
-you will need to modify how hosts are looked up. This can most easily
-be
-done by adding
-entries to the <code>hosts</code> file, making the host names refer to
-the
-local host (<code>127.0.0.1</code>). The Tomcat web server / servlet
-container then resolves to a virtual host by name. The following
-entries
-should be added
-to the <code>hosts</code> file of the given operating system on which
-the
-test server is running:
-<p><u>Under Linux/Unix, add to <code>/etc/hosts</code></u>
-</p>
-<ul>
-  <code>
-127.0.0.1 www.acmepubs.com acmepubs.com<br>
-127.0.0.1 www.megapubs.com megapubs.com<br>
-127.0.0.1 www.pubs.org pubs.org<br>
-127.0.0.1 www.go.org go.org<br>
-127.0.0.1 www.sgd.org sgd.org<br>
-127.0.0.1 www.s-moby.org s-moby.org<br>
-127.0.0.1 www.smobydev.org smobydev.org<br>
-  </code>
-</ul>
-<p>
-<u>Under Windows NT/2000/XP, add to
-<code>&lt;WIN_DIR&gt;/system32/drivers/etc/hosts</code></u>
-</p>
-<ul>
-  <code>
-127.0.0.1 acmepubs.com<br>
-127.0.0.1 www.acmepubs.com<br>
-127.0.0.1 megapubs.com<br>
-127.0.0.1 www.megapubs.com<br>
-127.0.0.1 go.org<br>
-127.0.0.1 www.go.org<br>
-127.0.0.1 sgd.org<br>
-127.0.0.1 www.sgd.org<br>
-127.0.0.1 pubs.org<br>
-127.0.0.1 www.pubs.org<br>
-127.0.0.1 s-moby.org<br>
-127.0.0.1 www.s-moby.org<br>
-  </code>
-</ul>
-</body>
+  <head>
+    <meta name="generator" content="HTML Tidy, see www.w3.org">
+
+    <title>Semantic MOBY Server - Hosted Pages</title>
+  </head>
+
+  <body>
+    <table style="WIDTH: 100%; TEXT-ALIGN: center" border="1"
+    cellpadding="0" cellspacing="0">
+      <tbody>
+        <tr>
+          <td style=
+          "VERTICAL-ALIGN: top; BACKGROUND-COLOR: rgb(204,204,204)">
+          <b>Semantic MOBY Server - Hosted Pages</b></td>
+        </tr>
+      </tbody>
+    </table>
+
+    <p>The Semantic MOBY reference implementation server hosts the
+    following pages:<br>
+    <br>
+    </p>
+
+    <table style="WIDTH: 100%; TEXT-ALIGN: left" border="1"
+    cellpadding="2" cellspacing="0">
+      <tbody>
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><span style=
+          "FONT-WEIGHT: bold">Page</span><br>
+          </td>
+
+          <td style="VERTICAL-ALIGN: top"><span style=
+          "FONT-WEIGHT: bold">Description</span><br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.acmepubs.com:8080">www.acmepubs.com</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of an acmepubs.com,
+          a hypothetical citation search provider.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td><a href=
+          "http://www.acmepubs.com:8080/terms">http://www.acmepubs.com/terms</a></td>
+
+          <td>The vocabulary of terms defined by acmepubs.com.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.acmepubs.com:8080/citationSearch">www.acmepubs.com/citationSearch</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Provider description graph
+          for acmepubs.com. Note that doing an HTTP GET on this URI
+          (e.g. by clicking on the link at the left), by definition
+          returns an RDF graph that describes the provider. Also note
+          that in this reference implementation, the URI is implemented
+          as a Java Servlet.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.megapubs.com:8080">www.megapubs.com</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of an megapubs.com,
+          another example citation search provider.</td>
+        </tr>
+
+        <tr>
+          <td><a href=
+          "http://www.megapubs.com:8080/terms">www.megapubs.com/terms</a></td>
+
+          <td>The vocabulary of terms defined by megapubs.com.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.megapubs.com:8080/citationSearch">www.megapubs.com/citationSearch</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Provider description graph
+          for megapubs.com. The notes regarding the
+          www.acmepubs.com/citationSearch also apply to this URI.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.pubs.org:8080">www.pubs.org</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of a hypothetical
+          vocabulary provider, pubs.org.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.pubs.org:8080/terms">www.pubs.org/terms</a></td>
+
+          <td style="VERTICAL-ALIGN: top">The vocabulary of terms
+          defined by pubs.org. Note that in this reference
+          implementation, unlike the two citation search providers,
+          this vocabulary is provided in a resource file (terms)
+          delivered as is by the web server - no servlets are
+          involved.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.go.org:8080">www.go.org</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of a hypothetical
+          vocabulary provider, go.org. This provider is meant to be
+          representative of the type of vocabulary information that the
+          real Gene Ontology (GO) Consortium would need to provide in
+          order to be a Semantic MOBY vocabulary provider.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.go.org:8080/terms">www.go.org/terms</a></td>
+
+          <td style="VERTICAL-ALIGN: top">The vocabulary of terms
+          defined by go.org. The notes regarding www.pubs.org/terms
+          apply here as well.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.sgd.org:8080/">www.sgd.org</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of a hypothetical
+          vocabulary provider, sgd.org. This provider is meant to be
+          representative of the type of vocabulary information that the
+          real <i>Saccharomyces Gene Database</i> would need to provide
+          in order to be a Semantic MOBY vocabulary provider.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.sgd.org:8080/terms">www.sgd.org/terms</a></td>
+
+          <td style="VERTICAL-ALIGN: top">The vocabulary of terms
+          defined by go.org. The notes regarding www.pubs.org/terms
+          apply here as well.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top">www.s-moby.org</td>
+
+          <td style="VERTICAL-ALIGN: top">This page you're currently
+          viewing.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.s-moby.org:8080/terms">www.s-moby.org/terms</a></td>
+
+          <td style="VERTICAL-ALIGN: top">The Semantic MOBY vocabulary
+          terms. The notes regarding www.pubs.org/terms apply here as
+          well.</td>
+        </tr>
+      </tbody>
+    </table>
+  </body>
 </html>

From gss at pub.open-bio.org  Thu Jun 17 13:37:05 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 17 13:21:14 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171737.i5HHb5Mf025523@pub.open-bio.org>


gss
Thu Jun 17 13:37:05 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv25498/S-MOBY/ref-impl/server/src/org/smoby/ref/tools

Modified Files:
	URIInvestigator.java 
Log Message:
Cleanup

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/06/16 23:33:25	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/06/17 17:37:05	1.5
@@ -176,10 +176,30 @@
         
         switch (status)
         {
+            case HttpServletResponse.SC_NOT_MODIFIED:
+                
+                // The resource has not been modified since it was
+                // registered, so there is nothing to do but log a message.
+                //
+            	syncLog.info("IN-SYNC : " + providerURI);
+                break;
+            
+            case HttpServletResponse.SC_NOT_FOUND:
+                
+                // The resource is no longer accessible, so de-register it
+                // from the database.
+                //
+                if (alreadyRegistered) {
+                	deregisterProvider(manager, true);
+                } else {
+                	syncLog.info("IGNORED : " + providerURI + " doesn't exist");
+                }
+                break;
+                
             case HttpServletResponse.SC_OK:
                 
-                // The call succeeded, so graphString should contain a valid graph.
-                // Try to parse it.
+                // The call succeeded, so see if graphString contains
+            	// a valid graph by trying to parse it.
                 //
                 lastModifiedDate = null;
                 
@@ -226,61 +246,30 @@
                     Parser parser = Parser.forInputStream(in, Parser.LANGUAGE_RDF_XML);
                     provider = parser.parseProvider();
                 }
-                catch (UnparsableGraphException e)
-                {
-                	syncLog.warn("Unparsable graph found at " + providerURI +
-                        (alreadyRegistered ? "; deregistering" : "; ignoring"));
-                    if (alreadyRegistered) {
-                        deregisterProvider(manager);
-                    }
-                    return;
-                }
+                catch (Throwable t) {}
                 
-                if (alreadyRegistered) {
-                    deregisterProvider(manager);
-                }
-                
-                try
-                {
-                    manager.registerProvider(provider, lastModifiedDate);
-                    
-                    // Log a message about successfully registering the graph:
-                    //
-                    syncLog.info((alreadyRegistered ? "UPDATED : " : "ADDED   : ") + providerURI);
-                }
-                catch (StorageException e) {
-                	syncLog.error("Error storing graph for " + providerURI, e);
-                }
-                
-                break;
-                
-            case HttpServletResponse.SC_NOT_MODIFIED:
-                
-                // The resource has not been modified since it was
-                // registered, so there is nothing to do but log a message.
+                // De-register the provider, printing a removal message if
+                // a provider couldn't be parsed
                 //
-            	syncLog.info("IN-SYNC : " + providerURI);
-                break;
-            
-            case HttpServletResponse.SC_NOT_FOUND:
+                deregisterProvider(manager, provider==null);
                 
-                // The resource is no longer accessible, so de-register it
-                // from the database.
+                // If a provider was parsed, then register it
                 //
-                if (alreadyRegistered)
-                {    
-                    try
-                    {
-                    	manager.deregisterProvider(providerURI);
-                    	syncLog.info("REMOVED : " + providerURI);
-                    }
-                    catch (StorageException e) {
-                    	syncLog.error("Unable to de-register provider " + providerURI, e);
-                    }
-                }
-                else {
-                	syncLog.info("IGNORED : " + providerURI + " doesn't exist");
+                if (provider != null)
+                {
+	                try
+	                {
+	                    manager.registerProvider(provider, lastModifiedDate);
+	                    
+	                    // Log a message about successfully registering the graph:
+	                    //
+	                    syncLog.info((alreadyRegistered ? "UPDATED : " : "ADDED   : ") + providerURI);
+	                }
+	                catch (StorageException e) {
+	                	syncLog.error("Error storing graph for " + providerURI, e);
+	                }
                 }
+                
                 break;
             
             default:
@@ -293,10 +282,13 @@
         }
     }
     
-    private void deregisterProvider(StorageManager manager)
+    private void deregisterProvider(StorageManager manager, boolean removing)
     {
         try {
         	manager.deregisterProvider(providerURI);
+        	if (removing) {
+            	syncLog.info("REMOVED : " + providerURI);
+        	}
         }
         catch (StorageException e) {
         	syncLog.error("Unable to de-register provider " + providerURI, e);

From gss at pub.open-bio.org  Thu Jun 17 13:37:58 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 17 13:22:07 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171737.i5HHbwhw025564@pub.open-bio.org>


gss
Thu Jun 17 13:37:58 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev
In directory pub.open-bio.org:/tmp/cvs-serv25539/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev

Modified Files:
	ProviderListServlet.java 
Log Message:
Since only global model saved, iterate over its rdf:type moby:Provider statements

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev ProviderListServlet.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/06/14 20:59:36	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/06/17 17:37:57	1.4
@@ -1,12 +1,10 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.servlet.*;
-import org.smoby.tools.*;
-import org.smoby.ref.servlets.BaseServlet;
+import org.smoby.vocabulary.*;
+import org.smoby.ref.servlets.*;
 import org.smoby.ref.tools.db.*;
-import org.smoby.ref.tools.*;
-
 import com.hp.hpl.jena.rdf.model.*;
+import com.hp.hpl.jena.vocabulary.*;
 import java.io.*;
 import java.util.*;
 import javax.servlet.*;
@@ -22,23 +20,19 @@
         
         try
         {
-            boolean showContents = (request.getParameter("show-contents") != null);
-            String globalModelName = MOBYProperties.getProperty("DB_REPOSITORY_NAME", true);
-            ModelMaker maker = manager.getModelMaker();
+        	Model dbModel = manager.openDBModel();
             int count = 0;
-            for (Iterator it = maker.listModels(); it.hasNext();) {
-            	String modelName = it.next().toString();
-                if (! modelName.equals(globalModelName)) {
-                    count++;
-                    if (showContents) {
-                        Model model = maker.openModel(modelName);
-                        model.write(out, "RDF/XML-ABBREV");
-                        model.close();
-                    } else {
-                    	out.println(modelName);
-                    }
-                }
+            StmtIterator it = dbModel.listStatements(
+            	null, RDF.type, MOBY.Provider);
+            
+            while (it.hasNext()) {
+            	Statement stmt = it.nextStatement();
+            	out.println(stmt.getSubject().getURI());
+            	count++;
             }
+            
+            dbModel.close();
+            
             if (count < 1) {
             	out.println("No providers are defined");
             }
@@ -46,8 +40,5 @@
         catch (StorageException e) {
             throw new ServletException(e);
         }
-        catch (MissingPropertyException e) {
-            throw new ServletException(e);
-        }
     }
 }
\ No newline at end of file

From gss at pub.open-bio.org  Thu Jun 17 13:38:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 17 13:23:10 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171738.i5HHcx4E025602@pub.open-bio.org>


gss
Thu Jun 17 13:38:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary

Modified Files:
	MegaPubs.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary MegaPubs.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java	2004/05/19 18:26:48	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java	2004/06/17 17:38:59	1.4
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.megapubs.com:8080/";
+        return "http://www.megapubs.com:8080/terms/";
     }
     
     public static final Property geneSymbol  = property(getURI(), "geneSymbol");

From gss at pub.open-bio.org  Thu Jun 17 13:38:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 17 13:23:11 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171738.i5HHcxiZ025621@pub.open-bio.org>


gss
Thu Jun 17 13:38:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary

Modified Files:
	Go.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary Go.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java	2004/05/19 18:26:55	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java	2004/06/17 17:38:59	1.3
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.go.org:8080/";
+        return "http://www.go.org:8080/terms/";
     }
     
     public static final Resource GeneSymbol = resource(getURI(), "GeneSymbol");

From gss at pub.open-bio.org  Thu Jun 17 13:39:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 17 13:23:12 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171739.i5HHd0wp025641@pub.open-bio.org>


gss
Thu Jun 17 13:38:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary

Modified Files:
	SGD.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary SGD.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java	2004/05/19 18:26:22	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java	2004/06/17 17:38:59	1.3
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.sgd.org:8080/";
+        return "http://www.sgd.org:8080/terms/";
     }
     
     public static final Resource LiteratureGuide = resource(getURI(), "LiteratureGuide");

From gss at pub.open-bio.org  Thu Jun 17 13:39:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 17 13:23:13 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171739.i5HHd0Ft025663@pub.open-bio.org>


gss
Thu Jun 17 13:38:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary

Modified Files:
	AcmePubs.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary AcmePubs.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java	2004/05/19 18:26:52	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java	2004/06/17 17:38:59	1.5
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.acmepubs.com:8080/";
+        return "http://www.acmepubs.com:8080/terms/";
     }
     
     public static final Property geneSymbol  = property(getURI(), "geneSymbol");

From gss at pub.open-bio.org  Thu Jun 17 13:39:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Jun 17 13:23:15 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171739.i5HHd0Fp025684@pub.open-bio.org>


gss
Thu Jun 17 13:39:00 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary

Modified Files:
	Pubs.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Pubs.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java	2004/05/19 18:26:25	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java	2004/06/17 17:39:00	1.4
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.pubs.org:8080/";
+        return "http://www.pubs.org:8080/terms/";
     }
     
     public static final Resource PubAbstract = resource(getURI(), "PubAbstract");

From gss at pub.open-bio.org  Fri Jun 18 17:37:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 18 17:21:55 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182137.i5ILbqHC029781@pub.open-bio.org>


gss
Fri Jun 18 17:37:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv29756/src/org/smoby/graph/impl

Modified Files:
	MOBYObjectFactory.java 
Added Files:
	MOBYProviderSetImpl.java 
Log Message:
New class to represent a set of providers

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl MOBYProviderSetImpl.java,NONE,1.1 MOBYObjectFactory.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java	2004/05/24 22:05:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java	2004/06/18 21:37:52	1.2
@@ -40,6 +40,11 @@
                 					underlying);
     }
     
+    public static MOBYProviderSet newProviderSet()
+    {
+    	return new MOBYProviderSetImpl();
+    }
+    
     public static MOBYGraph newGraph(String uri, MOBYGraphNode hasMapping, Model underlying)
     {
         return new MOBYGraphImpl(uri, hasMapping, underlying);

From gss at pub.open-bio.org  Fri Jun 18 17:37:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 18 17:21:57 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182137.i5ILbqEZ029796@pub.open-bio.org>


gss
Fri Jun 18 17:37:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv29756/src/org/smoby/graph

Added Files:
	MOBYProviderSet.java 
Log Message:
New class to represent a set of providers

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYProviderSet.java,NONE,1.1
From gss at pub.open-bio.org  Fri Jun 18 17:38:27 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 18 17:22:28 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182138.i5ILcRMk029838@pub.open-bio.org>


gss
Fri Jun 18 17:38:27 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv29813/src/org/smoby/parser

Modified Files:
	Parser.java 
Log Message:
Minor small fixes

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/17 17:35:01	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/18 21:38:27	1.4
@@ -6,6 +6,7 @@
 import org.smoby.graph.*;
 import org.smoby.graph.impl.*;
 import org.smoby.parser.*;
+import org.smoby.tools.Util;
 import org.smoby.vocabulary.*;
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.vocabulary.*;
@@ -100,7 +101,7 @@
     public static Parser forInputStream(InputStream is, String language)
 		throws UnparsableGraphException
     {
-        Model model = ModelFactory.createDefaultModel();
+        Model model = Util.newJenaModel();
         try {
             model.read(is, "", language);
         } catch (Throwable t) {
@@ -131,45 +132,14 @@
         while (it.hasNext())
         {
         	Statement stmt = it.nextStatement();
-        	Model subModel = ModelFactory.createDefaultModel();
+        	Model subModel = Util.newJenaModel();
         	subModel.setNsPrefixes(model.getNsPrefixMap());
         	Resource subject = stmt.getSubject();
-        	addReachableStmts(subModel, subject, subject.getURI());
+        	Util.addReachableStmts(model, subModel, subject, subject.getURI());
         	inferenceModels.put(subModel,
         		ModelFactory.createRDFSModel(subModel));
         }
     }
-    
-	private void addReachableStmts(Model model, Resource subject, String uri)
-	{
-		// For each statement whose subject is the given resource
-		//
-		StmtIterator it = subject.getModel().listStatements(
-			subject, null, (RDFNode) null);
-		
-		while (it.hasNext())
-		{
-			Statement stmt = it.nextStatement();
-			
-			// The statement itself should be added
-			//
-			model.add(model.createStatement(
-				stmt.getSubject(), stmt.getPredicate(), stmt.getObject()));
-			
-			// If the object of the statement is a blank node or a
-			// resource whose URI starts with the provider URI, then
-			// recursively add the statements that are reachable
-			// from the object
-			//
-			if (stmt.getObject().canAs(Resource.class))
-			{
-				Resource object = (Resource) stmt.getObject().as(Resource.class);
-				if (object.isAnon() || object.getURI().startsWith(uri)) {
-					addReachableStmts(model, object, uri);
-				}
-			}
-		}
-	}
 
     /**
      * Parse a provider from the model. If the model contains
@@ -196,14 +166,9 @@
     {
         ArrayList providers = new ArrayList();
         
-        // Find the statements that say something is of type Provider
-        //
-//        StmtIterator it = underlying.listStatements(null, RDF.type, MOBY.Provider);
-        
-        Iterator it = inferenceModels.keySet().iterator();
-        
         // Parse each provider
         //
+        Iterator it = inferenceModels.keySet().iterator();
         while (it.hasNext())
         {
         	Model model = (Model) it.next();

From gss at pub.open-bio.org  Fri Jun 18 17:38:46 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 18 17:22:47 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182138.i5ILckEJ029877@pub.open-bio.org>


gss
Fri Jun 18 17:38:46 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv29852/src/org/smoby/tools

Modified Files:
	Util.java 
Log Message:
New utility methods

moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools Util.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/Util.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/Util.java	2004/05/24 22:05:36	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/Util.java	2004/06/18 21:38:46	1.2
@@ -4,6 +4,15 @@
 import java.util.*;
 
 import org.apache.commons.httpclient.util.DateParser;
+import org.smoby.vocabulary.MOBY;
+
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.NsIterator;
+import com.hp.hpl.jena.rdf.model.RDFNode;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.rdf.model.StmtIterator;
 
 /**
  * This abstract class contains a miscellaneous set of useful static methods
@@ -26,4 +35,119 @@
     {
     	return HTTP_DATE_FORMAT.format(date);
     }
+    
+    public static Model newJenaModel()
+    {
+    	Model model = ModelFactory.createDefaultModel();
+    	MOBY.addNsPrefix(model);
+    	return model;
+    }
+    
+	public static void addReachableStmts(
+		Model source, Model dest, Resource subject, String uri)
+	{
+		// For each statement whose subject is the given resource
+		//
+		StmtIterator it = source.listStatements(
+			subject, null, (RDFNode) null);
+		
+		while (it.hasNext())
+		{
+			Statement stmt = it.nextStatement();
+			
+			// The statement itself should be added
+			//
+			dest.add(dest.createStatement(
+				stmt.getSubject(), stmt.getPredicate(), stmt.getObject()));
+			
+			// If the object of the statement is a blank node or a
+			// resource whose URI starts with the provider URI, then
+			// recursively add the statements that are reachable
+			// from the object
+			//
+			if (stmt.getObject().canAs(Resource.class))
+			{
+				Resource object = (Resource) stmt.getObject().as(Resource.class);
+				if (object.isAnon() || (uri != null && object.getURI().startsWith(uri))) {
+					addReachableStmts(source, dest, object, uri);
+				}
+			}
+		}
+	}
+	
+	/**
+	 * Add the namespace prefix mappings from a source model to a destination
+	 * model. A prefix mapping associates a qualified name (e.g. 'moby') with
+	 * a full URL (e.g. 'http://www.s-moby.org:8080/terms/'). In case a prefix
+	 * is already in the destination model, then use the next available prefix
+	 * formed by adding a number to the end of the prefix (e.g. if 'foo' is
+	 * taken, then add 'foo_1' if it is available, or 'foo_2' if not...).
+	 */
+	public static void addNsPrefixes(Model source, Model dest)
+	{
+		Map prefixes = source.getNsPrefixMap();
+		Iterator it = prefixes.keySet().iterator();
+		
+		while (it.hasNext())
+		{
+			// Prefix and associated URI to be added
+			//
+			String prefix = it.next().toString();
+			String uri = prefixes.get(prefix).toString();
+			
+			// Check to see if the prefix is already in the destination model
+			//
+			String prevURI = dest.getNsPrefixURI(prefix);
+			
+			if (prevURI == null)
+			{
+				// Not used, so just add it
+				//
+				dest.setNsPrefix(prefix, uri);
+			}
+			else if (! prevURI.equals(uri))
+			{
+				// Used and doesn't match previous, so add the next
+				// available prefix
+				//
+				boolean added = false;
+				for (int i = 1; (! added); i++)
+				{
+					String newPrefix = prefix + "_" + i;
+					if (dest.getNsPrefixURI(newPrefix) == null)
+					{
+						dest.setNsPrefix(newPrefix, uri);
+						added = true;
+					}
+				}
+			}
+		}
+	}
+	
+	/**
+	 * Remove unused namespace prefixes from the given model.
+	 */
+	public static void removeUnusedNsPrefixes(Model model)
+	{
+		Map newMap = new HashMap();
+		
+		for (NsIterator it = model.listNameSpaces(); it.hasNext();)
+		{
+			String uri = it.nextNs();
+			String prefix = model.getNsURIPrefix(uri);
+			newMap.put(prefix, uri);
+		}
+		
+		List toRemove = new ArrayList();
+		Iterator it = model.getNsPrefixMap().keySet().iterator();
+		while (it.hasNext()) {
+			toRemove.add(it.next());
+		}
+		it = toRemove.iterator();
+		while (it.hasNext()) {
+			model.removeNsPrefix(it.next().toString());
+		}
+		
+		model.setNsPrefixes(newMap);
+	}
 }

From gss at pub.open-bio.org  Fri Jun 18 17:39:42 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 18 17:23:43 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182139.i5ILdgl7029933@pub.open-bio.org>


gss
Fri Jun 18 17:39:42 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv29908/src/org/smoby/vocabulary

Modified Files:
	MOBY.java 
Log Message:
Added nsPrefix methods

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/17 17:34:17	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/18 21:39:42	1.4
@@ -13,6 +13,16 @@
         return "http://www.s-moby.org:8080/terms/";
     }
     
+    public static String getNsPrefix()
+    {
+    	return "moby";
+    }
+    
+    public static void addNsPrefix(Model model)
+    {
+    	model.setNsPrefix(getNsPrefix(), getURI()); 
+    }
+    
     public static final Resource Provider   		= resource(getURI(), "Provider");
     public static final Resource Graph      		= resource(getURI(), "Graph");
     public static final Resource Subject    		= resource(getURI(), "Subject");

From gss at pub.open-bio.org  Fri Jun 18 17:41:58 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 18 17:26:01 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182141.i5ILfwfr030037@pub.open-bio.org>


gss
Fri Jun 18 17:41:58 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools
In directory pub.open-bio.org:/tmp/cvs-serv30012/WebRoot/tools

Modified Files:
	client.html 
Log Message:
Minor small fixes

moby-live/S-MOBY/ref-impl/server/WebRoot/tools client.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html	2004/06/14 22:04:20	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html	2004/06/18 21:41:58	1.3
@@ -1,42 +1,53 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
 <html>
-<head>
-  <title>Semantic MOBY Client Tools</title>
-</head>
-<body>
-	<table style="text-align: center; width: 100%;" border="1"
+  <head>
+    <meta name="generator" content="HTML Tidy, see www.w3.org">
+
+    <title>Semantic MOBY Client Tools</title>
+  </head>
+
+  <body>
+    <table style="WIDTH: 100%; TEXT-ALIGN: center" border="1"
     cellspacing="0" cellpadding="0">
-    <tbody>
-      <tr>
-        <td style="vertical-align: top; background-color: rgb(204, 204, 204);">
-      	  <b>Semantic MOBY Client Tools</b>
-        </td>
-      </tr>
-    </tbody>
-  </table>
-
-<h4><u>Suggest a provider URL for S-MOBY to explore</u></h4>
-<form action="http://www.s-moby.org:8080/investigate" method="post">
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Provider URL:
-  <input size="60" name="provider-url">&nbsp;&nbsp;
-  <input value="Suggest" type="submit">
-</form>
-
-<h4><u>Discover matching graphs in the S-MOBY metadata repository</u></h4>
-<form action="http://www.s-moby.org:8080/find-providers" method="post">
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Paste a graph in RDF/XML format, select
-  statements to return, and press "Discover" to find matching graphs. &nbsp;&nbsp;
-  <p>
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-  Statements to return:&nbsp;&nbsp;
-  <input type="radio" name="statements" value="minimal">Minimal&nbsp;&nbsp;
-  <input type="radio" name="statements" value="query" CHECKED>Query only&nbsp;&nbsp;
-  <input type="radio" name="statements" value="cached">Cached&nbsp;&nbsp;
-  <input value="Discover" type="submit">
-  <p>
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-  <textarea cols="80" rows="15" name="query-graph"></textarea>
-</form>
+      <tbody>
+        <tr>
+          <td style=
+          "VERTICAL-ALIGN: top; BACKGROUND-COLOR: rgb(204,204,204)">
+          <b>Semantic MOBY Client Tools</b></td>
+        </tr>
+      </tbody>
+    </table>
+
+    <h4><u>Suggest a provider URL for S-MOBY to explore</u></h4>
+
+    <form action="http://www.s-moby.org:8080/investigate" method=
+    "post">
+      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Provider URL: <input size=
+      "60" name="provider-url">&nbsp;&nbsp; <input value="Suggest"
+      type="submit">
+    </form>
+
+    <h4><u>Discover matching graphs in the S-MOBY metadata
+    repository</u></h4>
+
+    <form action="http://www.s-moby.org:8080/find-providers" method=
+    "post">
+      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Paste a graph in RDF/XML
+      format, select statements to return, and press "Discover" to find
+      matching graphs. &nbsp;&nbsp; 
+
+      <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Statements to
+      return:&nbsp;&nbsp; <input type="radio" name="statements" value=
+      "minimal">Minimal&nbsp;&nbsp; <input type="radio" name=
+      "statements" value="query">Query only&nbsp;&nbsp; <input type=
+      "radio" name="statements" value="reachable" checked=
+      "">Reachable&nbsp; <input value="Discover" type="submit"></p>
 
-</body>
+      <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <textarea name=
+      "query-graph" rows="15" cols="80">
+          
+      </textarea></p>
+    </form>
+  </body>
 </html>

From gss at pub.open-bio.org  Fri Jun 18 17:42:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 18 17:26:36 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182142.i5ILgYdP030067@pub.open-bio.org>


gss
Fri Jun 18 17:42:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv30042/src/org/smoby/ref/tools

Modified Files:
	DiscoveryQuery.java 
Log Message:
Changes to utilize single model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/06/10 23:24:16	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/06/18 21:42:34	1.6
@@ -6,6 +6,7 @@
 
 import org.smoby.parser.*;
 import org.smoby.ref.tools.db.*;
+import org.smoby.tools.Util;
 import org.smoby.graph.*;
 import org.smoby.graph.impl.*;
 import org.smoby.vocabulary.*;
@@ -16,6 +17,7 @@
 import com.hp.hpl.jena.rdql.*;
 import com.hp.hpl.jena.shared.*;
 import com.hp.hpl.jena.util.iterator.*;
+import com.hp.hpl.jena.vocabulary.RDF;
 
 /**
  * This class finds graphs that match a query graph.
@@ -23,22 +25,24 @@
 public class DiscoveryQuery
 {
     /**
-     * Constant indicating that only the URI should be returned
-     * in each matching graph.
+     * Constant indicating that only the minimal statements should
+     * be returned in each matching graph.
      */
-    public final static int URI_ONLY = 0;
+    private final static int MINIMAL_STMTS = 0;
     
     /**
      * Constant indicating that only statements in the query should
      * be returned in each matching graph.
      */
-    public final static int QUERY_STMTS_ONLY = 1;
+    private final static int QUERY_STMTS = 1;
     
     /**
-     * Constants indicating that all statements (i.e. the ones found when
-     * the graph was registered) should be returned in each matching graph.
+     * Constant indicating that all reachable statements (i.e. the
+     * ones that can be traversed, starting with the provider node,
+     * without leaving the scope of the provider's URI) should be
+     * returned in each matching graph.
      */
-    public final static int ALL_STMTS = 2;
+    private final static int REACHABLE_STMTS = 2;
     
     /**
      * The graph that serves as a template for providers that match.
@@ -62,6 +66,21 @@
      */
     private int lastBnodeNumber;
     
+    public static DiscoveryQuery newMinimalStmtsQuery(MOBYProvider provider)
+    {
+    	return new DiscoveryQuery(provider, MINIMAL_STMTS);
+    }
+    
+    public static DiscoveryQuery newQueryStmtsQuery(MOBYProvider provider)
+    {
+    	return new DiscoveryQuery(provider, QUERY_STMTS);
+    }
+    
+    public static DiscoveryQuery newReachableStmtsQuery(MOBYProvider provider)
+    {
+    	return new DiscoveryQuery(provider, REACHABLE_STMTS);
+    }
+    
     /**
      * Create an instance for the given query graph and return statements
      * style.
@@ -69,7 +88,7 @@
      * @param statementsToReturn which statements should be returned: URI_ONLY,
      * QUERY_STMTS_ONLY, or ALL_STMTS (use the static constants on this class).
      */
-    public DiscoveryQuery(MOBYProvider queryProvider, int statementsToReturn)
+    private DiscoveryQuery(MOBYProvider queryProvider, int statementsToReturn)
     {
     	this.queryProvider = queryProvider;
         this.statementsToReturn = statementsToReturn;
@@ -85,21 +104,22 @@
         lastBnodeNumber = 0;
     }
     
-    public MOBYCollection findMatchingGraphs()
+    public MOBYProviderSet findMatchingGraphs()
 	{
         init();
         
+        Model dbModel = null;
 		try
 		{
 		    Model queryModel = ((MOBYProviderImpl) queryProvider).getUnderlying();
             String queryString = buildQueryString(queryModel);
             StorageManager manager = new StorageManager();
-            Model model = manager.openDBModel();
-            ((ModelRDB) model).setDoFastpath(false);
+            dbModel = manager.openDBModel();
+            ((ModelRDB) dbModel).setDoFastpath(false);
             
 			// Execute the query
 			//
-			QueryResults results = Query.exec(queryString, model);
+			QueryResults results = Query.exec(queryString, dbModel);
 			ArrayList matching = new ArrayList();
             
 			while (results.hasNext())
@@ -109,23 +129,27 @@
 			}
 			results.close();
 			
-			List returnList = new ArrayList();
+			MOBYProviderSet returnSet = MOBYObjectFactory.newProviderSet();
 			
 			for (Iterator it = matching.iterator(); it.hasNext();)
 			{
-				MOBYProvider mp = buildGraphModel(queryModel, (ResultBinding) it.next());
-				String uri = mp.getURI();
-				// YUCK!
-				Model providerModel = manager.openModel(uri);
-				Parser parser = new Parser(providerModel);
-				returnList.add(parser.parseProvider());
+				Object next = it.next();
+				MOBYProvider mp = buildGraphModel(dbModel,
+					queryModel, (ResultBinding) next);
+				returnSet.addProvider(mp);
 			}
 			
-			return MOBYObjectFactory.newUnorderedCollection(null, returnList, null);
+			return returnSet;
 			
 		} catch (Throwable t) {
 			return null;
 		}
+		finally
+		{
+			if (dbModel != null) {
+				dbModel.close();
+			}
+		}
 	}
 	
 	/**
@@ -221,11 +245,12 @@
 	 * @param binding bindings for variables
 	 * @return
 	 */
-	private MOBYProvider buildGraphModel(Model queryModel, ResultBinding binding)
+	private MOBYProvider buildGraphModel(
+		Model dbModel, Model queryModel, ResultBinding binding)
 	{
 		// Create a default model to return
 		//
-		Model model = ModelFactory.createDefaultModel();
+		Model model = Util.newJenaModel();
 		model.setNsPrefixes(queryModel.getNsPrefixMap());
 		
 		// For each statement in the query, create a new statement
@@ -244,10 +269,117 @@
 			Statement copy = model.createStatement(subject, property, object);
 			model.add(copy);
 		}
-		Parser parser = new Parser(model);
+		
+		// Add/remove statements based on the desired set, i.e.
+		// based on the value of statementsToReturn, and remove
+		// unused namespace prefixes from the model.
+		//
+		Model adjusted = adjustedModel(model, dbModel);
+		Util.removeUnusedNsPrefixes(adjusted);
+		
+		// Parse and return a MOBY provider using the adjusted model
+		//
+		Parser parser = new Parser(adjusted);
 		return parser.parseProvider();
 	}
 	
+	/**
+	 * Given a model built from the query template model, return a
+	 * model adjusted to include the statements to match the
+	 * statementsToReturn instance variable. The models that result
+	 * from performing a query consists of exactly the statements
+	 * that were in the query, with some blank nodes filled in. In
+	 * the case of QUERY_STMTS, that is the set that should be
+	 * returned. In the case of MINIMAL_STMTS, only the provider
+	 * type, name, one line description, and about URI statements
+	 * should be returned. In the case of REACHABLE_STMTS, all the
+	 * statements that are reachable from the provider URI, without
+	 * going outside the provider URI's scope, should be returned.
+	 */
+	private Model adjustedModel(Model original, Model dbModel)
+	{
+		switch (statementsToReturn)
+		{
+			case QUERY_STMTS	: return original;
+			case MINIMAL_STMTS	: return minimalModel(original, dbModel);
+			default				: return reachableModel(original, dbModel);
+		}
+	}
+	
+	/**
+	 * Return a model consisting of just the (rdf:type moby:Provider),
+	 * (moby:name <name>), (moby:oneLineDescription <description>), and
+	 * (moby:aboutURI <uri>) property statements for the provider.
+	 */
+	private Model minimalModel(Model original, Model dbModel)
+	{
+		Model minimal = Util.newJenaModel();
+		minimal.setNsPrefixes(dbModel.getNsPrefixMap());
+		
+		// Add the rdf:type MOBY:Provider statement
+		//
+		try {
+			Statement providerTypeStmt = original.listStatements(
+				null, RDF.type, MOBY.Provider).nextStatement();
+			minimal.add(providerTypeStmt);
+			
+			Resource subject = providerTypeStmt.getSubject();
+			
+			// Add a statement, if it exists in the repository, that
+			// says (<subject> moby:name <name>)
+			//
+			try {
+				minimal.add(dbModel.listStatements(subject,
+					MOBY.name, (RDFNode) null).nextStatement());
+			} catch (Throwable t) {} // There was no moby:name property
+
+			// Add a statement, if it exists in the repository, that
+			// says (<subject> moby:aboutURI <uri>)
+			//
+			try {
+				minimal.add(dbModel.listStatements(subject,
+					MOBY.aboutURI, (RDFNode) null).nextStatement());
+			} catch (Throwable t) {} // There was no moby:aboutURI property
+
+			// Add a statement, if it exists in the repository, that
+			// says <subject> moby:oneLineDescription <value>
+			//
+			try {
+				minimal.add(dbModel.listStatements(subject,
+					MOBY.oneLineDescription, (RDFNode) null).nextStatement());
+			} catch (Throwable t) {} // There was no moby:oneLineDescription
+		}
+		catch (Throwable t) {} // There was no (rdf:type moby:Provider)
+		
+		return minimal;
+	}
+	
+	/**
+	 * Return a model consisting of the statements in the original (query)
+	 * model, plus any statements not already in the model that are
+	 * reachable from the subject of the rdf:type moby:Provider statement.
+	 */
+	private Model reachableModel(Model original, Model dbModel)
+	{
+		// Start with a model consisting of the original statements
+		//
+		Model reachable = ModelFactory.createDefaultModel();
+		reachable.setNsPrefixes(dbModel.getNsPrefixMap());
+		reachable.add(original);
+		
+		// Find the subject of the (rdf:type MOBY:Provider) statement
+		//
+		try {
+			Statement providerTypeStmt = original.listStatements(
+				null, RDF.type, MOBY.Provider).nextStatement();
+			Resource subject = providerTypeStmt.getSubject();
+			Util.addReachableStmts(dbModel, reachable, subject, subject.getURI());
+		}
+		catch (Throwable t) {} // There was no (rdf:type moby:Provider)
+		
+		return reachable;
+	}
+	
 	private RDFNode getBinding(RDFNode node, ResultBinding binding)
 	{
 		// If the resource is not a blank node, then just return the
@@ -256,23 +388,16 @@
 		if (! node.asNode().isBlank()) {
 			return node;
 		}
-		//ResultBinding
 		ResultBindingIterator results = binding.iterator();
 		
 		while (results.hasNext())
 		{
-			Object object = results.next();
-			Value value = (Value) object;
+			results.next();
 			String varName = results.varName();
-//			Value value = results.value();
+			RDFNode value = (RDFNode) binding.get(varName);
 			Object cachedName = varNames.get(node.toString());
-			if (varName.equals(cachedName))
-			{
-//				if (value.isRDFLiteral()) {
-//					return value.getRDFLiteral();
-//				} else if (value.isRDFResource()) {
-//					return value.getRDFResource();
-//				}
+			if (varName.equals(cachedName)) {
+				return value;
 			}
 		}
 		return node;

From gss at pub.open-bio.org  Fri Jun 18 17:42:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 18 17:26:37 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182142.i5ILgYea030086@pub.open-bio.org>


gss
Fri Jun 18 17:42:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db
In directory pub.open-bio.org:/tmp/cvs-serv30042/src/org/smoby/ref/tools/db

Modified Files:
	StorageManager.java 
Log Message:
Changes to utilize single model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/06/16 23:33:00	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/06/18 21:42:34	1.5
@@ -3,6 +3,7 @@
 import org.smoby.graph.*;
 import org.smoby.graph.impl.*;
 import org.smoby.ref.tools.*;
+import org.smoby.tools.Util;
 import org.smoby.vocabulary.*;
 import com.hp.hpl.jena.db.*;
 import com.hp.hpl.jena.rdf.model.*;
@@ -83,11 +84,16 @@
             while (it.hasNext()) {
             	Statement stmt = it.nextStatement();
             	Resource subject = stmt.getSubject();
-            	if (subject.isAnon() || subject.getURI().startsWith(uriString)) {
+            	String subjectURI = subject.getURI();
+            	if (subject.isAnon() ||
+            		((subjectURI != null) &&
+            		  subjectURI.startsWith(uriString))) {
             		dbModel.add(stmt);
             	}
             }
             
+            Util.addNsPrefixes(model, dbModel);
+            
             // Add a statement asserting when the model was added
             //
             if (lastModifiedDate != null) {

From gss at pub.open-bio.org  Fri Jun 18 17:42:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 18 17:26:38 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182142.i5ILgYid030106@pub.open-bio.org>


gss
Fri Jun 18 17:42:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets
In directory pub.open-bio.org:/tmp/cvs-serv30042/src/org/smoby/ref/servlets

Modified Files:
	DiscoveryServlet.java 
Log Message:
Changes to utilize single model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets DiscoveryServlet.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/06/14 20:59:36	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/06/18 21:42:34	1.4
@@ -2,8 +2,7 @@
 
 import org.smoby.servlet.*;
 import org.smoby.graph.*;
-import org.smoby.parser.NonCanonicalException;
-import org.smoby.parser.Parser;
+import org.smoby.parser.*;
 import org.smoby.ref.tools.*;
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.rdql.*;
@@ -17,11 +16,15 @@
  * search the metadata repository for graphs that unify with a query graph
  * in the Prolog sense. The query graph should be sent via HTTP POST in a
  * parameter named "query-graph"; a set of matching graphs is returned in
- * the response body in either human-readable text format (the default),
- * or in an efficient, machine-readable binary format. To receive the
- * response in this binary format, the client should send a parameter
- * named "binary-return" in the request, with any value. The client can
- * obtain a Java object suitable for parsing either binary or text format
+ * the response body. The statements to be included in each matching graph
+ * is controlled by sending a parameter named "statements".  If the value
+ * of the parameter is "minimal", then only a small set of statements is
+ * returned, namely the statements that encode the name, one line
+ * description, and URI of the provider. If the value of the parameter is
+ * "reachable", then all statements reachable from the provider node are
+ * returned for each matching provider.
+ * 
+ * The client can obtain a Java object suitable for parsing the graph
  * into an array of ProviderDescriptionGraph objects, by calling the
  * GraphListTransceiverFactory.newReceiver() factory method.
  */
@@ -42,14 +45,30 @@
             //
 			Parser parser = Parser.forString(graphString, Parser.LANGUAGE_RDF_XML);
 			MOBYProvider provider = parser.parseProvider();
+			
+			// Find which statements the user wishes to have returned
+			//
+			String statements = ParamReader.getParameter(
+				"statements", request, false, new String[] {
+					"minimal", "query", "reachable"
+				});
             
             // Retrieve an array of provider description graphs that unify with
             // the query graph.
             //
-            DiscoveryQuery q = new DiscoveryQuery(provider, DiscoveryQuery.ALL_STMTS);
-			MOBYCollection matching = q.findMatchingGraphs();
+            DiscoveryQuery q = null;
+            
+            if (statements.equalsIgnoreCase("minimal")) {
+            	q = DiscoveryQuery.newMinimalStmtsQuery(provider);
+            } else if (statements.equalsIgnoreCase("query")) {
+            	q = DiscoveryQuery.newQueryStmtsQuery(provider);
+            } else {
+            	q = DiscoveryQuery.newReachableStmtsQuery(provider);
+            }
+            
+			MOBYProviderSet matching = q.findMatchingGraphs();
 			
-            if ((matching.size() == 0))
+            if ((matching == null) || (matching.size() == 0))
             {
                 // The client doesn't want the graphs sent in a binary
                 // format, so show a text message indicating that there
@@ -59,20 +78,10 @@
             }
             else
             {
-                for (Iterator it = matching.iterator(); it.hasNext();) {
-                    MOBYProvider p = (MOBYProvider) it.next();
-                    p.serialize(out);
-                }
+            	matching.serialize(out);
 			}
             
 		}
-//		catch (NonCanonicalException e)
-//		{
-//            // The query graph did not have the required canonical form
-//            //
-//			response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE,
-//				"Query graph is not canonical:\n" + e);
-//		}
 		catch (ParameterException e)
         {
             // The graph parameter was missing

From gss at pub.open-bio.org  Fri Jun 18 17:45:07 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri Jun 18 17:29:09 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182145.i5ILj7TR030161@pub.open-bio.org>


gss
Fri Jun 18 17:45:07 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery
In directory pub.open-bio.org:/tmp/cvs-serv30132/S-MOBY/ref-impl/queries/discovery

Modified Files:
	query.rdf query.n3 
Log Message:
Changed prefix mappings for go, sgd, and moby

moby-live/S-MOBY/ref-impl/queries/discovery query.rdf,1.2,1.3 query.n3,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf	2004/06/10 23:28:06	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf	2004/06/18 21:45:07	1.3
@@ -1,27 +1,27 @@
 <rdf:RDF
-    xmlns:go="http://www.go.org:8080/terms#"
+    xmlns:sgd="http://www.sgd.org:8080/terms/"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:moby="http://www.s-moby.org:8080/terms#"
-    xmlns:sgd="http://www.sgd.org:8080/terms#" >
+    xmlns:go="http://www.go.org:8080/terms/"
+    xmlns:moby="http://www.s-moby.org:8080/terms/" >
   <rdf:Description rdf:nodeID="A0">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <moby:hasMapping rdf:nodeID="A1"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-    <rdf:_1 rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Object"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms/LiteratureGuide"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A1">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <moby:mapsTo rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Provider"/>
+    <moby:operatesOn rdf:nodeID="A2"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A3">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Graph"/>
+    <moby:hasMapping rdf:nodeID="A4"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A2">
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A3"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A4">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <moby:operatesOn rdf:nodeID="A2"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms/GeneSymbol"/>
+    <moby:mapsTo rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Subject"/>
   </rdf:Description>
 </rdf:RDF>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3	2004/06/10 23:27:58	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3	2004/06/18 21:45:07	1.3
@@ -1,6 +1,6 @@
-@prefix go:       <http://www.go.org:8080/terms#> .
-@prefix sgd:      <http://www.sgd.org:8080/terms#> .
-@prefix moby:     <http://www.s-moby.org:8080/terms#> .
+@prefix go:       <http://www.go.org:8080/terms/> .
+@prefix sgd:      <http://www.sgd.org:8080/terms/> .
+@prefix moby:     <http://www.s-moby.org:8080/terms/> .
 @prefix rdf:      <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 
 _:provider

From mwilkinson at pub.open-bio.org  Thu Jun 24 18:30:38 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu Jun 24 18:14:01 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242230.i5OMUcqB032091@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:30:38 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor
In directory pub.open-bio.org:/tmp/cvs-serv32073/MOBY/Adaptor

Log Message:
Directory /home/repository/moby/moby-live/Perl/MOBY/Adaptor added to the repository

moby-live/Perl/MOBY/Adaptor - New directory
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/RCS/directory,v: No such file or directory

From mwilkinson at pub.open-bio.org  Thu Jun 24 18:30:52 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu Jun 24 18:14:14 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242230.i5OMUqtw032135@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:30:52 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby
In directory pub.open-bio.org:/tmp/cvs-serv32117/MOBY/Adaptor/moby

Log Message:
Directory /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby added to the repository

moby-live/Perl/MOBY/Adaptor/moby - New directory
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/directory,v: No such file or directory

From mwilkinson at pub.open-bio.org  Thu Jun 24 18:31:00 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu Jun 24 18:14:22 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242231.i5OMV0VT032179@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:31:00 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory pub.open-bio.org:/tmp/cvs-serv32161/MOBY/Adaptor/moby/queryapi

Log Message:
Directory /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi added to the repository

moby-live/Perl/MOBY/Adaptor/moby/queryapi - New directory
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/RCS/directory,v: No such file or directory

From mwilkinson at pub.open-bio.org  Thu Jun 24 18:32:38 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu Jun 24 18:16:00 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242232.i5OMWcgc032293@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:32:38 EDT 2004
Update of /home/repository/moby/moby-live/Perl
In directory pub.open-bio.org:/tmp/cvs-serv32274

Modified Files:
	MANIFEST 
Log Message:
stratifying the SQL away from the MOBY Central module so that we can have a variety of underlying databases or SW-based data stores with teh MOBY Central API on top of them

moby-live/Perl MANIFEST,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MANIFEST,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MANIFEST	2004/06/15 00:37:55	1.10
+++ /home/repository/moby/moby-live/Perl/MANIFEST	2004/06/24 22:32:38	1.11
@@ -4,9 +4,9 @@
 Makefile.PL
 MOBY/authority.pm
 MOBY/central_db_connection.pm
-MOBY/mysql.pm
 MOBY/OntologyServer.pm
 MOBY/Config.pm
+MOBY/dbConfig.pm
 MOBY/CommonSubs.pm
 MOBY/CrossReference.pm
 MOBY/service_instance.pm
@@ -22,6 +22,8 @@
 MOBY/Client/ServiceInstance.pm
 MOBY/Client/SimpleArticle.pm
 MOBY/Client/Service.pm
+MOBY/Adaptor/moby/queryapi.pm
+MOBY/Adaptor/moby/queryapi/mysql.pm
 t/Client-Central.t
 scripts/debugYourService
 scripts/MOBY-Central.pl

From mwilkinson at pub.open-bio.org  Thu Jun 24 18:32:39 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu Jun 24 18:16:02 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242232.i5OMWd8f032347@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:32:38 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv32274/MOBY

Modified Files:
	Central.pm Config.pm OntologyServer.pm 
	central_db_connection.pm collection_input.pm 
	collection_output.pm service_instance.pm simple_input.pm 
	simple_output.pm 
Added Files:
	dbConfig.pm 
Log Message:
stratifying the SQL away from the MOBY Central module so that we can have a variety of underlying databases or SW-based data stores with teh MOBY Central API on top of them

moby-live/Perl/MOBY dbConfig.pm,NONE,1.1 Central.pm,1.130,1.131 Config.pm,1.2,1.3 OntologyServer.pm,1.44,1.45 central_db_connection.pm,1.4,1.5 collection_input.pm,1.1,1.2 collection_output.pm,1.1,1.2 service_instance.pm,1.4,1.5 simple_input.pm,1.3,1.4 simple_output.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.130
retrieving revision 1.131
diff -u -r1.130 -r1.131
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/16 01:15:30	1.130
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/24 22:32:38	1.131
@@ -10,8 +10,6 @@
 use strict;
 use Carp;
 use vars qw($AUTOLOAD $WSDL_TEMPLATE);
-use DBI;
-use DBD::mysql;
 use XML::DOM;
 use MOBY::OntologyServer;
 use MOBY::service_type;
@@ -183,28 +181,6 @@
 	return 0;
 }
 
-sub _dbAccess {
-
-    my $conf = MOBY::Config->new;
-
-    my $username = $conf->{mobycentral}->{username};
-    my $password = $conf->{mobycentral}->{password};
-    my $port = $conf->{mobycentral}->{port};
-    my $dbname = $conf->{mobycentral}->{dbname};
-    my $url = $conf->{mobycentral}->{url};
-    
-	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
-	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
-	#my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
-	#my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
-	#my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
-	
-	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
-	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
-	
-	return ($dbh);
-}
-
 
 =head2 registerObjectClass
 
@@ -1264,7 +1240,7 @@
                     object_type_uri	=> $typeURI,
                     namespace_type_uris	=> $namespace_string,
                     article_name 	=> $article,
-                    collection_input_id 	=> 	$collid,
+                    collection_output_id 	=> 	$collid,
                     );
             unless ($soutput){
        			$SVC->DELETE_THYSELF; return (-1,"registration failed during registration of output object $typeURI.  Unknown reasons.");

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Config.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/Config.pm	2004/06/15 01:15:16	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/Config.pm	2004/06/24 22:32:38	1.3
@@ -6,8 +6,13 @@
 
 use strict;
 use Carp;
+use MOBY::dbConfig;
 use vars qw($AUTOLOAD);
 use Text::Shellwords;
+use vars '$VERSION','@ISA','@EXPORT','$CONFIG';
+
+@ISA = qw(Exporter);
+@EXPORT = ('$CONFIG');
 
 {
 	#Encapsulated class data
@@ -16,6 +21,11 @@
 	#ATTRIBUTES
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
+				   mobycentral	=> 	[undef,			'read/write'],
+				   mobyobject	=> 	[undef,			'read/write'],
+				   mobynamespace=> 	[undef,			'read/write'],
+				   mobyservice	=> 	[undef,			'read/write'],
+				   mobyrelationship	=> 	[undef,			'read/write'],
                     );
 
    #_____________________________________________________________
@@ -41,15 +51,14 @@
 
 }
 
-sub id {
-	my ($self, $val) =@_;
-	$self->registration_id($val) if defined $val;
-	return $self->registration_id;
-}
+# the expected sectionons (listed above) will have their dbCOnfig objects available
+# as methods.  The unexpected sections will have their dbConfig objects available
+# by $dbConfig = $CONFIG->{section_title}
 
 sub new {
 	my ($caller, %args) = @_;
 	
+#print STDERR "creating MOBY::Config\n";
 	my $caller_is_obj = ref($caller);
     my $class = $caller_is_obj || $caller;
 
@@ -65,32 +74,69 @@
     }
 
     my $file = $ENV{MOBY_CENTRAL_CONFIG};
-    chomp $file;
+	$file || die "can't open MOBY Configuration file $!\n";
+    
+	chomp $file;
     if ((-e $file) && (!(-d $file))){
         open IN, $file || die "can't open MOBY Configuration file $!\n";
     }
-    
-    while (my $l = <IN>){
-        chomp $l;
-        next if $l=~/\s*\#/;  # ignore comments
-        
-        if ($l=~/\[(\w+)\]/){
-            my $key = $1;
-            while (my $l2 = <IN>){
-                chomp $l2;
-                last unless ($l2 =~ /\S/);
-                my @terms = shellwords($l2);
-                last unless (scalar @terms > 2);
-                
-                $self->{$key}->{$terms[0]} = $terms[2];
-            }
-        }
-    }
+    my @sections = split /(\[\s*\S+\s*\][^\[]*)/s, join "", <IN>;
+#print STDERR "split into @sections\n";
+	foreach my $section (@sections){
+#print STDERR "calling MOBY::dbConfig\n";
+		my $dbConfig = MOBY::dbConfig->new(section => $section);  # this is an object full of strings, no actual connections.  It represents the information in the config file
+		next unless $dbConfig;
+		my $dbname = $dbConfig->section_title;
+		next unless $dbname;
+#print STDERR "setting the COnfig dbConfig for the title $dbname with object $dbConfig\n\n";
+		$self->{$dbname} = $dbConfig;
+	}
 
+	$CONFIG = $self;
     return $self;
 
 }
 
+sub getDataAdaptor {
+	my ($self, %args) = @_;
+	
+	my $source = $args{datasource};
+	$source ||= $args{source};
+	$source ||="mobycentral";
+	
+	if ($self->{"${source}Adaptor"}){return $self->{"${source}Adaptor"}};  # read from cache
+
+    my $username = $self->$source->{username};  # $self->source returns a MOBY::dbConfig object
+    my $password = $self->$source->{password};
+    my $port = $self->$source->{port};
+    my $dbname = $self->$source->{dbname};
+    my $url = $self->$source->{url};
+	my $adaptor = $self->$source->{adaptor};
+	my $sourcetype = $self->$source->{sourcetype};
+	
+	eval "require $adaptor";
+	return undef if $@;
+	eval "require $sourcetype";
+	return undef if $@;
+	
+	my $ADAPTOR = $adaptor->new(  # by default, this is queryapi
+								source => $source,
+								username => $username,
+								password => $password,
+								port => $port,
+								dbname => $dbname,
+								url => $url,
+								sourcetype => $sourcetype,
+							   );
+	if ($ADAPTOR){
+		$self->{"${source}Adaptor"} = $ADAPTOR;  # cache it
+		return $ADAPTOR;
+	} else {
+		return undef
+	}
+	
+}
+
 sub DESTROY {}
 
 sub AUTOLOAD {

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.44
retrieving revision 1.45
diff -u -r1.44 -r1.45
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 14:55:17	1.44
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/24 22:32:38	1.45
@@ -140,20 +140,23 @@
     $self->ontology eq 'service' && $self->database('mobyservice');
     $self->ontology eq 'relationship' && $self->database('mobyrelationship');
 
-	
-	my $conf = MOBY::Config->new;
-	$self->username($conf->{$self->database}->{username}) unless $self->username;
-    $self->password($conf->{$self->database}->{password}) unless $self->password;
-    $self->port($conf->{$self->database}->{port}) unless $self->port;
-    $self->host($conf->{$self->database}->{url}) unless $self->host;
+#print STDERR "\n\nCONFIG object is $CONFIG\n\n";
+	$CONFIG ||=MOBY::Config->new;
+#print STDERR "got username ",($CONFIG->{mobycentral}->{username})," for mobycentral\n";
+	$self->username($CONFIG->{$self->database}->{username}) unless $self->username;
+    $self->password($CONFIG->{$self->database}->{password}) unless $self->password;
+    $self->port($CONFIG->{$self->database}->{port}) unless $self->port;
+    $self->host($CONFIG->{$self->database}->{url}) unless $self->host;
  
 	my $host = $self->host?$self->host:$ENV{MOBY_CENTRAL_URL}; chomp $host;
 	my $username = $self->username?$self->username:$ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
 	my $password = $self->password?$self->password:$ENV{MOBY_CENTRAL_DBPASS}; chomp $password if $password; $password =~ s/\s//g if $password;
     my $port = $self->port?$self->port:$ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
     
-    my ($dsn) = "DBI:mysql:".($conf->{$self->database}->{dbname}).":".($host).":".($port);
+    my ($dsn) = "DBI:mysql:".($CONFIG->{$self->database}->{dbname}).":".($host).":".($port);
 
+#print STDERR "\n\nDSN was $dsn\n\n";
+	
     my $dbh;
 #	$debug && &_LOG("connecting to db with params ",$self->database, $self->username, $self->password,"\n");
     if (defined $password){

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/15 01:00:26	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/24 22:32:38	1.5
@@ -47,6 +47,7 @@
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
         db_connect_object => ["MOBY::mysql",        'read/write'],
+		datasource			=> ['mobycentral', 		'read/write'],
         #username => ["mobycentral",         'read/write'],
         #password => ["mobycentral",         'read/write'],        
         #dbname => ["mobycentral",       'read/write'],
@@ -108,25 +109,11 @@
     else {
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
-    #my $dbobj = $self->db_connect_object;
-    #my $dbh = &{$dbobj."::new"}(
-    #    $self->dbname,
-    #    $self->username,
-    #    $self->password,
-    #    $self->host,
-    #    $self->port);
-
-
-    my $conf = MOBY::Config->new;
-
-    my $username = $conf->{mobycentral}->{username};
-    my $password = $conf->{mobycentral}->{password};
-    my $port = $conf->{mobycentral}->{port};
-    my $dbname = $conf->{mobycentral}->{dbname};
-    my $url = $conf->{mobycentral}->{url};
-    	
-	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
-	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
+
+    $CONFIG ||= MOBY::Config->new;
+	
+	# getting the dbh is bad bad bad!!!
+	my $dbh = $CONFIG->getDataAdaptor(datasource => 'mobycentral')->dbh;
 	
     $self->dbh($dbh);
 	return $self;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/collection_input.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/collection_input.pm	2004/06/16 01:15:30	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/collection_input.pm	2004/06/24 22:32:38	1.2
@@ -1,9 +1,9 @@
-#!/usr/bin/perl -w
-
 package MOBY::collection_input;
 use strict;
 use Carp;
 use XML::DOM;
+use MOBY::Config;
+
 use vars qw($AUTOLOAD @ISA);
 
 
@@ -76,17 +76,6 @@
 
 }
 
-
-
-sub _dbh {
-    my ($self) = @_;
-    
-    my $central_connect = MOBY::central_db_connection->new();
-	$self->dbh($central_connect->dbh);
-	return $central_connect->dbh;
-	
-}
-
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -106,6 +95,7 @@
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
 
+
 	my $id = $self->WRITE;
 	$self->collection_input_id($id) if defined $id;
     return $self;
@@ -114,10 +104,13 @@
 
 sub WRITE {
 	my ($self) = @_;
-	my $dbh = $self->_dbh;
+	$CONFIG ||=MOBY::Config->new;  # exported by Config.pm
+	my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral');
+	my $id = $adaptor->insert_collection_input(
+									  service_instance => $self->service_instance_id,
+									  article_name	=> $self->article_name,
+									 );
 	
-	$dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($self->service_instance_id, $self->article_name));
-	my $id=$dbh->{mysql_insertid};
 	return $id;		
 }
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/collection_output.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/collection_output.pm	2004/06/16 01:15:30	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/collection_output.pm	2004/06/24 22:32:38	1.2
@@ -4,6 +4,8 @@
 use strict;
 use Carp;
 use XML::DOM;
+use MOBY::Config;
+
 use vars qw($AUTOLOAD @ISA);
 
 
@@ -76,17 +78,6 @@
 }
 
 
-
-sub _dbh {
-    my ($self) = @_;
-    
-    my $central_connect = MOBY::central_db_connection->new();
-	$self->dbh($central_connect->dbh);
-	return $central_connect->dbh;
-	
-}
-
-
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -115,10 +106,13 @@
 
 sub WRITE {
 	my ($self) = @_;
-	my $dbh = $self->_dbh;
+	$CONFIG ||=MOBY::Config->new;  # exported by Config.pm
+	my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral');
+	my $id = $adaptor->insert_collection_output(
+									  service_instance => $self->service_instance_id,
+									  article_name	=> $self->article_name,
+									 );
 	
-	$dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($self->service_instance_id, $self->article_name));
-	my $id=$dbh->{mysql_insertid};
 	return $id;		
 }
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm	2004/06/16 01:15:30	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm	2004/06/24 22:32:38	1.5
@@ -349,7 +349,7 @@
 				namespace_type_uris	=> $a{'namespace_type_uris'},
 				article_name 	=> $a{'article_name'},
 				service_instance_id	=> 	$self->service_instance_id,
-				collection_input_id 	=> 	$a{'collection_output_id'}
+				collection_output_id 	=> 	$a{'collection_output_id'}
 					   );
 
 	push @{$self->{outputs}}, $simple;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm	2004/06/16 01:15:30	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm	2004/06/24 22:32:38	1.4
@@ -4,6 +4,7 @@
 use strict;
 use Carp;
 use XML::DOM;
+use MOBY::Config;
 use vars qw($AUTOLOAD @ISA);
 
 
@@ -80,17 +81,6 @@
 
 }
 
-
-sub _dbh {
-    my ($self) = @_;
-    
-    my $central_connect = MOBY::central_db_connection->new();
-	$self->dbh($central_connect->dbh);
-	return $central_connect->dbh;
-	
-}
-
-
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -116,25 +106,20 @@
 
 }
 
+
 sub WRITE {
-	my ($self) = @_;	
-	my $dbh = $self->_dbh;
+	my ($self) = @_;
+	$CONFIG ||=MOBY::Config->new;  # exported by Config.pm
+	my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral');
+	my $id = $adaptor->insert_simple_input(
+		object_type_uri => $self->object_type_uri,
+		namespace_type_uris => $self->namespace_type_uris,
+		article_name => $self->article_name,
+		service_instance_id => $self->service_instance_id,
+		collection_input_id => $self->collection_input_id,
+									 );
 	
-	$dbh->do("insert into simple_input
-				 (object_type_uri,
-				  namespace_type_uris,
-				  article_name,
-				  service_instance_id,
-				  collection_input_id)
-				 values (?,?,?,?,?)",
-		undef,
-		($self->object_type_uri,
-		$self->namespace_type_uris,
-		$self->article_name,
-		$self->service_instance_id,
-		$self->collection_input_id));
-	my $id=$dbh->{mysql_insertid};
-	return $id;
+	return $id;		
 }
 
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm	2004/06/16 01:15:30	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm	2004/06/24 22:32:38	1.3
@@ -3,6 +3,7 @@
 package MOBY::simple_output;
 use strict;
 use Carp;
+use MOBY::Config;
 use XML::DOM;
 use vars qw($AUTOLOAD @ISA);
 
@@ -80,17 +81,6 @@
 }
 
 
-
-sub _dbh {
-    my ($self) = @_;
-    
-    my $central_connect = MOBY::central_db_connection->new();
-	$self->dbh($central_connect->dbh);
-	return $central_connect->dbh;
-	
-}
-
-
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -118,25 +108,20 @@
 
 sub WRITE {
 	my ($self) = @_;
-	my $dbh = $self->_dbh;	
-	$dbh->do("insert into simple_output
-				 (object_type_uri,
-				  namespace_type_uris,
-				  article_name,
-				  service_instance_id,
-				  collection_output_id)
-				 values (?,?,?,?,?)",
-		undef,
-		($self->object_type_uri,
-		$self->namespace_type_uris,
-		$self->article_name,
-		$self->service_instance_id,
-		$self->collection_output_id));
-	my $id=$dbh->{mysql_insertid};
+	$CONFIG ||=MOBY::Config->new;  # exported by Config.pm
+	my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral');
+	my $id = $adaptor->insert_simple_output(
+		object_type_uri => $self->object_type_uri,
+		namespace_type_uris => $self->namespace_type_uris,
+		article_name => $self->article_name,
+		service_instance_id => $self->service_instance_id,
+		collection_output_id => $self->collection_output_id,
+									 );
+	
 	return $id;		
-
 }
 
+
 sub AUTOLOAD {
     no strict "refs";
     my ($self, $newval) = @_;

From mwilkinson at pub.open-bio.org  Thu Jun 24 18:32:39 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu Jun 24 18:16:05 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242232.i5OMWd2M032362@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:32:39 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby
In directory pub.open-bio.org:/tmp/cvs-serv32274/MOBY/Adaptor/moby

Added Files:
	queryapi.pm 
Log Message:
stratifying the SQL away from the MOBY Central module so that we can have a variety of underlying databases or SW-based data stores with teh MOBY Central API on top of them

moby-live/Perl/MOBY/Adaptor/moby queryapi.pm,NONE,1.1
From mwilkinson at pub.open-bio.org  Thu Jun 24 18:32:39 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu Jun 24 18:16:07 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242232.i5OMWdAc032377@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:32:39 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory pub.open-bio.org:/tmp/cvs-serv32274/MOBY/Adaptor/moby/queryapi

Added Files:
	mysql.pm 
Log Message:
stratifying the SQL away from the MOBY Central module so that we can have a variety of underlying databases or SW-based data stores with teh MOBY Central API on top of them

moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,NONE,1.1
From mwilkinson at pub.open-bio.org  Tue Jun 29 12:24:00 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Jun 29 12:06:52 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406291624.i5TGO06q025875@pub.open-bio.org>


mwilkinson
Tue Jun 29 12:23:59 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv25852/MOBY

Modified Files:
	CommonSubs.pm dbConfig.pm 
Log Message:
CommonSubs now accepts HTML markup in the service provision block.  LocalServices (the example services that I run) now correctly credit the SeqHound project.

moby-live/Perl/MOBY CommonSubs.pm,1.52,1.53 dbConfig.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.52
retrieving revision 1.53
diff -u -r1.52 -r1.53
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/06/15 00:37:55	1.52
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/06/29 16:23:59	1.53
@@ -1425,7 +1425,8 @@
     foreach my $n(0..($responses->getLength - 1)){
         my $resp = $responses->item($n);
         foreach my $response_component($resp->getChildNodes){
-            $content .= $response_component->toString;
+#            $content .= $response_component->toString;
+            $content .= $response_component->getNodeValue if ($response_component->getNodeType == TEXT_NODE);
         }
     }
     return ($content);

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm	2004/06/24 22:32:38	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm	2004/06/29 16:23:59	1.2
@@ -78,6 +78,7 @@
     $key = $self->_readSections($self->section);
 	#if ($@){die "MOBY Configuration file is misconfigured: dbConfig line 71\n";}
 #print STDERR "I received the key $key\n";
+    return undef unless $key;
     return undef unless $key =~ /\S/;
 #print STDERR "returning the dbConfig object for database title $key\n";
     $self->section_title($key);

From mwilkinson at pub.open-bio.org  Tue Jun 29 12:24:00 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Jun 29 12:06:53 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406291624.i5TGO0OP025895@pub.open-bio.org>


mwilkinson
Tue Jun 29 12:24:00 EDT 2004
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv25852/scripts/Services

Modified Files:
	LocalServices.pm 
Log Message:
CommonSubs now accepts HTML markup in the service provision block.  LocalServices (the example services that I run) now correctly credit the SeqHound project.

moby-live/Perl/scripts/Services LocalServices.pm,1.62,1.63
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.62
retrieving revision 1.63
diff -u -r1.62 -r1.63
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2004/02/23 21:31:53	1.62
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2004/06/29 16:24:00	1.63
@@ -46,6 +46,8 @@
 
 my $debug = 1;
 
+my $SeqHoundCredit = "This data is provided by <a HREF='http://seqhound.blueprint.org'>SeqHound</a>; <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12401134&dopt=Abstract'>Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW.  SeqHound: biological sequence and structure database as a platform forbioinformatics research. BMC Bioinformatics. 2002 Oct 25;3(1):32</a>";
+
 use vars qw(@ISA);
 
 ##################################################
@@ -118,7 +120,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 
@@ -152,7 +154,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getSHoundProteinsFromOrganism {  # WORKS
@@ -185,7 +187,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 
@@ -219,7 +221,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 
@@ -253,7 +255,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getSHoundGODBGetParentOf {  # WORKS
@@ -290,7 +292,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getSHoundGODBGetChildrenOf {  # WORKS
@@ -327,7 +329,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getSHoundDNAFromOrganism {  # WORKS
@@ -360,7 +362,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getTaxChildNodes {  # WORKS
@@ -393,7 +395,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getTaxParent { # now it works.
@@ -419,7 +421,7 @@
 			$parent && ($MOBY_RESPONSE .= simpleResponse("<Object namespace='taxon' id='$parent'/>", "", $qID));
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 
@@ -449,7 +451,7 @@
 													   "</CrossReference>$name</String>", "", $qID));
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getGoTerm {
@@ -679,7 +681,7 @@
     }
 	$aa = SHoundFini();
 	#print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub _makeSeqObj {
@@ -778,7 +780,7 @@
     }
 	$aa = SHoundFini();
 #	print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub MOBYSHoundGetGenBankWhateverSequence {
@@ -865,7 +867,7 @@
     }
 	$aa = SHoundFini();
 #	print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub MOBYSHoundGetGenBankFasta {
@@ -927,7 +929,7 @@
     }
 	$aa = SHoundFini();
 	#print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 

From gss at pub.open-bio.org  Wed Jun 30 14:21:28 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 30 14:04:15 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406301821.i5UILSfv031022@pub.open-bio.org>


gss
Wed Jun 30 14:21:28 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv30997/S-MOBY/ref-impl

Modified Files:
	INSTALL.html 
Log Message:
Fixed installation instructions to reflect problems that Ardavan K found.

moby-live/S-MOBY/ref-impl INSTALL.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/INSTALL.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/INSTALL.html	2004/06/10 23:10:44	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/INSTALL.html	2004/06/30 18:21:28	1.2
@@ -1,13 +1,14 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <html>
 <head>
+  <meta name="generator" content="HTML Tidy, see www.w3.org">
   <title>Building and Installing Semantic MOBY</title>
 </head>
 <body>
 <h2 style="text-align: center;">Building and Installing the Semantic
 MOBY<br>
 Reference Implementation</h2>
-<div style="text-align: justify;">This page contains step-by-step
+<div style="text-align: justify;"> This page contains step-by-step
 instructions on building and installing the complete reference
 implementation of Semantic MOBY. The complete installation includes a
 reference implementation of a discovery/registration server
@@ -23,7 +24,7 @@
 </div>
 <br>
 <h3>Prerequisites</h3>
-<div style="text-align: justify;">Before beginning to build the
+<div style="text-align: justify;"> Before beginning to build the
 reference implementation, certain software must be installed on the
 machine that is to host the installation. In the following list, the
 recommended software versions are the only ones that the author has
@@ -39,19 +40,15 @@
     <br>
   </li>
   <li>
-    <div style="text-align: justify;"><a href="http://ant.apache.org">Apache
+    <div style="text-align: justify;"> <a href="http://ant.apache.org">Apache
 Ant</a> (tested with version 1.6.1) should be installed and on the
-executable path. To check, type <code>'ant -version</code><code>' </code>(without
-the quotes) on a command line.<br>
-    </div>
-    <br>
-  </li>
-  <li style="text-align: justify;">One of the open source databases,
-either <a href="http://www.postgresql.org">PostgreSQL</a> (tested with
-version 7.4.1) or <a href="http://www.mysql.com">MySQL</a> (tested
-with version 4.0.18) should be installed and running, and a database
-named <code>smoby-dev</code> has been created.<br>
+executable path. To check, type <code>'ant -version</code><code>'</code>
+(without the quotes) on a command line.One of the open source
+databases, either <a href="http://www.postgresql.org">PostgreSQL</a>
+(tested with version 7.4.1) or <a href="http://www.mysql.com">MySQL</a>
+(tested with version 4.0.18) should be installed and running.<br>
     <br>
+    </div>
   </li>
   <li style="text-align: justify;">The Semantic MOBY distribution has
 been retrieved from CVS and saved locally. As of this writing, there
@@ -69,83 +66,108 @@
 <h3>Installation steps</h3>
 <ol type="1">
   <li>
-    <div style="text-align: justify;">Modify the <code>hosts</code>
+    <div style="text-align: justify;"> Modify the <code>hosts</code>
 file of the computer that is to host the reference implementation, as
-described in the <code>for-hosts-file </code>file located in the <code>ref-impl/config-files/</code>
+described in the <code>for-hosts-file</code> file located in the <code>ref-impl/config-files/</code>
 subdirectory of the reference implementation directory. Since one
 computer is to host several example domains (s-moby.org, acmepubs.com,
 etc.), this is the easiest way to make these virtual domain, hosted by
 Apache Tomcat (see the next step) resolve to the local host.<br>
-    </div>
     <br>
+    </div>
   </li>
   <li>
-    <div style="text-align: justify;">Install <a
+    <div style="text-align: justify;"> Install <a
  href="http://jakarta.apache.org/tomcat">Apache Tomcat 5.0</a> (tested
 with version 5.0.25) and start it. If all went well, you should be able
 to open <a href="http://localhost:8080">http://localhost:8080</a> in a
 browser. After making sure it is properly installed, shutdown Tomcat.<br>
+    <br>
     </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"> Modify Tomcat's main
+configuration file (<code>server.xml</code>), located in the <code>conf/</code>
+subdirectory of the Tomcat installation directory as instructed in the <code>for-tomcat-conf-server.xml</code>
+file, located in the <code>config-files/</code> subdirectory of the
+reference implementation directory. This modification sets up virtual
+hosts, accessible by name, that are all served by Tomcat 5.<br>
     <br>
+    </div>
   </li>
   <li>
-    <div style="text-align: justify;">Modify <tomcat-top-dir>Tomcat's
-main configuration file (<code>server.xml</code>), located in the <code>conf/</code>
-subdirectory of the Tomcat installation directory as instructed in the </tomcat-top-dir><code>for-tomcat-conf-server.xml
-    </code>file, located in the <code>config-files/</code>
-subdirectory of the reference implementation directory. This
-modification sets up virtual hosts, accessible by name, that are all
-served by Tomcat 5.<br>
-    </div>
-    <tomcat-top-dir><br>
-    </tomcat-top-dir></li>
-  <li>
-    <div style="text-align: justify;">Save a copy of the <ref-impl-top-dir><code>common.example.properties</code>
-file, located in the reference implementation<span
- style="font-family: monospace;"></span><code></code> directory, as <code>common.properties</code>
+    <div style="text-align: justify;"> Save a copy of the <code>common.example.properties</code>
+file, located in the reference implementation directory, as <code>common.properties</code>
 (in the same directory). This file is used by the Ant build scripts,
 and should be modified to reflect the system on which the reference
-implementation is being installed.</ref-impl-top-dir><br>
-    <ref-impl-top-dir></ref-impl-top-dir></div>
-    <ref-impl-top-dir><br>
-    </ref-impl-top-dir></li>
-  <li>
-    <div style="text-align: justify;">From the command line, change
-directory to the reference implementation directory and <ref-impl-top-dir>run
-    <code>'ant third-party' </code>(without the quotes). This
-retrieves third party components from CVS and builds them. Retrieving
-the components from CVS is admittedly less predictable than storing a
-version of the components with the Semantic MOBY distribution, but as
-the components (especially <a href="http://jena.sourceforge.net">Jena2</a>)
-are constantly being improved, it is considered more important to have
-the latest versions than to have stable versions. Currently, this step
-takes about three minutes on a 2GHz P4 machine with a broadband
-connection.</ref-impl-top-dir><br>
-    <ref-impl-top-dir></ref-impl-top-dir></div>
-    <br>
-    <ref-impl-top-dir></ref-impl-top-dir></li>
-  <li>
-    <div style="text-align: justify;">From the command line, while
-still in the reference implementation directory,&nbsp;<ref-impl-top-dir>
-run '<code>ant deploy-to-tomcat</code>' (without the quotes). This
-compiles the Semantic MOBY reference implementation and deploys the
-various parts to run as Java Servlets under Tomcat 5.</ref-impl-top-dir><br>
-    <ref-impl-top-dir></ref-impl-top-dir></div>
-    <ref-impl-top-dir><br>
-    </ref-impl-top-dir></li>
-  <li>
-    <div style="text-align: justify;">Copy the appropriate JDBC driver
-jar file into the <tomcat-top-dir><code>shared/lib</code>
-subdirectory of the Tomcat 5 installation. As of this writing, the
-latest PostgreSQL JDBC jar file
+implementation is being installed.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"> From the command line, change
+directory to the reference implementation directory and run <code>'ant
+third-party'</code> (without the quotes). This retrieves third party
+components from CVS and builds them. Retrieving the components from CVS
+is admittedly less predictable than storing a version of the components
+with the Semantic MOBY distribution, but as the components (especially <a
+ href="http://jena.sourceforge.net">Jena2</a>) are constantly being
+improved, it is considered more important to have the latest versions
+than to have stable versions. Currently, this step takes about three
+minutes on a 2GHz P4 machine with a broadband connection.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"> From the command line, while
+still in the reference implementation directory,&nbsp; run '<code>ant
+deploy-to-tomcat</code>' (without the quotes). This compiles the
+Semantic MOBY reference implementation and deploys the various parts to
+run as Java Servlets under Tomcat 5.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"> Copy the appropriate JDBC driver
+jar file into the <code>shared/lib</code> subdirectory of the Tomcat 5
+installation. As of this writing, the latest PostgreSQL JDBC jar file
 was named <span style="font-style: italic;">postgresql.jar</span> and
-the latest MySQL driver was named <span style="font-style: italic;">mysql-connector-java-3.0.11-stable-bin.jar</span>.</tomcat-top-dir><br>
-    <tomcat-top-dir></tomcat-top-dir></div>
-    <tomcat-top-dir><br>
-    </tomcat-top-dir></li>
+the latest MySQL driver was named <span style="font-style: italic;">mysql-connector-java-3.0.11-stable-bin.jar</span>.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"><!--StartFragment --> Using
+whatever tools are appropriate for your DBMS, create a database user
+(e.g. <code>joe</code>) with a password (e.g. <code>foobar</code>).
+For MySQL, the free MySQL Control Center works well, and for
+PostgreSQL, PGAdmin III works well.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"><!--StartFragment --> Create a
+database, and give it a name (e.g. <code>my-smoby-repository</code>).
+Make the owner of the database the user (e.g. <code>joe</code>)
+created in step&nbsp;8.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"><!--StartFragment --> Modify <code>smoby.properties</code>,
+located in the <code>webapps/s-moby.org</code> subdirectory of the
+Tomcat installation directory, setting <code>DB_USER_ID</code> to the
+user (e.g. <code>joe</code>) created in step 8, <code>DB_PASSWORD</code>
+to the password (e.g. <code>foobar</code>) of the user created in step
+8, and <code>DB_REPOSITORY_NAME</code> to the database name (e.g. <code>my-smoby-repository</code>)
+used in step 8.Also modify <code>DB_URL</code> to include the name of
+the database used in&nbsp;step 9&nbsp;(e.g. <code>jdbc:postgresql://localhost/my-smoby-repository</code>).<br>
+    <br>
+    </div>
+  </li>
   <li>Start Tomcat. If all went well, you should be able to open <a
- href="http://www.s-moby.org:8080">http://www.s-moby.org:8080</a>
-in a browser. </li>
+ href="http://www.s-moby.org:8080">http://www.s-moby.org:8080</a> in a
+browser.</li>
 </ol>
 </body>
 </html>

From gss at pub.open-bio.org  Wed Jun 30 14:21:28 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed Jun 30 14:05:04 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406301821.i5UILSsL031041@pub.open-bio.org>


gss
Wed Jun 30 14:21:28 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv30997/S-MOBY/ref-impl/server/WebRoot

Modified Files:
	smoby.properties 
Log Message:
Fixed installation instructions to reflect problems that Ardavan K found.

moby-live/S-MOBY/ref-impl/server/WebRoot smoby.properties,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/smoby.properties,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/smoby.properties	2004/06/10 23:25:49	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/smoby.properties	2004/06/30 18:21:28	1.2
@@ -3,9 +3,9 @@
 
 # Common values for MySQL and PostgreSQL
 #
-DB_USER_ID            = smobydev
-DB_PASSWORD           = 
-DB_REPOSITORY_NAME    = smoby-dev
+DB_USER_ID            = <change-me>
+DB_PASSWORD           = <change-me>
+DB_REPOSITORY_NAME    = <change-me>
 
 # Uncomment if using MySQL
 #
@@ -17,4 +17,4 @@
 #
 DB_DRIVER_CLASS_NAME  = org.postgresql.Driver
 DB_TYPE               = PostgreSQL
-DB_URL                = jdbc:postgresql://localhost/smoby-dev
\ No newline at end of file
+DB_URL                = jdbc:postgresql://localhost/<change-me>
\ No newline at end of file

From simont at pub.open-bio.org  Tue Jun  1 12:51:27 2004
From: simont at pub.open-bio.org (Simon Twigger)
Date: Tue, 1 Jun 2004 12:51:27 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406011651.i51GpR7t003930@pub.open-bio.org>


simont
Tue Jun  1 12:51:26 EDT 2004
Update of /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege
In directory pub.open-bio.org:/tmp/cvs-serv3911

Modified Files:
	MOBY_Service_ontology.png 
Log Message:
update, no change to content

moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege MOBY_Service_ontology.png,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MOBY_Service_ontology.png,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
Binary files /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MOBY_Service_ontology.png	2004/04/28 18:48:41	1.2 and /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MOBY_Service_ontology.png	2004/06/01 16:51:26	1.3 differ
rcsdiff: /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MOBY_Service_ontology.png: diff failed



From gss at pub.open-bio.org  Thu Jun 10 14:47:42 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 14:47:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406101847.i5AIlger017252@pub.open-bio.org>


gss
Thu Jun 10 14:47:42 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files
In directory pub.open-bio.org:/tmp/cvs-serv17230/ref-impl/config-files

Removed Files:
	for-tomcat-conf-catalina.properties 
Log Message:
No longer needed

moby-live/S-MOBY/ref-impl/config-files for-tomcat-conf-catalina.properties,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files/RCS/for-tomcat-conf-catalina.properties,v: No such file or directory



From gss at pub.open-bio.org  Thu Jun 10 14:58:01 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 14:58:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406101858.i5AIw13A017320@pub.open-bio.org>


gss
Thu Jun 10 14:58:01 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files
In directory pub.open-bio.org:/tmp/cvs-serv17295/ref-impl/config-files

Modified Files:
	for-tomcat-conf-server.xml 
Added Files:
	for-hosts-file README 
Log Message:
Cleanup

moby-live/S-MOBY/ref-impl/config-files for-hosts-file,NONE,1.1 README,NONE,1.1 for-tomcat-conf-server.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files/for-tomcat-conf-server.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files/for-tomcat-conf-server.xml	2004/04/02 00:02:03	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files/for-tomcat-conf-server.xml	2004/06/10 18:58:01	1.2
@@ -1,32 +1,32 @@
 <!-- Put the following just after the last </Host> closing element
      in <tomcat-home>/conf/server.xml -->
 
-      <Host appBase="webapps" name="acmepubs.com">
+      <Host appBase="webapps/acmepubs.com" name="acmepubs.com">
           <Alias>www.acmepubs.com</Alias>
-          <Context path="" docBase="acmepubs.com" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="megapubs.com">
+      <Host appBase="webapps/megapubs.com" name="megapubs.com">
           <Alias>www.megapubs.com</Alias>
-          <Context path="" docBase="megapubs.com" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="go.org">
+      <Host appBase="webapps/go.org" name="go.org">
           <Alias>www.go.org</Alias>
-          <Context path="" docBase="go.org" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="sgd.org">
+      <Host appBase="webapps/sgd.org" name="sgd.org">
           <Alias>www.sgd.org</Alias>
-          <Context path="" docBase="sgd.org" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="pubs.org">
+      <Host appBase="webapps/pubs.org" name="pubs.org">
           <Alias>www.pubs.org</Alias>
-          <Context path="" docBase="pubs.org" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="s-moby.org">
+      <Host appBase="webapps/s-moby.org" name="s-moby.org">
           <Alias>www.s-moby.org</Alias>
-          <Context path="" docBase="s-moby.org" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>



From gss at pub.open-bio.org  Thu Jun 10 19:06:55 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:06:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102306.i5AN6tGb017989@pub.open-bio.org>


gss
Thu Jun 10 19:06:55 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv17968/ref-impl

Added Files:
	.cvsignore 
Log Message:
Ignore products of building the reference implementation

moby-live/S-MOBY/ref-impl .cvsignore,NONE,1.1


From gss at pub.open-bio.org  Thu Jun 10 19:09:39 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:09:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102309.i5AN9dXo018072@pub.open-bio.org>


gss
Thu Jun 10 19:09:39 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv18051/ref-impl

Added Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl build.xml,NONE,1.1


From gss at pub.open-bio.org  Thu Jun 10 19:10:02 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:10:02 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102310.i5ANA2ta018104@pub.open-bio.org>


gss
Thu Jun 10 19:10:02 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv18083/ref-impl

Added Files:
	common.example.properties 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl common.example.properties,NONE,1.1


From gss at pub.open-bio.org  Thu Jun 10 19:10:31 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:10:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102310.i5ANAVTl018142@pub.open-bio.org>


gss
Thu Jun 10 19:10:31 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv18117/ref-impl

Modified Files:
	index.html 
Log Message:
Reference installation/deployment document

moby-live/S-MOBY/ref-impl index.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/index.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/index.html	2004/03/12 17:48:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/index.html	2004/06/10 23:10:30	1.2
@@ -65,7 +65,8 @@
 </div>
 <br>
 The above links provide more information about each part of the
-reference implementation.<br>
+reference implementation. See the file <a href="INSTALL.html">INSTALL.html</a>
+for information on building and installing the reference implementation.<br>
 <div style="margin-left: 40px;">
 <div style="margin-left: 40px;"></div>
 </div>



From gss at pub.open-bio.org  Thu Jun 10 19:10:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:10:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102310.i5ANAiop018168@pub.open-bio.org>


gss
Thu Jun 10 19:10:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv18147/ref-impl

Added Files:
	servlet.xml common.xml INSTALL.html 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl servlet.xml,NONE,1.1 common.xml,NONE,1.1 INSTALL.html,NONE,1.1


From gss at pub.open-bio.org  Thu Jun 10 19:11:02 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:11:02 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102311.i5ANB25b018206@pub.open-bio.org>


gss
Thu Jun 10 19:11:02 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv18181/ref-impl/core

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/core build.xml,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/05/27 15:54:44	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/06/10 23:11:02	1.4
@@ -3,24 +3,42 @@
 <project name="smoby-core" default="jar" basedir=".">
 
     <!-- Import shared stuff -->
-    <import file="../library.xml"/>
+    <import file="../common.xml"/>
 
-    <!-- Package the compiled source files into the main jar file -->
-    <target name="jar" depends="compile">
-        <jar destfile="${core-jar-file}" basedir="${classes-dir}"/>
-    </target>
+    <!-- Relative path for where to put stuff that gets built -->
+    <property name="build-dir" value="build"/>
     
+    <!-- Relative path for where javac should output class files -->
+    <property name="classes-dir" value="${build-dir}/classes"/>
+
     <!-- Compile all the source files that go into the library -->
     <target name="compile">
         <mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="core.classpath"/>
         </javac>
     </target>
     
+    <!-- Package the compiled source files into the main jar file -->
+    <target name="jar" depends="compile">
+        <jar destfile="${core-jar-file}" basedir="${classes-dir}"/>
+    </target>
+
     <!-- Deploy the jar file to the Tomcat shared library directory -->
     <target name="deploy-to-tomcat" depends="jar">
-        <copy file="${core-jar-file}" todir="${tomcat-shared-lib-dir}"/>
+        <copy file="${core-jar-file}"
+              todir="${tomcat-shared-lib-dir}"/>
+    </target>
+    
+	<!-- Remove the build directory and its contents -->
+	<target name="clean">
+		<delete dir="${build-dir}" includeEmptyDirs="true"/>
+        <delete file="${core-jar-file}"/>
+	</target>
+    
+    <!-- Un-deploy the jar file from the Tomcat shared library directory -->
+    <target name="undeploy-from-tomcat">
+        <delete file="${tomcat-shared-lib-dir}/${core-jar-file}"/>
     </target>
     
 </project>



From gss at pub.open-bio.org  Thu Jun 10 19:13:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:13:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDi92018265@pub.open-bio.org>


gss
Thu Jun 10 19:13:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF web.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/web.xml	2004/03/27 01:34:51	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.2
@@ -1,4 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE web-app PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN" "http://java.sun.com/dtd/web-app_2_3.dtd">
 <web-app>
+  <display-name>Example MOBY provider pubs.org</display-name>
 </web-app>



From gss at pub.open-bio.org  Thu Jun 10 19:13:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:13:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDiBN018284@pub.open-bio.org>


gss
Thu Jun 10 19:13:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF web.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml	2004/03/27 01:17:58	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.3
@@ -2,6 +2,8 @@
 <!DOCTYPE web-app PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN" "http://java.sun.com/dtd/web-app_2_3.dtd">
 <web-app>
   
+  <display-name>Example MOBY provider megapubs.com</display-name>
+
   <servlet>
     <servlet-name>CitationSearchServlet</servlet-name>
     <display-name>Publication Search</display-name>



From gss at pub.open-bio.org  Thu Jun 10 19:13:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:13:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDiOa018303@pub.open-bio.org>


gss
Thu Jun 10 19:13:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/server/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF web.xml,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml	2004/03/27 01:23:21	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.4
@@ -3,6 +3,8 @@
 
 <web-app>
 
+  <display-name>Semantic MOBY Server</display-name>
+
   <servlet>
     <servlet-name>GraphConversionServlet</servlet-name>
     <display-name>Graph Converter</display-name>



From gss at pub.open-bio.org  Thu Jun 10 19:13:45 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:13:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDjAt018322@pub.open-bio.org>


gss
Thu Jun 10 19:13:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF web.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml	2004/03/19 00:37:48	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.2
@@ -1,6 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE web-app PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN" "http://java.sun.com/dtd/web-app_2_3.dtd">
 <web-app>
+
+  <display-name>Example MOBY provider acmepubs.com</display-name>
   
   <servlet>
     <servlet-name>CitationSearchServlet</servlet-name>



From gss at pub.open-bio.org  Thu Jun 10 19:13:45 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:13:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDjKv018344@pub.open-bio.org>


gss
Thu Jun 10 19:13:45 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/example-providers/go.org/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF web.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/web.xml	2004/04/01 00:30:50	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.2
@@ -1,4 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE web-app PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN" "http://java.sun.com/dtd/web-app_2_3.dtd">
 <web-app>
+  <display-name>Example MOBY provider go.org</display-name>
 </web-app>



From gss at pub.open-bio.org  Thu Jun 10 19:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbSC018409@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-clients

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-clients build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/build.xml	2004/03/12 17:48:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/build.xml	2004/06/10 23:15:37	1.2
@@ -1,2 +1,11 @@
-<project name="example-clients" basedir=".">
+<project name="example-clients" default="all" basedir=".">
+
+    <target name="all">
+        <ant dir="SimpleEngager"/>
+    </target>
+
+    <target name="clean">
+        <ant dir="SimpleEngager" target="clean"/>
+    </target>
+
 </project>



From gss at pub.open-bio.org  Thu Jun 10 19:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbBK018428@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/server

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/server build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/05/27 15:54:12	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/06/10 23:15:37	1.3
@@ -1,29 +1,42 @@
-<!-- Apache Ant format build file for s-moby.org example provider -->
+<!-- Apache Ant format build file for s-moby.org server -->
 
-<project name="s-moby.org" default="war" basedir=".">
+<project name="s-moby.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="s-moby.org.war"/>
+    <!-- The web application name -->
+    <property name="webapp-name" value="s-moby.org"/>
 	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
-	
-	<!-- Compile all the source files that go into the library -->
+    <!-- Compile all the source files that go into the library, and copy any
+         properties files (i.e. smoby.properties and log4j.properties) into
+         the classes directory -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
+        <copy toDir="${classes-dir}">
+            <fileset dir="WebRoot">
+                <include name="*.properties"/>
+            </fileset>
+        </copy>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>



From gss at pub.open-bio.org  Thu Jun 10 19:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbfV018512@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-providers/megapubs.com

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml	2004/05/27 15:54:28	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml	2004/06/10 23:15:37	1.3
@@ -1,29 +1,35 @@
-<!-- Apache Ant format build file for acmepubs.com example provider -->
+<!-- Apache Ant format build file for megapubs.com server -->
 
-<project name="megapubs.com" default="war" basedir=".">
+<project name="s-moby.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="megapubs.com.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="megapubs.com"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>



From gss at pub.open-bio.org  Thu Jun 10 19:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbjJ018489@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-clients/SimpleEngager

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml	2004/05/28 21:35:17	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml	2004/06/10 23:15:37	1.3
@@ -3,22 +3,34 @@
 <project name="simple-engager" default="jar" basedir=".">
 
     <!-- Import shared stuff -->
-    <import file="../../library.xml"/>
+    <import file="../../common.xml"/>
+
+    <!-- Relative path for where to put stuff that gets built -->
+    <property name="build-dir" value="build"/>
+    
+    <!-- Relative path for where javac should output class files -->
+    <property name="classes-dir" value="${build-dir}/classes"/>
 
     <!-- The main jar file -->
-    <property name="jar-file" value="${build-dir}/engager.jar"/>
+    <property name="jar-file" value="simple-engager.jar"/>
 
-    <!-- Package the compiled source files into the main jar file -->
-    <target name="jar" depends="compile">
-        <jar destfile="${jar-file}" basedir="${classes-dir}"/>
-    </target>
-    
     <!-- Compile all the source files that go into the library -->
     <target name="compile">
         <mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
     </target>
     
+    <!-- Package the compiled source files into the main jar file -->
+    <target name="jar" depends="compile">
+        <jar destfile="${jar-file}" basedir="${classes-dir}"/>
+    </target>
+    
+	<!-- Remove the build directory and its contents -->
+	<target name="clean">
+		<delete dir="${build-dir}" includeEmptyDirs="true"/>
+        <delete file="${jar-file}"/>
+	</target>
+    
 </project>



From gss at pub.open-bio.org  Thu Jun 10 19:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbtN018470@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-providers/go.org

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/go.org build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/build.xml	2004/05/27 16:23:59	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/build.xml	2004/06/10 23:15:37	1.2
@@ -1,29 +1,35 @@
 <!-- Apache Ant format build file for go.org example provider -->
 
-<project name="go.org" default="war" basedir=".">
+<project name="go.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="go.org.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="go.org"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>



From gss at pub.open-bio.org  Thu Jun 10 19:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbSU018534@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-providers/pubs.org

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/pubs.org build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/build.xml	2004/05/27 15:54:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/build.xml	2004/06/10 23:15:37	1.2
@@ -1,29 +1,35 @@
 <!-- Apache Ant format build file for pubs.org example provider -->
 
-<project name="pubs.org" default="war" basedir=".">
+<project name="s-moby.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="pubs.org.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="pubs.org"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>



From gss at pub.open-bio.org  Thu Jun 10 19:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFb1V018448@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-providers/acmepubs.com

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml	2004/05/27 15:54:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml	2004/06/10 23:15:37	1.3
@@ -1,29 +1,35 @@
 <!-- Apache Ant format build file for acmepubs.com example provider -->
 
-<project name="acmepubs.com" default="war" basedir=".">
+<project name="acmepubs.com" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="acmepubs.com.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="acmepubs.com"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>



From gss at pub.open-bio.org  Thu Jun 10 19:16:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:16:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102316.i5ANGmJn018573@pub.open-bio.org>


gss
Thu Jun 10 19:16:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data
In directory pub.open-bio.org:/tmp/cvs-serv18549/ref-impl/test-data

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data added to the repository

moby-live/S-MOBY/ref-impl/test-data - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Thu Jun 10 19:16:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:16:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102316.i5ANGmfG018591@pub.open-bio.org>


gss
Thu Jun 10 19:16:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser
In directory pub.open-bio.org:/tmp/cvs-serv18549/ref-impl/test-data/parser

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser added to the repository

moby-live/S-MOBY/ref-impl/test-data/parser - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Thu Jun 10 19:16:51 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:16:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102316.i5ANGpqR018636@pub.open-bio.org>


gss
Thu Jun 10 19:16:51 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser
In directory pub.open-bio.org:/tmp/cvs-serv18615/ref-impl/test-data/parser

Added Files:
	unparsable.n3 minimal.n3 three-providers.n3 README.txt 
Log Message:
Began writing JUnit test cases (feel free to help out, everyone :-)

moby-live/S-MOBY/ref-impl/test-data/parser unparsable.n3,NONE,1.1 minimal.n3,NONE,1.1 three-providers.n3,NONE,1.1 README.txt,NONE,1.1


From gss at pub.open-bio.org  Thu Jun 10 19:24:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:24:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102324.i5ANOGLl018745@pub.open-bio.org>


gss
Thu Jun 10 19:24:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv18720/ref-impl/server/src/org/smoby/ref/tools

Modified Files:
	DiscoveryQuery.java 
Log Message:
Commented out most functionality until I figure out the new
ResultBindingIterator protocol...

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/05/19 18:26:40	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/06/10 23:24:16	1.5
@@ -4,11 +4,10 @@
 import java.text.*;
 import java.util.*;
 
-import org.smoby.parser.Parser;
+import org.smoby.parser.*;
 import org.smoby.ref.tools.db.*;
 import org.smoby.graph.*;
-import org.smoby.graph.impl.MOBYObjectFactory;
-import org.smoby.graph.impl.MOBYProviderImpl;
+import org.smoby.graph.impl.*;
 import org.smoby.vocabulary.*;
 
 import com.hp.hpl.jena.db.*;
@@ -257,22 +256,23 @@
 		if (! node.asNode().isBlank()) {
 			return node;
 		}
-		
-		ResultBinding.ResultBindingIterator results = binding.iterator();
+		//ResultBinding
+		ResultBindingIterator results = binding.iterator();
 		
 		while (results.hasNext())
 		{
-			results.next();
+			Object object = results.next();
+			Value value = (Value) object;
 			String varName = results.varName();
-			Value value = results.value();
+//			Value value = results.value();
 			Object cachedName = varNames.get(node.toString());
 			if (varName.equals(cachedName))
 			{
-				if (value.isRDFLiteral()) {
-					return value.getRDFLiteral();
-				} else if (value.isRDFResource()) {
-					return value.getRDFResource();
-				}
+//				if (value.isRDFLiteral()) {
+//					return value.getRDFLiteral();
+//				} else if (value.isRDFResource()) {
+//					return value.getRDFResource();
+//				}
 			}
 		}
 		return node;



From gss at pub.open-bio.org  Thu Jun 10 19:25:49 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:25:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102325.i5ANPnGe018783@pub.open-bio.org>


gss
Thu Jun 10 19:25:49 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src
In directory pub.open-bio.org:/tmp/cvs-serv18760/ref-impl/server/src

Removed Files:
	log4j.properties smoby.properties 
Log Message:
Moved from src/ to WebRoot/

moby-live/S-MOBY/ref-impl/server/src log4j.properties,1.1,NONE smoby.properties,1.4,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/log4j.properties,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/smoby.properties,v: No such file or directory



From gss at pub.open-bio.org  Thu Jun 10 19:25:49 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:25:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102325.i5ANPn6V018798@pub.open-bio.org>


gss
Thu Jun 10 19:25:49 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv18760/ref-impl/server/WebRoot

Added Files:
	smoby.properties 
Log Message:
Moved from src/ to WebRoot/

moby-live/S-MOBY/ref-impl/server/WebRoot smoby.properties,NONE,1.1


From gss at pub.open-bio.org  Thu Jun 10 19:26:31 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:26:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102326.i5ANQV5p018845@pub.open-bio.org>


gss
Thu Jun 10 19:26:31 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage
In directory pub.open-bio.org:/tmp/cvs-serv18822/ref-impl/queries/engage

Removed Files:
	engage-megapubs-citationSearch.rdf 
	engage-megapubs-citationSearch.n3 
Log Message:
No longer needed

moby-live/S-MOBY/ref-impl/queries/engage engage-megapubs-citationSearch.rdf,1.1,NONE engage-megapubs-citationSearch.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/RCS/engage-megapubs-citationSearch.rdf,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/RCS/engage-megapubs-citationSearch.n3,v: No such file or directory



From gss at pub.open-bio.org  Thu Jun 10 19:27:12 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:27:12 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102327.i5ANRCR3018875@pub.open-bio.org>


gss
Thu Jun 10 19:27:12 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage
In directory pub.open-bio.org:/tmp/cvs-serv18850/ref-impl/queries/engage

Modified Files:
	engage-acmepubs-citationSearch.n3 
Log Message:
Simplified N3 by using un-named blank nodes

moby-live/S-MOBY/ref-impl/queries/engage engage-acmepubs-citationSearch.n3,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3	2004/04/02 00:05:16	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3	2004/06/10 23:27:12	1.2
@@ -10,28 +10,44 @@
 
 acmepubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
-    rdfs:comment "Industry standard search" ;
-    moby:operatesOn _:bnode1 .
-
-_:bnode1
-    a moby:Graph, rdf:Bag ;
-    moby:hasMapping _:bnode2 .
-
-_:bnode2
-    a moby:Subject, go:GeneSymbol ;
-    moby:mapsTo _:bnode3 ;
-    acmepubs:geneSymbol "REV7" .
-
-_:bnode3
-    a moby:Object, sgd:LiteratureGuide ;
-    acmepubs:literatureGuideURL _:bnode6 .
+    moby:name "AcmePubs Citation Search" ;
+    moby:oneLineDescription "Industry standard search" ;
+    moby:aboutURI "http://www.acmepubs.com/about/citationSearch" ;
+    moby:operatesOn [
+        a rdf:Bag ;
+        rdf:_1 [
+            a moby:Graph ;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                acmepubs:geneSymbol "REV5" ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide ;
+                    acmepubs:literatureGuideURL _:bnode1
+                ]
+            ]
+        ] ;
+        rdf:_2 [
+            a moby:Graph ;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                acmepubs:geneSymbol "REV7" ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide ;
+                    acmepubs:literatureGuideURL _:bnode2
+                ]
+            ]
+        ] ;
+    ] .
 
 acmepubs:geneSymbol
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain go:GeneSymbol ;
     rdfs:range xsd:string .
 
 acmepubs:literatureGuideURL
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain sgd:LiteratureGuide ;
     rdfs:range xsd:anyURI .
+



From gss at pub.open-bio.org  Thu Jun 10 19:27:41 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:27:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102327.i5ANRfwJ018915@pub.open-bio.org>


gss
Thu Jun 10 19:27:41 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage
In directory pub.open-bio.org:/tmp/cvs-serv18890/ref-impl/queries/engage

Modified Files:
	engage-acmepubs-citationSearch.rdf 
Log Message:
Use un-named blank nodes

moby-live/S-MOBY/ref-impl/queries/engage engage-acmepubs-citationSearch.rdf,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf	2004/04/02 00:05:16	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf	2004/06/10 23:27:41	1.2
@@ -12,31 +12,54 @@
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A0">
     <moby:hasMapping rdf:nodeID="A1"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A1">
-    <moby:mapsTo rdf:nodeID="A2"/>
+  <rdf:Description rdf:nodeID="A2">
+    <moby:mapsTo rdf:nodeID="A3"/>
     <acmepubs:geneSymbol>REV7</acmepubs:geneSymbol>
     <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
   </rdf:Description>
+  <rdf:Description rdf:nodeID="A4">
+    <acmepubs:literatureGuideURL rdf:nodeID="A5"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A6">
+    <moby:hasMapping rdf:nodeID="A2"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <acmepubs:literatureGuideURL rdf:nodeID="A7"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A8">
+    <rdf:_2 rdf:nodeID="A6"/>
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A0"/>
+  </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <moby:oneLineDescription>Industry standard search</moby:oneLineDescription>
+    <moby:operatesOn rdf:nodeID="A8"/>
+    <moby:aboutURI>http://www.acmepubs.com/about/citationSearch</moby:aboutURI>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <rdfs:comment>Industry standard search</rdfs:comment>
-    <moby:operatesOn rdf:nodeID="A0"/>
+    <moby:name>AcmePubs Citation Search</moby:name>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <acmepubs:literatureGuideURL rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  <rdf:Description rdf:nodeID="A1">
+    <acmepubs:geneSymbol>REV5</acmepubs:geneSymbol>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <moby:mapsTo rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/literatureGuideURL">
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>



From gss at pub.open-bio.org  Thu Jun 10 19:27:58 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:27:58 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102327.i5ANRwYw018953@pub.open-bio.org>


gss
Thu Jun 10 19:27:58 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery
In directory pub.open-bio.org:/tmp/cvs-serv18928/ref-impl/queries/discovery

Modified Files:
	query.n3 
Log Message:
Simplified N3 by using un-named blank nodes

moby-live/S-MOBY/ref-impl/queries/discovery query.n3,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3	2004/04/02 00:05:16	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3	2004/06/10 23:27:58	1.2
@@ -5,15 +5,15 @@
 
 _:provider
     a moby:Provider ;
-    moby:operatesOn _:bnode1 .
-
-_:bnode1
-    a moby:Graph, rdf:Bag ;
-    moby:hasMapping _:bnode2 .
-
-_:bnode2
-    a moby:Subject, go:GeneSymbol ;
-    moby:mapsTo _:bnode3 .
-
-_:bnode3
-    a moby:Object, sgd:LiteratureGuide .
+    moby:operatesOn [
+        a rdf:Bag ;
+        rdf:_1 [
+            a moby:Graph;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide
+                ]
+            ]
+        ]
+    ] .



From gss at pub.open-bio.org  Thu Jun 10 19:28:06 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:28:06 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102328.i5ANS68x018983@pub.open-bio.org>


gss
Thu Jun 10 19:28:06 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery
In directory pub.open-bio.org:/tmp/cvs-serv18958/ref-impl/queries/discovery

Modified Files:
	query.rdf 
Log Message:
Use un-named blank nodes

moby-live/S-MOBY/ref-impl/queries/discovery query.rdf,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf	2004/04/02 00:05:16	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf	2004/06/10 23:28:06	1.2
@@ -4,21 +4,24 @@
     xmlns:moby="http://www.s-moby.org:8080/terms#"
     xmlns:sgd="http://www.sgd.org:8080/terms#" >
   <rdf:Description rdf:nodeID="A0">
-    <moby:mapsTo rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+    <moby:hasMapping rdf:nodeID="A1"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A2">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <moby:operatesOn rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A0"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A1">
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <moby:mapsTo rdf:nodeID="A3"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
     <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A3">
-    <moby:hasMapping rdf:nodeID="A0"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+  <rdf:Description rdf:nodeID="A4">
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
+    <moby:operatesOn rdf:nodeID="A2"/>
   </rdf:Description>
 </rdf:RDF>



From gss at pub.open-bio.org  Thu Jun 10 19:30:53 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:30:53 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102330.i5ANUr5l019096@pub.open-bio.org>


gss
Thu Jun 10 19:30:53 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv19071/ref-impl/example-providers/sgd.org

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/sgd.org build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/build.xml	2004/05/27 15:54:20	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/build.xml	2004/06/10 23:30:53	1.2
@@ -1,29 +1,35 @@
 <!-- Apache Ant format build file for sgd.org example provider -->
 
-<project name="sgd.org" default="war" basedir=".">
+<project name="sgd.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="sgd.org.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="sgd.org"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>



From gss at pub.open-bio.org  Thu Jun 10 19:31:51 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:31:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102331.i5ANVp4D019169@pub.open-bio.org>


gss
Thu Jun 10 19:31:51 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv19144/ref-impl/example-providers/sgd.org

Modified Files:
	.cvsignore 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-providers/sgd.org .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore	2004/05/27 15:54:20	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore	2004/06/10 23:31:50	1.2
@@ -1 +1,5 @@
 *.war
+.classpath
+.encoding
+.mymetadata
+.project



From gss at pub.open-bio.org  Thu Jun 10 19:32:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:32:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102332.i5ANW9GK019207@pub.open-bio.org>


gss
Thu Jun 10 19:32:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers
In directory pub.open-bio.org:/tmp/cvs-serv19182/ref-impl/example-providers

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/build.xml	2004/03/12 17:48:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/build.xml	2004/06/10 23:32:09	1.2
@@ -1,2 +1,39 @@
-<project name="example-providers" basedir=".">
+<project name="example-providers" basedir="." default="all">
+
+    <!-- Build all the example providers -->
+    <target name="all">
+        <ant dir="acmepubs.com"/>
+        <ant dir="go.org"/>
+        <ant dir="megapubs.com"/>
+        <ant dir="pubs.org"/>
+        <ant dir="sgd.org"/>
+    </target>
+
+    <!-- Clean all the example providers -->
+    <target name="clean">
+        <ant dir="acmepubs.com" target="clean"/>
+        <ant dir="go.org" target="clean"/>
+        <ant dir="megapubs.com" target="clean"/>
+        <ant dir="pubs.org" target="clean"/>
+        <ant dir="sgd.org" target="clean"/>
+    </target>
+
+    <!-- Deploy all the example providers to Tomcat -->
+    <target name="deploy-to-tomcat">
+        <ant dir="acmepubs.com" target="deploy-to-tomcat"/>
+        <ant dir="go.org" target="deploy-to-tomcat"/>
+        <ant dir="megapubs.com" target="deploy-to-tomcat"/>
+        <ant dir="pubs.org" target="deploy-to-tomcat"/>
+        <ant dir="sgd.org" target="deploy-to-tomcat"/>
+    </target>
+
+    <!-- Un-deploy all the example providers from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <ant dir="acmepubs.com" target="undeploy-from-tomcat"/>
+        <ant dir="go.org" target="undeploy-from-tomcat"/>
+        <ant dir="megapubs.com" target="undeploy-from-tomcat"/>
+        <ant dir="pubs.org" target="undeploy-from-tomcat"/>
+        <ant dir="sgd.org" target="undeploy-from-tomcat"/>
+    </target>
+
 </project>



From gss at pub.open-bio.org  Fri Jun 11 14:26:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:26:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111826.i5BIQQnt022787@pub.open-bio.org>


gss
Fri Jun 11 14:26:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv22758/S-MOBY/ref-impl

Modified Files:
	build.xml common.xml 
Log Message:
Needed to copy another jar file to Tomcat in deploy-to-tomcat target

moby-live/S-MOBY/ref-impl build.xml,1.1,1.2 common.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/build.xml	2004/06/10 23:09:39	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/build.xml	2004/06/11 18:26:25	1.2
@@ -72,9 +72,11 @@
         <!-- Copy jar files to the Tomcat shared library directory -->
         <copy toDir="${tomcat-shared-lib-dir}">
             <!-- Copy the HTTPClient jar files -->
+            <fileset dir="${http-client-lib-dir}">
+                <include name="*.jar"/>
+            </fileset>
             <fileset dir="${http-client-dist-dir}">
                 <include name="commons-httpclient.jar"/>
-                <include name="lib/*.jar"/>
             </fileset>
             <!-- Copy the jena jar files -->
             <fileset dir="${jena-lib-dir}">

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/common.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/common.xml	2004/06/10 23:10:44	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/common.xml	2004/06/11 18:26:25	1.2
@@ -25,6 +25,8 @@
         <property name="http-client-package" value="jakarta-commons/httpclient"/>
         <!-- Top level directory of the package -->
         <property name="http-client-top-dir" value="${third-party-dir}/${http-client-package}"/>
+        <!-- Library directory -->
+        <property name="http-client-lib-dir" value="${http-client-top-dir}/lib"/>
         <!-- Distribution directory -->
         <property name="http-client-dist-dir" value="${http-client-top-dir}/dist"/>
 



From gss at pub.open-bio.org  Fri Jun 11 14:43:15 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:43:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111843.i5BIhFkb022876@pub.open-bio.org>


gss
Fri Jun 11 14:43:15 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv22851/S-MOBY/ref-impl/core

Modified Files:
	.cvsignore 
Log Message:
Don't include smoby.jar in CVS

moby-live/S-MOBY/ref-impl/core .cvsignore,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/05/27 15:30:40	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/06/11 18:43:15	1.5
@@ -1,2 +1,2 @@
-classes
-build
\ No newline at end of file
+build
+smoby.jar
\ No newline at end of file



From gss at pub.open-bio.org  Fri Jun 11 14:44:07 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:44:07 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111844.i5BIi7jR022915@pub.open-bio.org>


gss
Fri Jun 11 14:44:07 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv22890/S-MOBY/ref-impl/example-clients/SimpleEngager

Modified Files:
	.cvsignore 
Log Message:
Don't include simple-engager.jar in CVS

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .cvsignore,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/05/27 19:37:10	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/11 18:44:07	1.3
@@ -1,2 +1,2 @@
-classes
 build
+simple-engager.jar
\ No newline at end of file



From gss at pub.open-bio.org  Fri Jun 11 14:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGtV022950@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-providers/acmepubs.com

Removed Files:
	.mymetadata .project .xdoclet .classpath 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .mymetadata,1.5,NONE .project,1.6,NONE .xdoclet,1.3,NONE .classpath,1.4,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.mymetadata,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.xdoclet,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.classpath,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 14:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGHd022967@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/core

Removed Files:
	.classpath .project 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/core .classpath,1.4,NONE .project,1.4,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/.project,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 14:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGfc022986@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-providers/pubs.org

Removed Files:
	.mymetadata .classpath .project 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-providers/pubs.org .mymetadata,1.1,NONE .classpath,1.2,NONE .project,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/.mymetadata,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/.project,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 14:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGex023009@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/server

Removed Files:
	.project .classpath xdoclet-build.xml .xdoclet .mymetadata 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/server .project,1.2,NONE .classpath,1.4,NONE xdoclet-build.xml,1.1,NONE .xdoclet,1.1,NONE .mymetadata,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/xdoclet-build.xml,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/.xdoclet,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/.mymetadata,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 14:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGmj023028@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY

Removed Files:
	.project 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY .project,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/RCS/.project,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 14:45:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjHcq023069@pub.open-bio.org>


gss
Fri Jun 11 14:45:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-clients/SimpleEngager

Removed Files:
	.classpath .project 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .classpath,1.2,NONE .project,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/.project,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 14:45:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjHnQ023049@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-providers/go.org

Removed Files:
	.mymetadata .project .classpath 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-providers/go.org .mymetadata,1.1,NONE .project,1.1,NONE .classpath,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/.mymetadata,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/.classpath,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 14:45:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjHCS023090@pub.open-bio.org>


gss
Fri Jun 11 14:45:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-providers/megapubs.com

Removed Files:
	.project .classpath .mymetadata 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .project,1.2,NONE .classpath,1.2,NONE .mymetadata,1.3,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/.mymetadata,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 14:45:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjH6W023108@pub.open-bio.org>


gss
Fri Jun 11 14:45:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/server/.externalToolBuilders

Removed Files:
	XDoclet Builder.launch 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/server/.externalToolBuilders XDoclet Builder.launch,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/XDoclet,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/Builder.launch,v: No such file or directory



From ambrose at pub.open-bio.org  Fri Jun 11 18:06:56 2004
From: ambrose at pub.open-bio.org (Ambrose Ng)
Date: Fri, 11 Jun 2004 18:06:56 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406112206.i5BM6uPZ023829@pub.open-bio.org>


ambrose
Fri Jun 11 18:06:56 EDT 2004
Update of /home/repository/moby/moby-live/Perl/Accessories
In directory pub.open-bio.org:/tmp/cvs-serv23807

Added Files:
	SearchDatabase.cgi 
Log Message:
adding Namespace Database search page

moby-live/Perl/Accessories SearchDatabase.cgi,NONE,1.1


From gss at pub.open-bio.org  Mon Jun 14 12:24:12 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:24:12 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141624.i5EGOCrf009597@pub.open-bio.org>


gss
Mon Jun 14 12:24:12 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv9572

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/core .cvsignore,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/06/11 18:43:15	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/06/14 16:24:12	1.6
@@ -1,2 +1,4 @@
 build
-smoby.jar
\ No newline at end of file
+smoby.jar
+.classpath
+.project



From gss at pub.open-bio.org  Mon Jun 14 12:30:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:30:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141630.i5EGUxLx009701@pub.open-bio.org>


gss
Mon Jun 14 12:30:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com
In directory pub.open-bio.org:/tmp/cvs-serv9676

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.cvsignore	2004/05/27 15:54:40	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.cvsignore	2004/06/14 16:30:58	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project



From gss at pub.open-bio.org  Mon Jun 14 12:35:27 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:35:27 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141635.i5EGZRma009780@pub.open-bio.org>


gss
Mon Jun 14 12:35:26 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com
In directory pub.open-bio.org:/tmp/cvs-serv9755

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.cvsignore	2004/05/27 15:54:28	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.cvsignore	2004/06/14 16:35:26	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project



From gss at pub.open-bio.org  Mon Jun 14 12:44:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:44:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141644.i5EGiiFa010077@pub.open-bio.org>


gss
Mon Jun 14 12:44:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org
In directory pub.open-bio.org:/tmp/cvs-serv10052

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/pubs.org .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.cvsignore	2004/05/27 15:54:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.cvsignore	2004/06/14 16:44:44	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project



From gss at pub.open-bio.org  Mon Jun 14 12:44:45 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:44:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141644.i5EGijjL010107@pub.open-bio.org>


gss
Mon Jun 14 12:44:45 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv10082

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .cvsignore,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/11 18:44:07	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/14 16:44:45	1.4
@@ -1,2 +1,4 @@
 build
-simple-engager.jar
\ No newline at end of file
+simple-engager.jar
+.classpath
+.project



From gss at pub.open-bio.org  Mon Jun 14 12:44:46 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:44:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141644.i5EGikoR010137@pub.open-bio.org>


gss
Mon Jun 14 12:44:46 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org
In directory pub.open-bio.org:/tmp/cvs-serv10112

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/go.org .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.cvsignore	2004/05/27 16:23:59	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.cvsignore	2004/06/14 16:44:46	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project



From gss at pub.open-bio.org  Mon Jun 14 12:45:53 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:45:53 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141645.i5EGjrJs010177@pub.open-bio.org>


gss
Mon Jun 14 12:45:53 EDT 2004
Update of /home/repository/moby/moby-live
In directory pub.open-bio.org:/tmp/cvs-serv10156

Added Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live .cvsignore,NONE,1.1


From gss at pub.open-bio.org  Mon Jun 14 12:49:24 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:49:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141649.i5EGnOhi010210@pub.open-bio.org>


gss
Mon Jun 14 12:49:23 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv10185/S-MOBY/ref-impl/example-clients/SimpleEngager

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .cvsignore,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/14 16:44:45	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/14 16:49:23	1.5
@@ -2,3 +2,4 @@
 simple-engager.jar
 .classpath
 .project
+classes



From gss at pub.open-bio.org  Mon Jun 14 12:52:32 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:52:32 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141652.i5EGqWqV010289@pub.open-bio.org>


gss
Mon Jun 14 12:52:32 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv10265/S-MOBY/ref-impl/example-providers/sgd.org

Removed Files:
	.project .mymetadata .classpath 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/sgd.org .project,1.1,NONE .mymetadata,1.1,NONE .classpath,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/.mymetadata,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/.classpath,v: No such file or directory



From gss at pub.open-bio.org  Mon Jun 14 13:17:57 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 13:17:57 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141717.i5EHHvJx010453@pub.open-bio.org>


gss
Mon Jun 14 13:17:56 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv10428

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/server .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore	2004/05/27 18:31:46	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore	2004/06/14 17:17:56	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project



From gss at pub.open-bio.org  Mon Jun 14 16:58:13 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 16:58:13 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142058.i5EKwD3K010951@pub.open-bio.org>


gss
Mon Jun 14 16:58:12 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv10926/src/org/smoby/ref/tools

Modified Files:
	MOBYProperties.java 
Log Message:
Use servlet context to find properties file

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools MOBYProperties.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/MOBYProperties.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/MOBYProperties.java	2004/03/20 00:36:48	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/MOBYProperties.java	2004/06/14 20:58:12	1.2
@@ -3,6 +3,8 @@
 import java.io.*;
 import java.util.*;
 
+import javax.servlet.ServletContext;
+
 
 /**
  * This abstract class contains a set of static methods for retrieving
@@ -32,25 +34,12 @@
     public static String getProperty(String propName, boolean required)
         throws MissingPropertyException
     {
-        try {
-            String value = getProps().getProperty(propName);
-            if (required && (value == null)) {
-                throw new MissingPropertyException(propName,
-                    "Property " + propName + " not found in " + PROP_FILE_NAME);
-            }
-            return value;
-        } catch (FileNotFoundException e) {
-            if (required) {
-                throw new MissingPropertyException(propName,
-                    "Properties file " + PROP_FILE_NAME + " not found on classpath", e);
-            }
-        } catch (IOException e) {
-            if (required) {
-            	throw new MissingPropertyException(propName,
-                    "Error while reading " + PROP_FILE_NAME, e);
-            }
+        String value = props.getProperty(propName);
+        if (required && (value == null)) {
+            throw new MissingPropertyException(propName,
+                "Property " + propName + " not found in " + PROP_FILE_NAME);
         }
-        return null;
+        return value;
     }
 
     /**
@@ -68,21 +57,22 @@
     }
     
     /**
-     * Use lazy evaluation to create a Properties object and load the
-     * properties file into it.
-     * @return the Properties object.
-     * @throws FileNotFoundException
-     * @throws IOException
+     * Read the properties file
+     * @throws FileNotFoundException if the file cannot be located
+     * @throws IOException if the file cannot be read
      */
-    private static Properties getProps()
-        throws FileNotFoundException, IOException
+    public static void initProps(ServletContext context)
+    	throws FileNotFoundException, IOException
     {
-        if (props == null) {
+        if (props == null) // Only try to read it once
+        {
         	props = new Properties();
-            InputStream is = MOBYProperties.class.getClassLoader().
-                getResourceAsStream(PROP_FILE_NAME);
-            props.load(is);
+            InputStream is = context.getResourceAsStream(PROP_FILE_NAME);
+            if (is == null) {
+            	throw new FileNotFoundException(
+            		"Properties file \"" + PROP_FILE_NAME + "\" not found");
+            }
+        	props.load(is);
         }
-        return props;
     }
 }



From gss at pub.open-bio.org  Mon Jun 14 16:58:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 16:58:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142058.i5EKwxLf010977@pub.open-bio.org>


gss
Mon Jun 14 16:58:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets
In directory pub.open-bio.org:/tmp/cvs-serv10956/src/org/smoby/ref/servlets

Added Files:
	BaseServlet.java 
Log Message:
Base class that does common initialization tasks

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets BaseServlet.java,NONE,1.1


From gss at pub.open-bio.org  Mon Jun 14 16:59:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 16:59:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142059.i5EKxae0011019@pub.open-bio.org>


gss
Mon Jun 14 16:59:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets
In directory pub.open-bio.org:/tmp/cvs-serv10990/src/org/smoby/ref/servlets

Modified Files:
	ProviderInvestigationServlet.java DiscoveryServlet.java 
Log Message:
Make subclass of new common superclass BaseServlet

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets ProviderInvestigationServlet.java,1.3,1.4 DiscoveryServlet.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java	2004/05/19 18:26:40	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java	2004/06/14 20:59:36	1.4
@@ -7,7 +7,7 @@
 import org.apache.commons.logging.*;
 import org.smoby.ref.tools.db.*;
 import org.smoby.graph.*;
-import org.smoby.ref.tools.URIInvestigator;
+import org.smoby.ref.tools.*;
 import org.smoby.servlet.*;
 
 /**
@@ -17,7 +17,7 @@
  * The only feedback given is that if the provider-url is missing, the response
  * status is set to 406 NOT ACCEPTABLE; otherwise, the status is set to 200 OK.
  */
-public class ProviderInvestigationServlet extends HttpServlet
+public class ProviderInvestigationServlet extends BaseServlet
 {
     private final static Log syncLog = LogFactory.getLog("SYNC");
     

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/06/14 20:59:36	1.3
@@ -25,7 +25,7 @@
  * into an array of ProviderDescriptionGraph objects, by calling the
  * GraphListTransceiverFactory.newReceiver() factory method.
  */
-public class DiscoveryServlet extends HttpServlet
+public class DiscoveryServlet extends BaseServlet
 {
 	public void doPost(HttpServletRequest request, HttpServletResponse response)
 		throws ServletException, IOException



From gss at pub.open-bio.org  Mon Jun 14 16:59:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 16:59:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142059.i5EKxaxO011055@pub.open-bio.org>


gss
Mon Jun 14 16:59:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev
In directory pub.open-bio.org:/tmp/cvs-serv10990/src/org/smoby/ref/servlets/dev

Modified Files:
	OWLValidationServlet.java MOBYGraphValidationServlet.java 
	GraphConversionServlet.java RepositoryPrintServlet.java 
	ProviderListServlet.java 
Log Message:
Make subclass of new common superclass BaseServlet

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev OWLValidationServlet.java,1.2,1.3 MOBYGraphValidationServlet.java,1.2,1.3 GraphConversionServlet.java,1.2,1.3 RepositoryPrintServlet.java,1.1,1.2 ProviderListServlet.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java	2004/06/14 20:59:36	1.3
@@ -1,5 +1,6 @@
 package org.smoby.ref.servlets.dev;
 
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.servlet.ParamReader;
 import org.smoby.servlet.ParameterException;
 
@@ -13,7 +14,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class OWLValidationServlet extends HttpServlet
+public class OWLValidationServlet extends BaseServlet
 {
 	public void doPost(HttpServletRequest request, HttpServletResponse response)
 		throws ServletException, IOException

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java	2004/06/14 20:59:36	1.3
@@ -1,6 +1,7 @@
 package org.smoby.ref.servlets.dev;
 
 import org.smoby.parser.Parser;
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.servlet.*;
 import org.smoby.graph.*;
 
@@ -11,7 +12,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class MOBYGraphValidationServlet extends HttpServlet
+public class MOBYGraphValidationServlet extends BaseServlet
 {
 	public void doPost(HttpServletRequest request, HttpServletResponse response)
 		throws ServletException, IOException

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java	2004/06/14 20:59:36	1.3
@@ -1,5 +1,6 @@
 package org.smoby.ref.servlets.dev;
 
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.servlet.ParamReader;
 import org.smoby.servlet.ParameterException;
 
@@ -9,7 +10,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class GraphConversionServlet extends HttpServlet
+public class GraphConversionServlet extends BaseServlet
 {
 	public void doPost(HttpServletRequest request, HttpServletResponse response)
 		throws ServletException, IOException

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java	2004/06/14 20:59:36	1.2
@@ -1,5 +1,6 @@
 package org.smoby.ref.servlets.dev;
 
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.ref.tools.db.*;
 
 import com.hp.hpl.jena.rdf.model.*;
@@ -8,7 +9,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class RepositoryPrintServlet extends HttpServlet
+public class RepositoryPrintServlet extends BaseServlet
 {
     public void doGet(HttpServletRequest request, HttpServletResponse response)
         throws ServletException, IOException

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/06/14 20:59:36	1.3
@@ -2,6 +2,7 @@
 
 import org.smoby.servlet.*;
 import org.smoby.tools.*;
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.ref.tools.db.*;
 import org.smoby.ref.tools.*;
 
@@ -11,7 +12,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class ProviderListServlet extends HttpServlet
+public class ProviderListServlet extends BaseServlet
 {
     public void doGet(HttpServletRequest request, HttpServletResponse response)
         throws ServletException, IOException



From gss at pub.open-bio.org  Mon Jun 14 17:07:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 17:07:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142107.i5EL7ZId011109@pub.open-bio.org>


gss
Mon Jun 14 17:07:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv11084

Modified Files:
	build.xml 
Log Message:
No longer need to copy properties files to WEB-INF/classes

moby-live/S-MOBY/ref-impl/server build.xml,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/06/10 23:15:37	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/06/14 21:07:35	1.4
@@ -16,11 +16,6 @@
         <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
-        <copy toDir="${classes-dir}">
-            <fileset dir="WebRoot">
-                <include name="*.properties"/>
-            </fileset>
-        </copy>
 	</target>
 
     <!-- Deploy the application to Tomcat -->



From gss at pub.open-bio.org  Mon Jun 14 18:04:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 18:04:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142204.i5EM4KjS011316@pub.open-bio.org>


gss
Mon Jun 14 18:04:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools
In directory pub.open-bio.org:/tmp/cvs-serv11291/WebRoot/tools

Modified Files:
	client.html 
Log Message:
Added radio buttons on Discover form

moby-live/S-MOBY/ref-impl/server/WebRoot/tools client.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html	2004/03/30 22:25:51	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html	2004/06/14 22:04:20	1.2
@@ -24,8 +24,14 @@
 
 <h4><u>Discover matching graphs in the S-MOBY metadata repository</u></h4>
 <form action="http://www.s-moby.org:8080/find-providers" method="post">
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Paste a graph in RDF/XML format
-  and press "Discover" to find matching graphs. &nbsp;&nbsp;
+  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Paste a graph in RDF/XML format, select
+  statements to return, and press "Discover" to find matching graphs. &nbsp;&nbsp;
+  <p>
+  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+  Statements to return:&nbsp;&nbsp;
+  <input type="radio" name="statements" value="minimal">Minimal&nbsp;&nbsp;
+  <input type="radio" name="statements" value="query" CHECKED>Query only&nbsp;&nbsp;
+  <input type="radio" name="statements" value="cached">Cached&nbsp;&nbsp;
   <input value="Discover" type="submit">
   <p>
   &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;



From mwilkinson at pub.open-bio.org  Mon Jun 14 20:08:14 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 20:08:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150008.i5F08EAc011629@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:08:14 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11614

Added Files:
	Config.pm 
Log Message:
added a configuration module.  MOBY Central will no longer use environment variables to get the database connection information

moby-live/Perl/MOBY Config.pm,NONE,1.1


From mwilkinson at pub.open-bio.org  Mon Jun 14 20:09:37 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 20:09:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150009.i5F09bw9011701@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:09:36 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11678

Modified Files:
	Central.pm Central.html 
Log Message:
modified the way Central gets its configuration.  Also fixed a bug that allowed object names to be registered with spaces

moby-live/Perl/MOBY Central.pm,1.127,1.128 Central.html,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.127
retrieving revision 1.128
diff -u -r1.127 -r1.128
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/04/20 23:24:25	1.127
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/15 00:09:36	1.128
@@ -18,6 +18,7 @@
 use MOBY::authority;
 use MOBY::service_instance;
 use MOBY::central_db_connection;
+use MOBY::Config;
 
 my $debug = 0;
 
@@ -72,6 +73,43 @@
 Servers/Services, or queryiong for available services given certain input/output
 or service type constraints.
 
+=cut
+
+
+=head1 CONFIGURATION
+
+This depends on a config file to get its database connection information.  At a minimum
+this config file must have the following clause:
+
+ [mobycentral]
+ url = some.url 
+ username = foo
+ password = bar
+ port = portnumber
+ dbname = mobycentral
+
+
+The space before and after the '=' is critical.
+
+The end of a clause is indicated by a blank line.
+
+Additional identically formatted clauses may be added for each of:
+
+  [mobyobject]
+  [mobynamespace]
+  [mobyservice]
+  [mobyrelationship]
+
+if these ontologies are being served from a local database (via the
+OntologyServer module).  These clauses will be read by the OntologyServer
+module if they are present, otherwise default connections will be made
+to the MOBY Central ontology server.
+
+The config file must be readable by the webserver, and the webserver
+environment should include the following ENV variable:
+
+$ENV{MOBY_CENTRAL_CONFIG} = /path/to/config/file.name
+
 
 =head1 AUTHORS
 
@@ -141,21 +179,20 @@
 }
 
 sub _dbAccess {
-	
-# this configuration system was stoopid and is now defunkt.
-	
-#    my $filename = "./MOBY/central.cfg";# $self->config;
-#	$debug && &_LOG("trying to open file $filename\n");
-#	open (IN, $filename) || die "can't open configuration file $filename:  $!";
-#	my $url = <IN>; chomp $url;
-#	my $dbname = <IN>; chomp $dbname;
-#	my $username = <IN>; chomp $username;
-#	my $password = <IN>; chomp $password;
-	my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
-	my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
-	my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
-	my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
-	my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
+
+    my $conf = MOBY::Config->new;
+
+    $username = $conf->{mobycentral}->{username};
+    $password = $conf->{mobycentral}->{password};
+    $port = $conf->{mobycentral}->{port};
+    $dbname = $conf->{mobycentral}->{dbname};
+    $url = $conf->{mobycentral}->{url};
+    
+	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
+	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
+	#my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
+	#my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
+	#my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
 	
 	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
 	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
@@ -237,6 +274,10 @@
 	return &_error("Malformed authURI - must not have an http:// prefix","") if $auth =~ '[/:]';
 	return &_error("Malformed authURI - must take the form NNN.NNN.NNN","") unless $auth =~ /\./;
 	return &_error("Malformed email - must be a valid email address of the form name\@organization.foo","") unless $email =~ /\S\@\S+\.\S+/;
+	return &_error("Object name may not contain spaces or other characters invalid in a URN","") if $term =~ /\s\"\&\<\>\[\]\^\`\{\|\}\~/;
+	if ($term =~ m"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?"){  # matches a URI
+        return &_error("Object name may not be an URN or URI","") if $1;
+    }
 
 	# validate that the final ontology will be valid by testing against existing relationships and such
 	while (my ($reltype, $obj) = each %{$relationships}){

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.html,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOBY/Central.html	2004/04/15 14:38:22	1.13
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.html	2004/06/15 00:09:36	1.14
@@ -15,6 +15,7 @@
 	<li><a href="#name">NAME</a></li>
 	<li><a href="#synopsis">SYNOPSIS</a></li>
 	<li><a href="#description">DESCRIPTION</a></li>
+	<li><a href="#configuration">CONFIGURATION</a></li>
 	<li><a href="#authors">AUTHORS</a></li>
 	<li><a href="#registration_xml_object">Registration XML Object</a></li>
 	<li><a href="#methods">METHODS</a></li>
@@ -107,6 +108,34 @@
 <p>
 </p>
 <hr />
+<h1><a name="configuration">CONFIGURATION</a></h1>
+<p>This depends on a config file to get its database connection information.  At a minimum
+this config file must have the following clause:</p>
+<pre>
+ [mobycentral]
+ url = some.url 
+ username = foo
+ password = bar
+ port = portnumber
+ dbname = mobycentral</pre>
+<p>The space before and after the '=' is critical.</p>
+<p>The end of a clause is indicated by a blank line.</p>
+<p>Additional identically formatted clauses may be added for each of:</p>
+<pre>
+  [mobyobject]
+  [mobynamespace]
+  [mobyservice]
+  [mobyrelationship]</pre>
+<p>if these ontologies are being served from a local database (via the
+OntologyServer module).  These clauses will be read by the OntologyServer
+module if they are present, otherwise default connections will be made
+to the MOBY Central ontology server.</p>
+<p>The config file must be readable by the webserver, and the webserver
+environment should include the following ENV variable:</p>
+<p>$ENV{MOBY_CENTRAL_CONFIG} = /path/to/config/file.name</p>
+<p>
+</p>
+<hr />
 <h1><a name="authors">AUTHORS</a></h1>
 <p>Mark Wilkinson (<a href="mailto:markw at illuminae.com">markw at illuminae.com</a>)</p>
 <p>BioMOBY Project:  <a href="http://www.biomoby.org">http://www.biomoby.org</a></p>



From mwilkinson at pub.open-bio.org  Mon Jun 14 20:22:05 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 20:22:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150022.i5F0M5db011857@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:22:05 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11838

Modified Files:
	OntologyServer.pm 
Log Message:
OntologyServer now reads the config file as well

moby-live/Perl/MOBY OntologyServer.pm,1.41,1.42
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.41
retrieving revision 1.42
diff -u -r1.41 -r1.42
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/05/11 15:48:45	1.41
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 00:22:05	1.42
@@ -74,6 +74,7 @@
 use vars qw($AUTOLOAD);
 use DBI;
 use DBD::mysql;
+use MOBY::Config;
 
 my $debug = 0;
 
@@ -139,6 +140,14 @@
     $self->ontology eq 'service' && $self->database('mobyservice');
     $self->ontology eq 'relationship' && $self->database('mobyrelationship');
 
+	
+	my $conf = MOBY::Config->new;
+	$self->username = $conf->{$self->database}->{username} unless $self->username;
+    $self->password = $conf->{$self->database}->{password} unless $self->password;
+    $self->port = $conf->{$self->database}->{port} unless $self->port;
+    $self->dbname = $self->database unless $self->dbname;
+    $self->host = $conf->{$self->database}->{url} unless $self->host;
+ 
 	my $host = $self->host?$self->host:$ENV{MOBY_CENTRAL_URL}; chomp $host;
 	my $username = $self->username?$self->username:$ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
 	my $password = $self->password?$self->password:$ENV{MOBY_CENTRAL_DBPASS}; chomp $password if $password; $password =~ s/\s//g if $password;



From mwilkinson at pub.open-bio.org  Mon Jun 14 20:37:55 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 20:37:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150037.i5F0btA2011994@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:37:55 EDT 2004
Update of /home/repository/moby/moby-live/Perl
In directory pub.open-bio.org:/tmp/cvs-serv11975

Modified Files:
	MANIFEST 
Log Message:
using config file here too

moby-live/Perl MANIFEST,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MANIFEST,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MANIFEST	2004/03/18 23:10:34	1.9
+++ /home/repository/moby/moby-live/Perl/MANIFEST	2004/06/15 00:37:55	1.10
@@ -6,6 +6,7 @@
 MOBY/central_db_connection.pm
 MOBY/mysql.pm
 MOBY/OntologyServer.pm
+MOBY/Config.pm
 MOBY/CommonSubs.pm
 MOBY/CrossReference.pm
 MOBY/service_instance.pm



From mwilkinson at pub.open-bio.org  Mon Jun 14 20:37:55 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 20:37:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150037.i5F0btjl012018@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:37:55 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11975/MOBY

Modified Files:
	CommonSubs.pm central_db_connection.pm 
Log Message:
using config file here too

moby-live/Perl/MOBY CommonSubs.pm,1.51,1.52 central_db_connection.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.51
retrieving revision 1.52
diff -u -r1.51 -r1.52
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/04 23:54:16	1.51
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/06/15 00:37:55	1.52
@@ -200,6 +200,7 @@
     getResponseArticles
     getCrossReferences
     genericServiceInputParser
+    genericServiceInputParserAsObject
     complexServiceInputParser
     whichDeepestParentObject
     getServiceNotes
@@ -233,6 +234,7 @@
     getResponseArticles
     getCrossReferences
     genericServiceInputParser
+    genericServiceInputParserAsObject
     complexServiceInputParser
     whichDeepestParentObject
     getServiceNotes
@@ -327,6 +329,48 @@
 
 
 
+=head2 serviceInputParser
+
+ name     : DO NOT USE!!
+ function : to take a MOBY message and break the objects out of it.  This is identical
+            to the genericServiceInputParser method above, except that it returns the data as
+            Objects rather than XML::DOM nodes.  This is an improvement!
+ usage    : my @inputs = serviceInputParser($MOBY_mssage));
+ args     : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message
+ returns  : @inputs - the structure of @inputs is a list of listrefs.
+            Each listref has three components:
+                1. COLLECTION|SIMPLE|SECONDARY (i.e. constants 1, 2, 3)
+                2. queryID (undef for Secondary parameters)
+                3. $data - either MOBY::Client::SimpleArticle, CollectionArticle, or SecondaryArticle
+
+=cut
+
+
+sub serviceInputParser {
+    my ($message) = @_;  # get the incoming MOBY query XML
+    my @inputs;           # set empty response
+    my @queries = getInputs($message);  # returns XML::DOM nodes <mobyData>...</mobyData>
+
+
+# mark, this doesn't work for complex services.  We need to allow more than one input per invocation
+    foreach my $query(@queries){
+        my $queryID = getInputID($query);  # get the queryID attribute of the mobyData
+        my @input_articles = getArticlesAsObjects($query); # get the Simple/Collection articles making up this query <Simple>...</Simple> or <Collection>...</Collection> or <Parameter>...</Parameter
+        foreach my $article(@input_articles){       # input is a listref
+            if ($article->isCollection){
+                my @simples = getCollectedSimples($article->XML);
+                push @inputs, [COLLECTION,$queryID, \@simples];
+            } elsif ($article->isSimple){
+                push @inputs, [SIMPLE,$queryID,$article];
+            } elsif ($article->isSecondary){
+                push @inputs, [SECONDARY,$queryID,$article];
+            }
+        }
+    }
+    return @inputs;
+}
+
+
 =head2 complexServiceInputParser
 
  name     : complexServiceInputParser
@@ -487,46 +531,6 @@
 
 
 
-=head2 genericServiceInputParserAsObject
-
- name     : DO NOT USE!
- function : to take a MOBY message and break the objects out of it.  This is identical
-            to the subroutine above, except that it returns the data as
-            Objects rather than XML::DOM nodes
- usage    : my @inputs = genericServiceInputParser($MOBY_mssage));
- args     : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message
- returns  : @inputs - the structure of @inputs is a list of listrefs.
-            Each listref has three components:
-                1. COLLECTION|SIMPLE|SECONDARY (i.e. constants 1, 2, 3)
-                2. queryID (undef for Secondary parameters)
-                3. $data - either MOBY::Client::SimpleArticle, CollectionArticle, or SecondaryArticle
-
-=cut
-
-
-sub genericServiceInputParserAsObject {
-    my ($message) = @_;  # get the incoming MOBY query XML
-    my @inputs;           # set empty response
-    my @queries = getInputs($message);  # returns XML::DOM nodes <mobyData>...</mobyData>
-
-    foreach my $query(@queries){
-        my $queryID = getInputID($query);  # get the queryID attribute of the mobyData
-        my @input_articles = getArticlesAsObjects($query); # get the Simple/Collection articles making up this query <Simple>...</Simple> or <Collection>...</Collection> or <Parameter>...</Parameter
-        foreach my $article(@input_articles){       # input is a listref
-            if ($article->isCollection){
-                my @simples = getCollectedSimples($article->XML);
-                push @inputs, [COLLECTION,$queryID, \@simples];
-            } elsif ($article->isSimple){
-                push @inputs, [SIMPLE,$queryID,$article];
-            } elsif ($article->isSecondary){
-                push @inputs, [SECONDARY,$queryID,$article];
-            }
-        }
-    }
-    return @inputs;
-}
-
-
 #################################################
 					 ##################################
 					 ##################################

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2003/06/10 17:12:52	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/15 00:37:55	1.3
@@ -3,7 +3,7 @@
 use Carp;
 use XML::DOM;
 use vars qw($AUTOLOAD @ISA);
-
+use MOBY::Config;
 
 =head1 NAME
 
@@ -116,6 +116,26 @@
     #    $self->host,
     #    $self->port);
 
+
+    my $conf = MOBY::Config->new;
+
+    $username = $conf->{mobycentral}->{username};
+    $password = $conf->{mobycentral}->{password};
+    $port = $conf->{mobycentral}->{port};
+    $dbname = $conf->{mobycentral}->{dbname};
+    $url = $conf->{mobycentral}->{url};
+    
+	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
+	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
+	#my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
+	#my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
+	#my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
+	
+	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
+	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
+	
+	return ($dbh);
+
 	my $host = $ENV{MOBY_CENTRAL_URL}; chomp $host;
 	my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
 	my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;



From mwilkinson at pub.open-bio.org  Mon Jun 14 20:37:55 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 20:37:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150037.i5F0btFP012043@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:37:55 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv11975/MOBY/Client

Modified Files:
	CollectionArticle.pm SimpleArticle.pm 
Log Message:
using config file here too

moby-live/Perl/MOBY/Client CollectionArticle.pm,1.7,1.8 SimpleArticle.pm,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm	2004/04/14 19:56:59	1.7
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm	2004/06/15 00:37:55	1.8
@@ -9,12 +9,39 @@
 
 =head1 NAME
 
-MOBY::Client::CollectionArticle - a small object describing the Collection articles from the findService Response message of MOBY Central
+MOBY::Client::CollectionArticle - a small object describing the Collection articles from the findService Response message of MOBY Central or representing the collection part of a MOBY invocation or response block
 
 =head1 SYNOPSIS
 
-experimental - please do not use in your code
+This module can be used in two ways.  One is to represent the Collection
+portion of a findService response.  The other is to represent the Collecion
+portion of a MOBY service invocation or response message.
+
+Parsing a MOBY Service Invocation
+
+ use MOBY::CommonSubs qw(:all);
+ 
+ sub myService {
+    my ($caller, $data) = @_;
+	
+    my (@inputs)= serviceInputParser($data);
+
+    foreach (@inputs){
+        my ($articleType, $qID, $OBJECT) = @{$_};
+        if ($articleType == COLLECTION){
+            $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;  # send back a blank response for this queryID
+            next;
+        } elsif ($articleType == SIMPLE) {
+        
+        } elsif ($articleType == SECONDARY){
+        
+        }
+    }
+ }
 
+ 
+ 
+ 
 =cut
 
 =head1 DESCRIPTION

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm	2004/04/14 19:56:59	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm	2004/06/15 00:37:55	1.5
@@ -328,6 +328,11 @@
     return $self;
 }
 
+sub value {
+    my ($self) = @_;
+    # ?????  what to do here ????
+    
+}
 sub AUTOLOAD {
     no strict "refs";
     my ($self, $newval) = @_;



From mwilkinson at pub.open-bio.org  Mon Jun 14 21:00:26 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 21:00:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150100.i5F10QMf012399@pub.open-bio.org>


mwilkinson
Mon Jun 14 21:00:26 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv12372/MOBY

Modified Files:
	Central.pm OntologyServer.pm central_db_connection.pm 
Log Message:
a few bugfixes for undeclared variables etc

moby-live/Perl/MOBY Central.pm,1.128,1.129 OntologyServer.pm,1.42,1.43 central_db_connection.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.128
retrieving revision 1.129
diff -u -r1.128 -r1.129
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/15 00:09:36	1.128
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/15 01:00:26	1.129
@@ -182,11 +182,11 @@
 
     my $conf = MOBY::Config->new;
 
-    $username = $conf->{mobycentral}->{username};
-    $password = $conf->{mobycentral}->{password};
-    $port = $conf->{mobycentral}->{port};
-    $dbname = $conf->{mobycentral}->{dbname};
-    $url = $conf->{mobycentral}->{url};
+    my $username = $conf->{mobycentral}->{username};
+    my $password = $conf->{mobycentral}->{password};
+    my $port = $conf->{mobycentral}->{port};
+    my $dbname = $conf->{mobycentral}->{dbname};
+    my $url = $conf->{mobycentral}->{url};
     
 	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
 	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.42
retrieving revision 1.43
diff -u -r1.42 -r1.43
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 00:22:05	1.42
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 01:00:26	1.43
@@ -142,11 +142,10 @@
 
 	
 	my $conf = MOBY::Config->new;
-	$self->username = $conf->{$self->database}->{username} unless $self->username;
-    $self->password = $conf->{$self->database}->{password} unless $self->password;
-    $self->port = $conf->{$self->database}->{port} unless $self->port;
-    $self->dbname = $self->database unless $self->dbname;
-    $self->host = $conf->{$self->database}->{url} unless $self->host;
+	$self->username($conf->{$self->database}->{username}) unless $self->username;
+    $self->password($conf->{$self->database}->{password}) unless $self->password;
+    $self->port($conf->{$self->database}->{port}) unless $self->port;
+    $self->host($conf->{$self->database}->{url}) unless $self->host;
  
 	my $host = $self->host?$self->host:$ENV{MOBY_CENTRAL_URL}; chomp $host;
 	my $username = $self->username?$self->username:$ENV{MOBY_CENTRAL_DBUSER}; chomp $username;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/15 00:37:55	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/15 01:00:26	1.4
@@ -119,40 +119,17 @@
 
     my $conf = MOBY::Config->new;
 
-    $username = $conf->{mobycentral}->{username};
-    $password = $conf->{mobycentral}->{password};
-    $port = $conf->{mobycentral}->{port};
-    $dbname = $conf->{mobycentral}->{dbname};
-    $url = $conf->{mobycentral}->{url};
-    
-	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
-	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
-	#my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
-	#my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
-	#my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
-	
+    my $username = $conf->{mobycentral}->{username};
+    my $password = $conf->{mobycentral}->{password};
+    my $port = $conf->{mobycentral}->{port};
+    my $dbname = $conf->{mobycentral}->{dbname};
+    my $url = $conf->{mobycentral}->{url};
+    	
 	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
 	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
 	
-	return ($dbh);
-
-	my $host = $ENV{MOBY_CENTRAL_URL}; chomp $host;
-	my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
-	my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
-	my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
-    my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
-    
-    #my $dbname = $self->dbname;
-    #my $host = $self->host;
-    #my $port = $self->port;
-    #my $username = $self->username;
-    #my $password = $self->password;
-    my ($dsn) = "DBI:mysql:$dbname:$host:$port";
-
-    my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
-
     $self->dbh($dbh);
-    return $self;
+	return $self;
 
 }
 



From mwilkinson at pub.open-bio.org  Mon Jun 14 21:15:16 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 21:15:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150115.i5F1FGWS012533@pub.open-bio.org>


mwilkinson
Mon Jun 14 21:15:16 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv12514/MOBY

Modified Files:
	Config.pm 
Log Message:
Doh.  I hard-coded a testing path in there.

moby-live/Perl/MOBY Config.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Config.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/Config.pm	2004/06/15 00:08:14	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/Config.pm	2004/06/15 01:15:16	1.2
@@ -65,7 +65,6 @@
     }
 
     my $file = $ENV{MOBY_CENTRAL_CONFIG};
-    $file = "/home/markw/conf.conf";
     chomp $file;
     if ((-e $file) && (!(-d $file))){
         open IN, $file || die "can't open MOBY Configuration file $!\n";



From mwilkinson at pub.open-bio.org  Tue Jun 15 10:55:17 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 15 Jun 2004 10:55:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406151455.i5FEtHJL014835@pub.open-bio.org>


mwilkinson
Tue Jun 15 10:55:17 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv14816/MOBY

Modified Files:
	OntologyServer.pm 
Log Message:
be sure to extract the database name from the config file in the case of a non-standard installation of the registry

moby-live/Perl/MOBY OntologyServer.pm,1.43,1.44
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.43
retrieving revision 1.44
diff -u -r1.43 -r1.44
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 01:00:26	1.43
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 14:55:17	1.44
@@ -152,7 +152,7 @@
 	my $password = $self->password?$self->password:$ENV{MOBY_CENTRAL_DBPASS}; chomp $password if $password; $password =~ s/\s//g if $password;
     my $port = $self->port?$self->port:$ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
     
-    my ($dsn) = "DBI:mysql:".($self->database).":".($host).":".($port);
+    my ($dsn) = "DBI:mysql:".($conf->{$self->database}->{dbname}).":".($host).":".($port);
 
     my $dbh;
 #	$debug && &_LOG("connecting to db with params ",$self->database, $self->username, $self->password,"\n");



From mwilkinson at pub.open-bio.org  Tue Jun 15 21:15:30 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 15 Jun 2004 21:15:30 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406160115.i5G1FU0T016502@pub.open-bio.org>


mwilkinson
Tue Jun 15 21:15:30 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv16447/MOBY/Client

Modified Files:
	Central.pm SecondaryArticle.pm 
Added Files:
	SimpleInput.pm 
Log Message:
all sorts of additions and changes.  Secondary parameters now work for me on two systems, so that problem should now be solved.  I am starting to rip out the SQL that is in MOBY Central into other modules, and it will eventually end up in a single mysql-specific module with an API to make it easier to code MOBY onto other data back-ends.  Various bug fixes here and there as well.

moby-live/Perl/MOBY/Client SimpleInput.pm,NONE,1.1 Central.pm,1.75,1.76 SecondaryArticle.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.75
retrieving revision 1.76
diff -u -r1.75 -r1.76
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/05/03 19:49:18	1.75
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/06/16 01:15:30	1.76
@@ -10,6 +10,7 @@
 use MOBY::Client::Registration;
 use MOBY::Client::SimpleArticle;
 use MOBY::Client::CollectionArticle;
+use MOBY::Client::SecondaryArticle;
 use MOBY::Client::OntologyServer;
 
 use vars qw($AUTOLOAD @ISA $MOBY_server $MOBY_uri);
@@ -722,8 +723,8 @@
 
 	if ($Category eq "moby" || $Category eq 'soap') {
 		my %SEC;
-		if ($a{'secondary'} && ref($a{'secondary'} =~ /hash/i)){
-			%SEC = %{$a{secondary}}
+		if ($a{'secondary'} && (ref($a{'secondary'}) =~ /hash/i)){
+			%SEC = %{$a{secondary}};
 		} elsif ($a{'secondary'} && !(ref($a{'secondary'}) =~ /hash/i)){
 			return $self->errorRegXML("invalid structure of secondary parameters.  Expected hashref.")
 		}
@@ -799,13 +800,14 @@
 			my $min = $data{min};
 			my $datatype = $data{datatype};
 			unless ($datatype){return $self->errorRegXML("a secondaryArticle must contain at least a datatype value in secondary article $param");}
+			unless (($datatype =~ /Integer/) || ($datatype =~ /Float/) || ($datatype =~ /String/) || ($datatype =~ /DateTime/)){return $self->errorRegXML("a secondaryArticle must have a datatype of Integer, Float, String, or DateTime");}
 			unless ((ref($data{enum})) =~ /array/i){return $self->errorRegXML("invalid structure of enum limits in secondary article $param; expected arrayref")}
 			my @enums = @{$data{enum}};
 			$message .="<Parameter articleName='$param'>\n";
 			$message .="<default>$default</default>\n";
 			$message .="<datatype>$datatype</datatype>\n";
-			$message .="<max></max>\n";
-			$message .="<min></min>\n";
+			$message .="<max>$max</max>\n";
+			$message .="<min>$min</min>\n";
 			foreach (@enums){
 				$message .="<enum>$_</enum>\n";
 			}

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm	2004/05/03 19:49:18	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm	2004/06/16 01:15:30	1.2
@@ -185,7 +185,7 @@
 
     sub addEnum {
         my ($self, $enum) = @_;
-        return $self->{enum} unless $enum;
+        return $self->{enum} unless defined($enum);
         push @{$self->{enum}}, $enum;
         return $self->{enum};
     }
@@ -265,36 +265,46 @@
 
     my $objects = $dom->getElementsByTagName("datatype");
     if ($objects->item(0)){
+        my $data;
         foreach my $child($objects->item(0)->getChildNodes){ 
             next unless $child->getNodeType == TEXT_NODE;
-            $self->datatype($self->datatype . $child->toString);
+            $data .= $child->toString;
+            $data =~ s/\s//g;
         }
+        $self->datatype($data);
     }
-    $self->datatype($self->datatype =~ s/^\s//);
-    $self->datatype($self->datatype =~ s/\s$//);
     
     $objects = $dom->getElementsByTagName("default");
     if ($objects->item(0)){
+        my $def;
         foreach my $child($objects->item(0)->getChildNodes){ 
             next unless $child->getNodeType == TEXT_NODE;
-            $self->default($self->default . $child->toString);
+            $def .= $child->toString;
+            $def =~ s/\s//g;
         }
+        $self->default($def);
     }
     
     $objects = $dom->getElementsByTagName("max");
     if ($objects->item(0)){
+        my $max;
         foreach my $child($objects->item(0)->getChildNodes){ 
             next unless $child->getNodeType == TEXT_NODE;
-            $self->max($self->max . $child->toString);
+            $max .= $child->toString;
+            $max =~ s/\s//g;
         }
+        $self->max($max);
     }
     
     $objects = $dom->getElementsByTagName("min");
     if ($objects->item(0)){
+        my $min;
         foreach my $child($objects->item(0)->getChildNodes){ 
             next unless $child->getNodeType == TEXT_NODE;
-            $self->min($self->min . $child->toString);
+            $min .= $child->toString;
+            $min =~ s/\s//g;
         }
+        $self->min($min);
     }
     
     $objects = $dom->getElementsByTagName("enum");
@@ -303,7 +313,8 @@
             foreach my $child($objects->item($_)->getChildNodes){
                 my $val;
                 next unless $child->getNodeType == TEXT_NODE;
-                next unless $val = $child->toString;
+                $val = $child->toString;
+                next unless defined($val);
                 $val =~ s/^\s//; $val =~ s/\s$//;
                 $self->addEnum($val);
             }



From mwilkinson at pub.open-bio.org  Tue Jun 15 21:15:30 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 15 Jun 2004 21:15:30 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406160115.i5G1FURZ016478@pub.open-bio.org>


mwilkinson
Tue Jun 15 21:15:30 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv16447/MOBY

Modified Files:
	Central.pm service_instance.pm simple_input.pm 
	simple_output.pm 
Added Files:
	collection_input.pm collection_output.pm secondary_input.pm 
Log Message:
all sorts of additions and changes.  Secondary parameters now work for me on two systems, so that problem should now be solved.  I am starting to rip out the SQL that is in MOBY Central into other modules, and it will eventually end up in a single mysql-specific module with an API to make it easier to code MOBY onto other data back-ends.  Various bug fixes here and there as well.

moby-live/Perl/MOBY collection_input.pm,NONE,1.1 collection_output.pm,NONE,1.1 secondary_input.pm,NONE,1.1 Central.pm,1.129,1.130 service_instance.pm,1.3,1.4 simple_input.pm,1.2,1.3 simple_output.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.129
retrieving revision 1.130
diff -u -r1.129 -r1.130
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/15 01:00:26	1.129
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/16 01:15:30	1.130
@@ -17,6 +17,11 @@
 use MOBY::service_type;
 use MOBY::authority;
 use MOBY::service_instance;
+use MOBY::simple_input;
+use MOBY::simple_output;
+use MOBY::collection_input;
+use MOBY::collection_output;
+use MOBY::secondary_input;
 use MOBY::central_db_connection;
 use MOBY::Config;
 
@@ -1150,7 +1155,7 @@
 	return &_error("Service with this authority/servicename already exists","") if ($SVC == -1);
 
 	$debug && &_LOG("new service instance created\n");
-	
+    
 	foreach my $IN(@IN){
 		my ($success,$msg) = &_registerArticles($SVC, "input", $IN, undef); 
 		return &_error("Registration Failed During INPUT Article Registration: $msg","") unless ($success==1);
@@ -1160,7 +1165,7 @@
 		return &_error("Registration Failed During OUTPUT Article Registration: $msg","") unless ($success==1);
 	}
 	foreach my $SEC(@SECS){
-		my ($success,$msg) = &_registerArticles($SVC, "secondary", $SEC, undef); 
+    	my ($success,$msg) = &_registerArticles($SVC, "secondary", $SEC, undef); 
 		return &_error("Registration Failed During SECONDARY Article Registration: $msg","") unless ($success==1);
 	}
 	
@@ -1172,7 +1177,7 @@
     my $dbh = $SVC->dbh;
     return  (-1,'Bad node') unless $node->getNodeType == ELEMENT_NODE;
 
-    # this is a Simple or a Collection object
+    # this is a Simple, Collection, or Parameter object
     my $simp_coll = $node->getTagName;
 	$debug && &_LOG("TAGNAME in $inout _registerArticle is $simp_coll");
 	
@@ -1183,9 +1188,20 @@
     my ($object_type, @namespaces);
 
     if ($simp_coll eq "Collection"){
-		$debug && &_LOG("Collection!\n");  # the following SQl belongs in the service_instance object, but screw it, I'm running out of time!
-		$dbh->do("insert into collection_$inout (service_instance_id, article_name) values (?,?)", undef, ($SVC->service_instance_id, $article));
-		my $collection_id=$dbh->{mysql_insertid};
+		$debug && &_LOG("Collection!\n");
+        my $collection_id;
+        if ($inout eq 'input'){
+            $collection_id = $SVC->add_collection_input(article_name => $article);
+        } elsif ($inout eq 'output') {
+            $collection_id = $SVC->add_collection_output(article_name => $article);            
+        } else {
+            $SVC->DELETE_THYSELF; return (-1,"found article that was neither input nor output");
+        }
+        
+        # the following SQl belongs in the service_instance object, but screw it, I'm running out of time!
+		#$dbh->do("insert into collection_$inout (service_instance_id, article_name) values (?,?)", undef, ($SVC->service_instance_id, $article));
+		#my $collection_id=$dbh->{mysql_insertid};
+        
 		my $Simples = $node->getElementsByTagName('Simple');
 		my $length = $Simples->getLength;
 		for (my $x=0; $x<$length; ++$x){
@@ -1227,67 +1243,88 @@
 		chop($namespace_string);  # remove trailing comma
 		my $dbh = $SVC->dbh;
 		my $service_instance_id;
-		unless ($collid) {
+		unless ($collid) {  # this SIMPLE is either alone, or is part of a COLLECTION ($collid > 0)
+                            # therefore we want either its service instance ID, or its Collection ID.
 			$service_instance_id = $SVC->service_instance_id;
 		}				# one or the other, but not both
-		$dbh->do("insert into simple_".$inout."
-				 (object_type_uri,
-				  namespace_type_uris,
-				  article_name,
-				  service_instance_id,
-				  collection_".$inout."_id)
-				 values (?,?,?,?,?)",
-		undef,
-		($typeURI,
-		$namespace_string,
-		$article,
-		$service_instance_id,
-		$collid));
-
+        
+        if ($inout eq 'input'){
+            my $sinput = $SVC->add_simple_input(
+                    object_type_uri	=> $typeURI,
+                    namespace_type_uris	=> $namespace_string,
+                    article_name 	=> $article,
+                    collection_input_id 	=> 	$collid,
+                    );
+            unless ($sinput){
+       			$SVC->DELETE_THYSELF; return (-1,"registration failed during registration of input object $typeURI.  Unknown reasons.");
+            }
+
+        } elsif ($inout eq 'output'){
+            my $soutput = $SVC->add_simple_output(
+                    object_type_uri	=> $typeURI,
+                    namespace_type_uris	=> $namespace_string,
+                    article_name 	=> $article,
+                    collection_input_id 	=> 	$collid,
+                    );
+            unless ($soutput){
+       			$SVC->DELETE_THYSELF; return (-1,"registration failed during registration of output object $typeURI.  Unknown reasons.");
+            }
+        }
+        
     } elsif ($simp_coll eq "Parameter"){
-	    my $article = $node->getAttributeNode("articleName");
-		$article = $article->getValue() if $article;
-        my $types =  $node->getElementsByTagName('datatype');
-	    my ($datatype, $def, $max, $min, @enums);
+        my $parameter = $node;
+        my $article = $parameter->getAttributeNode("articleName");
+        $article = $article->getValue() if $article;
+        my ($datatype, $def, $max, $min, @enums);
+        my $types =  $parameter->getElementsByTagName('datatype');
         if ($types->item(0)){
-			foreach ($types->item(0)->getChildNodes){ # should only ever be one!
+            foreach ($types->item(0)->getChildNodes){ # should only ever be one!
             ($_->getNodeType == TEXT_NODE) && ($datatype = $_->toString);
-	        }
-		}
-        my $defs =  $node->getElementsByTagName('default');
+            }
+        }
+        my $defs =  $parameter->getElementsByTagName('default');
         if ($defs->item(0)){
-			foreach ($defs->item(0)->getChildNodes){ # should only ever be one!
-				($_->getNodeType == TEXT_NODE) && ($def = $_->toString);
-			}
-		}
-        my $maxs =  $node->getElementsByTagName('max');
+            foreach ($defs->item(0)->getChildNodes){ # should only ever be one!
+                ($_->getNodeType == TEXT_NODE) && ($def = $_->toString);
+            }
+        }
+        my $maxs =  $parameter->getElementsByTagName('max');
         if ($maxs->item(0)){
-			foreach ($maxs->item(0)->getChildNodes){ # should only ever be one!
-				($_->getNodeType == TEXT_NODE) && ($max = $_->toString);
-			}
-		}
-        my $mins =  $node->getElementsByTagName('min');
+            foreach ($maxs->item(0)->getChildNodes){ # should only ever be one!
+                ($_->getNodeType == TEXT_NODE) && ($max = $_->toString);
+            }
+        }
+        my $mins =  $parameter->getElementsByTagName('min');
         if ($mins->item(0)){
-			foreach ($mins->item(0)->getChildNodes){ # should only ever be one!
-				($_->getNodeType == TEXT_NODE) && ($min = $_->toString);
-			}
-		}
-        my $enums =  $node->getElementsByTagName('enum');
-		my $numenums = $enums->getLength;
-		for (my $n=0;$n<$numenums;++$n){
-			foreach ($enums->item($n)->getChildNodes){ # should only ever be one!
-				($_->getNodeType == TEXT_NODE) && (push @enums, $_->toString);
-			}
-		}
-		my $enum_string = join "",(map {$_.","} @enums);
-		chop $enum_string; # get rid of trailing comma
-		my $dbh = $SVC->dbh;
-		$dbh->do(q{insert into secondary_input (default_value,maximum_value,minimum_value,enum_value,datatype,article_name,service_instance_id) values (?,?,?,?,?,?,?)},
-				 undef,
-				 ($def, $max, $min, $enum_string, $datatype, $article, $SVC->service_instance_id));		
+            foreach ($mins->item(0)->getChildNodes){ # should only ever be one!
+                ($_->getNodeType == TEXT_NODE) && ($min = $_->toString);
+            }
+        }
+        my $enums =  $parameter->getElementsByTagName('enum');
+        my $numenums = $enums->getLength;
+        for (my $n=0;$n<$numenums;++$n){
+            foreach ($enums->item($n)->getChildNodes){ # should only ever be one!
+                ($_->getNodeType == TEXT_NODE) && (push @enums, $_->toString);
+            }
+        }
+        my $enum_string = join "",(map {$_.","} @enums);
+        chop $enum_string; # get rid of trailing comma
+        my $sec = $SVC->add_secondary_input(
+                    default_value => $def,
+                    maximum_value => $max,
+                    minimum_value => $min,
+                    enum_value   => $enum_string,
+                    datatype     => $datatype,
+                    article_name => $article,
+                                            );
+        unless ($sec){
+            $SVC->DELETE_THYSELF; return (-1,"registration failed during registration of parameter $article.  Must be of type Integer, String, DateTime, or Float.");
+        }       
 	}
 	return 1;
 }
+
+
 sub _registerServicePayload {
 	my ($payload) = @_;
 	my $Parser = new XML::DOM::Parser;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm	2003/12/02 00:23:23	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm	2004/06/16 01:15:30	1.4
@@ -43,7 +43,7 @@
 
 =head1 AUTHORS
 
-Mark Wilkinson (mwilkinson at gene.pbi.nrc.ca)
+Mark Wilkinson (mwilkinson at mrl.ubc.ca)
 
 
 =cut
@@ -321,6 +321,94 @@
     return $authority;
 }
 
+sub add_simple_input {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $simple = MOBY::simple_input->new(
+				object_type_uri	=> $a{'object_type_uri'},
+				namespace_type_uris	=> $a{'namespace_type_uris'},
+				article_name 	=> $a{'article_name'},
+				service_instance_id	=> 	$self->service_instance_id,
+				collection_input_id 	=> 	$a{'collection_input_id'}
+					   );
+
+	push @{$self->{inputs}}, $simple;
+	return $simple->simple_input_id;
+}
+
+
+sub add_simple_output {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $simple = MOBY::simple_output->new(
+				object_type_uri	=> $a{'object_type_uri'},
+				namespace_type_uris	=> $a{'namespace_type_uris'},
+				article_name 	=> $a{'article_name'},
+				service_instance_id	=> 	$self->service_instance_id,
+				collection_input_id 	=> 	$a{'collection_output_id'}
+					   );
+
+	push @{$self->{outputs}}, $simple;
+	return $simple->simple_output_id;
+}
+
+
+sub add_collection_input {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $coll = MOBY::collection_input->new(
+				article_name 	=> $a{'article_name'},
+				service_instance_id	=> 	$self->service_instance_id,
+					   );
+
+	push @{$self->{inputs}}, $coll;
+	return $coll->collection_input_id;
+}
+
+
+sub add_collection_output {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $coll = MOBY::collection_output->new(
+				article_name 	=> $a{'article_name'},
+				service_instance_id	=> 	$self->service_instance_id,
+					   );
+
+	push @{$self->{outputs}}, $coll;
+	return $coll->collection_output_id;
+}
+
+
+sub add_secondary_input {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $sec = MOBY::secondary_input->new(
+		default_value => $a{'default_value'},
+		maximum_value => $a{'maximum_value'},
+		minimum_value => $a{'minimum_value'},
+		enum_value   => $a{'enum_value'},
+		datatype     => $a{'datatype'},
+		article_name => $a{'article_name'},
+		service_instance_id => $self->service_instance_id,
+					   );
+
+	push @{$self->{inputs}}, $sec;
+	return $sec->secondary_input_id;	
+
+}
+
+
+
 sub AUTOLOAD {
     no strict "refs";
     my ($self, $newval) = @_;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm	2003/12/28 20:41:59	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm	2004/06/16 01:15:30	1.3
@@ -9,11 +9,13 @@
 
 =head1 NAME
 
-MOBY::authority - a lightweight connection to the
+MOBY::simple_input - a lightweight connection to the
 simple_input table in the database
 
 =head1 SYNOPSIS
 
+NON FUNCTIONAL AT THIS TIME
+
  use MOBY::simple_input;
  my $Instance = MOBY::simple_input->new(
           object_type => "Sequence",
@@ -28,7 +30,7 @@
 
 =head1 DESCRIPTION
 
-representation of the authority table.  Can write to the database
+representation of the simple_input table.  Can write to the database
 
 =head1 AUTHORS
 
@@ -46,11 +48,13 @@
 	#ATTRIBUTES
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
-                    object_type          => [undef,        'read/write'],
-                    namespaces => [undef,        'read/write'],
-                    article_name         => [undef,       'read/write'],
-                    simple_input_id         => [undef,       'read/write'],
-                    service_instance_id         => [undef,       'read/write'],
+				simple_input_id	=> 	[undef, 		'read/write'],
+				object_type_uri	=> 	[undef, 		'read/write'],
+				namespace_type_uris	=> 	[undef, 		'read/write'],
+				article_name 	=> 	[undef, 		'read/write'],
+				service_instance_id	=> 	[undef, 		'read/write'],
+				collection_input_id 	=> 	[undef, 		'read/write'],
+				dbh 	=> 	[undef, 		'read/write'],
 				);
 
    #_____________________________________________________________
@@ -76,6 +80,17 @@
 
 }
 
+
+sub _dbh {
+    my ($self) = @_;
+    
+    my $central_connect = MOBY::central_db_connection->new();
+	$self->dbh($central_connect->dbh);
+	return $central_connect->dbh;
+	
+}
+
+
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -95,10 +110,33 @@
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
 
+	my $id = $self->WRITE;
+	$self->simple_input_id($id) if defined $id;
     return $self;
 
 }
 
+sub WRITE {
+	my ($self) = @_;	
+	my $dbh = $self->_dbh;
+	
+	$dbh->do("insert into simple_input
+				 (object_type_uri,
+				  namespace_type_uris,
+				  article_name,
+				  service_instance_id,
+				  collection_input_id)
+				 values (?,?,?,?,?)",
+		undef,
+		($self->object_type_uri,
+		$self->namespace_type_uris,
+		$self->article_name,
+		$self->service_instance_id,
+		$self->collection_input_id));
+	my $id=$dbh->{mysql_insertid};
+	return $id;
+}
+
 
 sub AUTOLOAD {
     no strict "refs";

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm	2003/05/07 19:20:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm	2004/06/16 01:15:30	1.2
@@ -14,6 +14,7 @@
 
 =head1 SYNOPSIS
 
+NON FUNCTIONAL AT THIS TIME
  use MOBY::simple_output;
  my $Instance = MOBY::simple_output->new(
           object_type => "Sequence",
@@ -28,7 +29,7 @@
 
 =head1 DESCRIPTION
 
-representation of the authority table.  Can write to the database
+representation of the simple_output table.  Can write to the database
 
 =head1 AUTHORS
 
@@ -46,11 +47,13 @@
 	#ATTRIBUTES
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
-                    object_type          => [undef,        'read/write'],
-                    namespaces => [undef,        'read/write'],
-                    article_name         => [undef,       'read/write'],
-                    simple_output_id         => [undef,       'read/write'],
-                    service_instance_id         => [undef,       'read/write'],
+				simple_output_id	=> 	[undef, 		'read/write'],
+				object_type_uri	=> 	[undef, 		'read/write'],
+				namespace_type_uris	=> 	[undef, 		'read/write'],
+				article_name 	=> 	[undef, 		'read/write'],
+				service_instance_id	=> 	[undef, 		'read/write'],
+				collection_output_id 	=> 	[undef, 		'read/write'],
+				dbh 	=> 	[undef, 		'read/write'],
 				);
 
    #_____________________________________________________________
@@ -76,6 +79,18 @@
 
 }
 
+
+
+sub _dbh {
+    my ($self) = @_;
+    
+    my $central_connect = MOBY::central_db_connection->new();
+	$self->dbh($central_connect->dbh);
+	return $central_connect->dbh;
+	
+}
+
+
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -95,15 +110,31 @@
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
 
+	my $id = $self->WRITE;
+	$self->simple_output_id($id) if defined $id;
     return $self;
 
 }
 
-sub object_type
 sub WRITE {
-    my ($caller, $dbh) = @_;
-    my $sth = $dbh->prepare("insert into simple_input (object_type_id, namespace_type_ids, article_name, service_instance_id) values (?,?,?,?)");
-    
+	my ($self) = @_;
+	my $dbh = $self->_dbh;	
+	$dbh->do("insert into simple_output
+				 (object_type_uri,
+				  namespace_type_uris,
+				  article_name,
+				  service_instance_id,
+				  collection_output_id)
+				 values (?,?,?,?,?)",
+		undef,
+		($self->object_type_uri,
+		$self->namespace_type_uris,
+		$self->article_name,
+		$self->service_instance_id,
+		$self->collection_output_id));
+	my $id=$dbh->{mysql_insertid};
+	return $id;		
+
 }
 
 sub AUTOLOAD {



From mwilkinson at pub.open-bio.org  Tue Jun 15 21:15:30 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 15 Jun 2004 21:15:30 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406160115.i5G1FUai016521@pub.open-bio.org>


mwilkinson
Tue Jun 15 21:15:30 EDT 2004
Update of /home/repository/moby/moby-live/Perl/scripts
In directory pub.open-bio.org:/tmp/cvs-serv16447/scripts

Modified Files:
	testMOBYClientCentral_v05.pl 
Log Message:
all sorts of additions and changes.  Secondary parameters now work for me on two systems, so that problem should now be solved.  I am starting to rip out the SQL that is in MOBY Central into other modules, and it will eventually end up in a single mysql-specific module with an API to make it easier to code MOBY onto other data back-ends.  Various bug fixes here and there as well.

moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.15,1.16
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl	2004/04/20 23:24:25	1.15
+++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl	2004/06/16 01:15:30	1.16
@@ -24,10 +24,10 @@
 }
 
 my $C = MOBY::Client::Central->new(
-#Registries => {
-#	mobycentral => {URL => 'http://localhost/cgi-bin/MOBY-Central.pl',
-#                       URI => 'http://localhost/MOBY/Central'}
-#		}
+Registries => {
+  mobycentral => {URL => $ENV{MOBY_SERVER}?$ENV{MOBY_SERVER}:'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl',
+		  URI => $ENV{MOBY_URI}?$ENV{MOBY_URI}:'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'}
+						}
 );
 
 



From mwilkinson at pub.open-bio.org  Tue Jun 15 21:15:30 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 15 Jun 2004 21:15:30 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406160115.i5G1FU7Y016541@pub.open-bio.org>


mwilkinson
Tue Jun 15 21:15:30 EDT 2004
Update of /home/repository/moby/moby-live/Perl/t
In directory pub.open-bio.org:/tmp/cvs-serv16447/t

Modified Files:
	Client-Central.t 
Log Message:
all sorts of additions and changes.  Secondary parameters now work for me on two systems, so that problem should now be solved.  I am starting to rip out the SQL that is in MOBY Central into other modules, and it will eventually end up in a single mysql-specific module with an API to make it easier to code MOBY onto other data back-ends.  Various bug fixes here and there as well.

moby-live/Perl/t Client-Central.t,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/t/Client-Central.t,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/t/Client-Central.t	2004/01/08 19:05:58	1.3
+++ /home/repository/moby/moby-live/Perl/t/Client-Central.t	2004/06/16 01:15:30	1.4
@@ -12,9 +12,11 @@
 
 # Test 2
 my $C = MOBY::Client::Central->new(
-    #MOBY_server => "http://localhost/cgi-bin/MOBY-Central.pl",
-    #MOBY_uri  => "http://localhost/MOBY/Central"
-    );
+		Registries => {
+						mobycentral => {	URL => 'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl',
+											URI => 'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'}
+						}
+                                  );
 
 isa_ok( $C,'MOBY::Client::Central',"Connected to test MOBY Central") or
     die("Cannot Connect to MOBY Central... cannot continue?");



From gss at pub.open-bio.org  Wed Jun 16 14:37:19 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:37:19 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161837.i5GIbJHC020447@pub.open-bio.org>


gss
Wed Jun 16 14:37:19 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20422/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 14:49:45 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:49:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161849.i5GInjsF020496@pub.open-bio.org>


gss
Wed Jun 16 14:49:45 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20472/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 14:50:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:50:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161850.i5GIoxcl020538@pub.open-bio.org>


gss
Wed Jun 16 14:50:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20517/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms

Added Files:
	literatureGuideURI.n3 literatureGuideURI geneSymbol 
	geneSymbol.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms literatureGuideURI.n3,NONE,1.1 literatureGuideURI,NONE,1.1 geneSymbol,NONE,1.1 geneSymbol.n3,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 14:50:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:50:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161850.i5GIox5V020562@pub.open-bio.org>


gss
Wed Jun 16 14:50:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv20517/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot

Modified Files:
	citationSearch.rdf citationSearch.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.6,1.7 citationSearch.n3,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/05/19 20:42:37	1.6
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/06/16 18:50:59	1.7
@@ -1,50 +1,37 @@
 <rdf:RDF
-    xmlns:go="http://www.go.org:8080/terms#"
+    xmlns:sgd="http://www.sgd.org:8080/terms/"
     xmlns:acmepubs="http://www.acmepubs.com:8080/"
+    xmlns:pubs="http://www.pubs.org:8080/terms/"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+    xmlns:acmeterms="http://www.acmepubs.com:8080/terms/"
+    xmlns:go="http://www.go.org:8080/terms/"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
-    xmlns:pubs="http://www.pubs.org:8081/terms#"
-    xmlns:moby="http://www.s-moby.org:8080/terms#"
-    xmlns:sgd="http://www.sgd.org:8080/terms#" >
-  <rdf:Description rdf:about="http://www.acmepubs.com:8080/geneSymbol">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
-  </rdf:Description>
+    xmlns:moby="http://www.s-moby.org:8080/terms/" >
   <rdf:Description rdf:nodeID="A0">
-    <moby:hasMapping rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A1">
-    <acmepubs:geneSymbol rdf:nodeID="A2"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <moby:mapsTo rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms/GeneSymbol"/>
+    <acmeterms:geneSymbol rdf:nodeID="A1"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Subject"/>
+    <moby:mapsTo rdf:nodeID="A2"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A2">
+    <acmeterms:literatureGuideURI rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms/LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Object"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A4">
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-    <rdf:_1 rdf:nodeID="A0"/>
+    <moby:hasMapping rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Graph"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/citationSearch">
-    <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
-    <moby:operatesOn rdf:nodeID="A4"/>
-    <moby:oneLineDescription>Industry standard search</moby:oneLineDescription>
-    <moby:aboutURI>http://www.acmepubs.com/about/citationSearch</moby:aboutURI>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
     <moby:name>AcmePubs Citation Search</moby:name>
+    <moby:oneLineDescription>Industry standard search</moby:oneLineDescription>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Provider"/>
+    <moby:operatesOn rdf:nodeID="A5"/>
+    <rdf:type rdf:resource="http://www.pubs.org:8080/terms/citationSearch"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A3">
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <acmepubs:literatureGuideURL rdf:nodeID="A5"/>
-  </rdf:Description>
-  <rdf:Description rdf:about="http://www.acmepubs.com:8080/literatureGuideURL">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
-    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  <rdf:Description rdf:nodeID="A5">
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A4"/>
   </rdf:Description>
 </rdf:RDF>
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3	2004/05/19 20:42:37	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3	2004/06/16 18:50:59	1.6
@@ -1,41 +1,28 @@
- at prefix pubs:     <http://www.pubs.org:8081/terms#> .
- at prefix xsd:      <http://www.w3.org/2001/XMLSchema#> .
- at prefix acmepubs: <http://www.acmepubs.com:8080/> .
- at prefix go:       <http://www.go.org:8080/terms#> .
- at prefix sgd:      <http://www.sgd.org:8080/terms#> .
- at prefix moby:     <http://www.s-moby.org:8080/terms#> .
- at prefix rdfs:     <http://www.w3.org/2000/01/rdf-schema#> .
- at prefix rdf:      <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
- at prefix owl:      <http://www.w3.org/2002/07/owl#> .
+ at prefix acmepubs:   <http://www.acmepubs.com:8080/> .
+ at prefix acmeterms:  <http://www.acmepubs.com:8080/terms/> .
+ at prefix pubs:       <http://www.pubs.org:8080/terms/> .
+ at prefix go:         <http://www.go.org:8080/terms/> .
+ at prefix sgd:        <http://www.sgd.org:8080/terms/> .
+ at prefix moby:       <http://www.s-moby.org:8080/terms/> .
+ at prefix rdfs:       <http://www.w3.org/2000/01/rdf-schema#> .
+ at prefix rdf:        <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+ at prefix owl:        <http://www.w3.org/2002/07/owl#> .
 
 acmepubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
     moby:name "AcmePubs Citation Search" ;
     moby:oneLineDescription "Industry standard search" ;
-    moby:aboutURI "http://www.acmepubs.com/about/citationSearch" ;
     moby:operatesOn [
         a rdf:Bag ;
         rdf:_1 [
             a moby:Graph ;
             moby:hasMapping [
                 a moby:Subject, go:GeneSymbol ;
-                acmepubs:geneSymbol _:bnode1 ;
+                acmeterms:geneSymbol _:bnode1 ;
                 moby:mapsTo [
                     a moby:Object, sgd:LiteratureGuide ;
-                    acmepubs:literatureGuideURL _:bnode2
+                    acmeterms:literatureGuideURI _:bnode2
                 ]
             ]
         ]
-    ] .
-
-acmepubs:geneSymbol
-    a owl:DataTypeProperty ;
-    rdfs:subPropertyOf moby:Property ;
-    rdfs:domain go:GeneSymbol ;
-    rdfs:range xsd:string .
-
-acmepubs:literatureGuideURL
-    a owl:DataTypeProperty ;
-    rdfs:subPropertyOf moby:Property ;
-    rdfs:domain sgd:LiteratureGuide ;
-    rdfs:range xsd:anyURI .
\ No newline at end of file
+    ] .
\ No newline at end of file



From gss at pub.open-bio.org  Wed Jun 16 14:51:13 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:51:13 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161851.i5GIpDk0020600@pub.open-bio.org>


gss
Wed Jun 16 14:51:13 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20579/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms

Added Files:
	literatureGuideURI.n3 geneSymbol geneSymbol.n3 
	literatureGuideURI 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms literatureGuideURI.n3,NONE,1.1 geneSymbol,NONE,1.1 geneSymbol.n3,NONE,1.1 literatureGuideURI,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 14:51:13 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:51:13 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161851.i5GIpDCp020624@pub.open-bio.org>


gss
Wed Jun 16 14:51:13 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv20579/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot

Modified Files:
	citationSearch.n3 citationSearch.rdf 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.5,1.6 citationSearch.rdf,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3	2004/05/19 20:42:33	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3	2004/06/16 18:51:13	1.6
@@ -1,41 +1,28 @@
- at prefix pubs:     <http://www.pubs.org:8081/terms#> .
- at prefix xsd:      <http://www.w3.org/2001/XMLSchema#> .
- at prefix megapubs: <http://www.megapubs.com:8080/> .
- at prefix go:       <http://www.go.org:8080/terms#> .
- at prefix sgd:      <http://www.sgd.org:8080/terms#> .
- at prefix moby:     <http://www.s-moby.org:8080/terms#> .
- at prefix rdfs:     <http://www.w3.org/2000/01/rdf-schema#> .
- at prefix rdf:      <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
- at prefix owl:      <http://www.w3.org/2002/07/owl#> .
+ at prefix megapubs:   <http://www.megapubs.com:8080/> .
+ at prefix megaterms:  <http://www.megapubs.com:8080/terms/> .
+ at prefix pubs:       <http://www.pubs.org:8080/terms/> .
+ at prefix go:         <http://www.go.org:8080/terms/> .
+ at prefix sgd:        <http://www.sgd.org:8080/terms/> .
+ at prefix moby:       <http://www.s-moby.org:8080/terms/> .
+ at prefix rdfs:       <http://www.w3.org/2000/01/rdf-schema#> .
+ at prefix rdf:        <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+ at prefix owl:        <http://www.w3.org/2002/07/owl#> .
 
 megapubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
     moby:name "MegaPubs Citation Search" ;
     moby:oneLineDescription "Cool new search" ;
-    moby:aboutURI "http://www.megapubs.com/about/citationSearch" ;
     moby:operatesOn [
         a rdf:Bag ;
         rdf:_1 [
             a moby:Graph ;
             moby:hasMapping [
                 a moby:Subject, go:GeneSymbol ;
-                megapubs:geneSymbol _:bnode1 ;
+                megaterms:geneSymbol _:bnode1 ;
                 moby:mapsTo [
                     a moby:Object, sgd:LiteratureGuide ;
-                    megapubs:literatureGuideURL _:bnode2
+                    megaterms:literatureGuideURI _:bnode2
                 ]
             ]
         ]
-    ] .
-
-megapubs:geneSymbol
-    a owl:DataTypeProperty ;
-    rdfs:subPropertyOf moby:Property ;
-    rdfs:domain go:GeneSymbol ;
-    rdfs:range xsd:string .
-
-megapubs:literatureGuideURL
-    a owl:DataTypeProperty ;
-    rdfs:subPropertyOf moby:Property ;
-    rdfs:domain sgd:LiteratureGuide ;
-    rdfs:range xsd:anyURI .
\ No newline at end of file
+    ] .
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/05/19 20:42:34	1.6
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/06/16 18:51:13	1.7
@@ -1,50 +1,37 @@
 <rdf:RDF
-    xmlns:go="http://www.go.org:8080/terms#"
+    xmlns:sgd="http://www.sgd.org:8080/terms/"
+    xmlns:pubs="http://www.pubs.org:8080/terms/"
     xmlns:megapubs="http://www.megapubs.com:8080/"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+    xmlns:go="http://www.go.org:8080/terms/"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
-    xmlns:pubs="http://www.pubs.org:8081/terms#"
-    xmlns:moby="http://www.s-moby.org:8080/terms#"
-    xmlns:sgd="http://www.sgd.org:8080/terms#" >
+    xmlns:moby="http://www.s-moby.org:8080/terms/"
+    xmlns:megaterms="http://www.megapubs.com:8080/terms/" >
   <rdf:Description rdf:nodeID="A0">
-    <moby:hasMapping rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-  </rdf:Description>
-  <rdf:Description rdf:about="http://www.megapubs.com:8080/literatureGuideURL">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
-    <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <megaterms:geneSymbol rdf:nodeID="A1"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Subject"/>
+    <moby:mapsTo rdf:nodeID="A2"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms/GeneSymbol"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/citationSearch">
-    <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Provider"/>
+    <moby:operatesOn rdf:nodeID="A3"/>
     <moby:oneLineDescription>Cool new search</moby:oneLineDescription>
-    <moby:operatesOn rdf:nodeID="A2"/>
-    <moby:aboutURI>http://www.megapubs.com/about/citationSearch</moby:aboutURI>
+    <rdf:type rdf:resource="http://www.pubs.org:8080/terms/citationSearch"/>
     <moby:name>MegaPubs Citation Search</moby:name>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <rdf:_1 rdf:nodeID="A0"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A1">
-    <moby:mapsTo rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <megapubs:geneSymbol rdf:nodeID="A4"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A3">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <megapubs:literatureGuideURL rdf:nodeID="A5"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:_1 rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
-  <rdf:Description rdf:about="http://www.megapubs.com:8080/geneSymbol">
-    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
-    <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
+  <rdf:Description rdf:nodeID="A2">
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms/LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Object"/>
+    <megaterms:literatureGuideURI rdf:nodeID="A5"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A4">
+    <moby:hasMapping rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Graph"/>
   </rdf:Description>
 </rdf:RDF>



From gss at pub.open-bio.org  Wed Jun 16 14:52:04 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:52:04 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161852.i5GIq4QV020656@pub.open-bio.org>


gss
Wed Jun 16 14:52:04 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv20631/S-MOBY/ref-impl/example-providers/sgd.org

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/sgd.org .cvsignore,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore	2004/06/10 23:31:50	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore	2004/06/16 18:52:04	1.3
@@ -3,3 +3,4 @@
 .encoding
 .mymetadata
 .project
+.settings



From gss at pub.open-bio.org  Wed Jun 16 14:55:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:55:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161855.i5GItaBd020712@pub.open-bio.org>


gss
Wed Jun 16 14:55:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv20690/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot

Removed Files:
	terms 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot terms,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/RCS/terms,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 14:57:56 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:57:56 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161857.i5GIvutQ020758@pub.open-bio.org>


gss
Wed Jun 16 14:57:56 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv20736/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot

Removed Files:
	terms.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot terms.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/RCS/terms.n3,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 15:00:29 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 15:00:29 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161900.i5GJ0Tdc020857@pub.open-bio.org>


gss
Wed Jun 16 15:00:29 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20833/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 15:00:31 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 15:00:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161900.i5GJ0VRJ020891@pub.open-bio.org>


gss
Wed Jun 16 15:00:31 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20870/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms

Added Files:
	LiteratureGuide LiteratureGuide.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms LiteratureGuide,NONE,1.1 LiteratureGuide.n3,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 15:01:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 15:01:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161901.i5GJ1K3b020933@pub.open-bio.org>


gss
Wed Jun 16 15:01:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv20908/S-MOBY/ref-impl/server

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/server .cvsignore,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore	2004/06/14 17:17:56	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore	2004/06/16 19:01:20	1.3
@@ -2,3 +2,4 @@
 .classpath
 .mymetadata
 .project
+.settings



From mwilkinson at pub.open-bio.org  Wed Jun 16 15:07:34 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed, 16 Jun 2004 15:07:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161907.i5GJ7Y7o021017@pub.open-bio.org>


mwilkinson
Wed Jun 16 15:07:34 EDT 2004
Update of /home/repository/moby/moby-live/Perl/scripts
In directory pub.open-bio.org:/tmp/cvs-serv20998/scripts

Modified Files:
	testMOBYClientCentral_v05.pl 
Log Message:
fixed test script

moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.16,1.17
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl	2004/06/16 01:15:30	1.16
+++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl	2004/06/16 19:07:34	1.17
@@ -148,7 +148,7 @@
 	         ],
 	secondary => {
         parametername1 => {
-            datatype => 'Int',
+            datatype => 'Integer',
     		default => 0,
 			max => 10,
 			min => -10,



From mwilkinson at pub.open-bio.org  Wed Jun 16 15:08:05 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed, 16 Jun 2004 15:08:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161908.i5GJ85Qi021064@pub.open-bio.org>


mwilkinson
Wed Jun 16 15:08:05 EDT 2004
Update of /home/repository/moby/moby-live/Perl/t
In directory pub.open-bio.org:/tmp/cvs-serv21045/t

Modified Files:
	Client-Central.t 
Log Message:
fixing an incorrect test in the test suite

moby-live/Perl/t Client-Central.t,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/t/Client-Central.t,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/t/Client-Central.t	2004/06/16 01:15:30	1.4
+++ /home/repository/moby/moby-live/Perl/t/Client-Central.t	2004/06/16 19:08:05	1.5
@@ -100,7 +100,7 @@
 	         ],
 	secondary => {
         parametername1 => {
-            datatype => 'Int',
+            datatype => 'Integer',
     		default => 0,
 			max => 10,
 			min => -10,



From gss at pub.open-bio.org  Wed Jun 16 15:19:54 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 15:19:54 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161919.i5GJJsei021114@pub.open-bio.org>


gss
Wed Jun 16 15:19:54 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv21093/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms

Added Files:
	index.html 
Log Message:
Index of OWL terms

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms index.html,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 15:21:57 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 15:21:57 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161921.i5GJLvAF021170@pub.open-bio.org>


gss
Wed Jun 16 15:21:57 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv21149/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms

Added Files:
	index.html 
Log Message:
Index of OWL terms

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms index.html,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 18:07:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:07:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162207.i5GM70mA021799@pub.open-bio.org>


gss
Wed Jun 16 18:07:00 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir
In directory pub.open-bio.org:/tmp/cvs-serv21775/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir added to the repository

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 18:07:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:07:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162207.i5GM73iE021841@pub.open-bio.org>


gss
Wed Jun 16 18:07:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir
In directory pub.open-bio.org:/tmp/cvs-serv21820/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir

Added Files:
	CitationSearch CitationSearch.n3 index.html PubAbstract 
	PubAbstract.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir CitationSearch,NONE,1.1 CitationSearch.n3,NONE,1.1 index.html,NONE,1.1 PubAbstract,NONE,1.1 PubAbstract.n3,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 18:08:53 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:08:53 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162208.i5GM8rkW021880@pub.open-bio.org>


gss
Wed Jun 16 18:08:53 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv21857/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot

Removed Files:
	terms terms.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot terms,1.1,NONE terms.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/terms,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/terms.n3,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 18:11:54 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:11:54 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162211.i5GMBsNP021939@pub.open-bio.org>


gss
Wed Jun 16 18:11:54 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv21915/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 18:13:13 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:13:13 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162213.i5GMDDUL021984@pub.open-bio.org>


gss
Wed Jun 16 18:13:13 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv21963/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms

Added Files:
	index.html PubAbstract CitationSearch PubAbstract.n3 
	CitationSearch.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms index.html,NONE,1.1 PubAbstract,NONE,1.1 CitationSearch,NONE,1.1 PubAbstract.n3,NONE,1.1 CitationSearch.n3,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 18:14:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:14:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162214.i5GMEIpb022021@pub.open-bio.org>


gss
Wed Jun 16 18:14:18 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir
In directory pub.open-bio.org:/tmp/cvs-serv21995/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir

Removed Files:
	CitationSearch CitationSearch.n3 index.html PubAbstract 
	PubAbstract.n3 
Log Message:
Moved to terms/ directory

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir CitationSearch,1.1,NONE CitationSearch.n3,1.1,NONE index.html,1.1,NONE PubAbstract,1.1,NONE PubAbstract.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/CitationSearch,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/CitationSearch.n3,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/index.html,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/PubAbstract,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/PubAbstract.n3,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 18:18:50 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:18:50 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162218.i5GMIoag022108@pub.open-bio.org>


gss
Wed Jun 16 18:18:50 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22079/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms

Modified Files:
	LiteratureGuide LiteratureGuide.n3 
Added Files:
	index.html 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms index.html,NONE,1.1 LiteratureGuide,1.1,1.2 LiteratureGuide.n3,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide	2004/06/16 19:00:30	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide	2004/06/16 22:18:50	1.2
@@ -1,8 +1,8 @@
 <rdf:RDF
+    xmlns:sgd="http://www.sgd.org:8080/terms/"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:owl="http://www.w3.org/2002/07/owl#"
-    xmlns:sgd="http://www.sgd.org:8080/terms#" >
-  <rdf:Description rdf:about="http://www.sgd.org:8080/terms#LiteratureGuide">
+    xmlns:owl="http://www.w3.org/2002/07/owl#" >
+  <rdf:Description rdf:about="http://www.sgd.org:8080/terms/LiteratureGuide">
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
   </rdf:Description>
 </rdf:RDF>
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide.n3,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide.n3	2004/06/16 19:00:30	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide.n3	2004/06/16 22:18:50	1.2
@@ -1,4 +1,4 @@
- at prefix sgd: <http://www.sgd.org:8080/terms#> .
+ at prefix sgd: <http://www.sgd.org:8080/terms/> .
 @prefix owl: <http://www.w3.org/2002/07/owl#> .
 
 sgd:LiteratureGuide



From gss at pub.open-bio.org  Wed Jun 16 18:23:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:23:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162223.i5GMNxai022173@pub.open-bio.org>


gss
Wed Jun 16 18:23:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv22150/S-MOBY/ref-impl/example-providers/go.org/WebRoot

Removed Files:
	terms terms.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot terms,1.1,NONE terms.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/RCS/terms,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/RCS/terms.n3,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 18:25:14 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:25:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162225.i5GMPEj3022216@pub.open-bio.org>


gss
Wed Jun 16 18:25:14 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22192/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 18:25:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:25:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162225.i5GMPGCH022258@pub.open-bio.org>


gss
Wed Jun 16 18:25:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22237/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms

Added Files:
	index.html GeneSymbol GeneSymbol.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms index.html,NONE,1.1 GeneSymbol,NONE,1.1 GeneSymbol.n3,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 18:27:14 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:27:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162227.i5GMRExb022299@pub.open-bio.org>


gss
Wed Jun 16 18:27:14 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools
In directory pub.open-bio.org:/tmp/cvs-serv22274/S-MOBY/ref-impl/server/WebRoot/tools

Modified Files:
	developer.html 
Log Message:
Added developer tool to list statements in metadata repository

moby-live/S-MOBY/ref-impl/server/WebRoot/tools developer.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html	2004/03/30 23:54:34	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html	2004/06/16 22:27:14	1.3
@@ -1,67 +1,112 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
 <html>
-<head>
-  <title>Semantic MOBY Developer Tools</title>
-</head>
-<body>
-	<table style="text-align: center; width: 100%;" border="1"
+  <head>
+    <meta name="generator" content="HTML Tidy, see www.w3.org">
+
+    <title>Semantic MOBY Developer Tools</title>
+  </head>
+
+  <body>
+    <table style="WIDTH: 100%; TEXT-ALIGN: center" border="1"
     cellspacing="0" cellpadding="0">
-    <tbody>
-      <tr>
-        <td style="vertical-align: top; background-color: rgb(204, 204, 204);">
-      	  <b>Semantic MOBY Developer Tools</b>
-        </td>
-      </tr>
-    </tbody>
-  </table>
-  <br>
-  <h4><u>Convert a graph to a different format</u></h4>
-<form method="POST" action="http://www.s-moby.org:8080/convert-graph">
-  Paste a graph, select its input format,
-  and press "Convert Graph" to convert to the other format
-  <p>
-  Input format:&nbsp;&nbsp;&nbsp;
-  <input type="radio" name="input-format" value="N3" CHECKED>N3&nbsp;&nbsp;
-  <input type="radio" name="input-format" value="RDF/XML">RDF/XML
-  <input type="radio" name="input-format" value="N-TRIPLE">N-Triples&nbsp;&nbsp;
-  <br>
-  Output format:
-  <input type="radio" name="output-format" value="N3">N3&nbsp;&nbsp;
-  <input type="radio" name="output-format" value="RDF/XML" CHECKED>RDF/XML
-  <input type="radio" name="output-format" value="N-TRIPLE">N-Triples&nbsp;&nbsp;
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-  <input type="submit" value="Convert Graph">
-  <p>
-  <textarea name="graph" rows="15" cols="80"></textarea>
-  &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;
-
-</form>
-<H4><U>List the providers in the S-MOBY metadata repository</U></H4>
-<FORM method="GET" action="http://www.s-moby.org:8080/list-providers">
-  &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;
-  <INPUT type="submit" value="List Providers">&nbsp;&nbsp;
-  <INPUT type="checkbox" name="show-contents" value=true>
-  Show provider description graphs
-</FORM>
-<h4><u>Validate an OWL Graph using Jena</u></h4>
-<form method="POST" action="http://www.s-moby.org:8080/validate-owl-graph">
-  Paste a graph in RDF/XML format and press "Validate" to see what type of
-  OWL the graph represents
-  <p>
-  <input type="submit" value="Validate">
-  <p>
-  <textarea name="graph" rows="15" cols="80"></textarea>
-</form>
-
-<h4><u>Validate that a graph is MOBY canonical form</u></h4>
-<form method="POST" action="http://www.s-moby.org:8080/validate-canonical-graph">
-  Paste a graph in RDF/XML format and press "Validate" to see if it is
-  MOBY canonical form
-  <p>
-  <input type="submit" value="Validate">
-  <p>
-  <textarea name="graph" rows="15" cols="80"></textarea>
-</form>
-  
-</body>
+      <tbody>
+        <tr>
+          <td style=
+          "VERTICAL-ALIGN: top; BACKGROUND-COLOR: rgb(204,204,204)">
+          <b>Semantic MOBY Developer Tools</b></td>
+        </tr>
+      </tbody>
+    </table><br>
+     
+
+    <h4><u>Convert a graph to a different format</u></h4>
+
+    <form method="post" action=
+    "http://www.s-moby.org:8080/convert-graph">
+      Paste a graph, select its input format, and press "Convert Graph"
+      to convert to the other format 
+
+      <p>Input format:&nbsp;&nbsp;&nbsp; <input type="radio" name=
+      "input-format" value="N3" checked>N3&nbsp;&nbsp; <input type=
+      "radio" name="input-format" value="RDF/XML">RDF/XML <input type=
+      "radio" name="input-format" value=
+      "N-TRIPLE">N-Triples&nbsp;&nbsp;<br>
+       Output format: <input type="radio" name="output-format" value=
+      "N3">N3&nbsp;&nbsp; <input type="radio" name="output-format"
+      value="RDF/XML" checked>RDF/XML <input type="radio" name=
+      "output-format" value="N-TRIPLE">N-Triples&nbsp;&nbsp;
+      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <input type="submit" value=
+      "Convert Graph"></p>
+
+      <p><textarea name="graph" rows="15" cols="80">
+                                              
+                                               
+                                       
+                                 
+                         
+                   
+           
+      </textarea> &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;</p>
+    </form>
+
+    <h4><u>List the providers in the S-MOBY metadata
+    repository</u></h4>
+
+    <form method="get" action=
+    "http://www.s-moby.org:8080/list-providers">
+      &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; <input type="submit"
+      value="List Providers">&nbsp;&nbsp; <input type="checkbox" name=
+      "show-contents" value="true"> Show provider description graphs
+    </form>
+
+    <h4><u>List&nbsp;all statements&nbsp;in the S-MOBY metadata
+    repository</u></h4>
+
+    <form name="List statements" action=
+    "http://www.s-moby.org:8080/print-repository" method="get">
+      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;<input type=
+      "submit" value="List Statements in Repository">
+    </form>
+
+    <h4><u>Validate an OWL Graph using Jena</u></h4>
+
+    <form method="post" action=
+    "http://www.s-moby.org:8080/validate-owl-graph">
+      Paste a graph in RDF/XML format and press "Validate" to see what
+      type of OWL the graph represents 
+
+      <p><input type="submit" value="Validate"></p>
+
+      <p><textarea name="graph" rows="15" cols="80">
+                                              
+                                               
+                                       
+                                 
+                         
+                   
+           
+      </textarea></p>
+    </form>
+
+    <h4><u>Validate that a graph is MOBY canonical form</u></h4>
+
+    <form method="post" action=
+    "http://www.s-moby.org:8080/validate-canonical-graph">
+      Paste a graph in RDF/XML format and press "Validate" to see if it
+      is MOBY canonical form 
+
+      <p><input type="submit" value="Validate"></p>
+
+      <p><textarea name="graph" rows="15" cols="80">
+                                              
+                                               
+                                       
+                                 
+                         
+                   
+           
+      </textarea></p>
+    </form>
+  </body>
 </html>



From gss at pub.open-bio.org  Wed Jun 16 18:27:47 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:27:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162227.i5GMRln5022326@pub.open-bio.org>


gss
Wed Jun 16 18:27:47 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv22304/S-MOBY/ref-impl/server/WebRoot

Removed Files:
	terms 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/server/WebRoot terms,1.2,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/terms,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 19:27:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:27:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162327.i5GNRQwk022472@pub.open-bio.org>


gss
Wed Jun 16 19:27:26 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22448/S-MOBY/ref-impl/server/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/server/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 19:27:29 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:27:29 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162327.i5GNRTDB022514@pub.open-bio.org>


gss
Wed Jun 16 19:27:29 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22493/S-MOBY/ref-impl/server/WebRoot/terms

Added Files:
	operatesOn oneLineDescription objectProperty.n3 __Seq.n3 
	__NonCollection.n3 providerAboutURI.n3 index.html Provider 
	Subject mapsTo __Collection.n3 __List.n3 Object.n3 hasMapping 
	providerAboutURI Graph.n3 subjectProperty mapsTo.n3 __List 
	name.n3 oneLineDescription.n3 __Alt __Bag.n3 __Bag Graph __Seq 
	objectProperty name operatesOn.n3 Provider.n3 hasMapping.n3 
	subjectProperty.n3 __NonCollection __Collection __Alt.n3 
	Subject.n3 Object 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/server/WebRoot/terms operatesOn,NONE,1.1 oneLineDescription,NONE,1.1 objectProperty.n3,NONE,1.1 __Seq.n3,NONE,1.1 __NonCollection.n3,NONE,1.1 providerAboutURI.n3,NONE,1.1 index.html,NONE,1.1 Provider,NONE,1.1 Subject,NONE,1.1 mapsTo,NONE,1.1 __Collection.n3,NONE,1.1 __List.n3,NONE,1.1 Object.n3,NONE,1.1 hasMapping,NONE,1.1 providerAboutURI,NONE,1.1 Graph.n3,NONE,1.1 subjectProperty,NONE,1.1 mapsTo.n3,NONE,1.1 __List,NONE,1.1 name.n3,NONE,1.1 oneLineDescription.n3,NONE,1.1 __Alt,NONE,1.1 __Bag.n3,NONE,1.1 __Bag,NONE,1.1 Graph,NONE,1.1 __Seq,NONE,1.1 objectProperty,NONE,1.1 name,NONE,1.1 operatesOn.n3,NONE,1.1 Provider.n3,NONE,1.1 hasMapping.n3,NONE,1.1 subjectProperty.n3,NONE,1.1 __NonCollection,NONE,1.1 __Collection,NONE,1.1 __Alt.n3,NONE,1.1 Subject.n3,NONE,1.1 Object,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 19:28:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:28:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162328.i5GNS0EK022541@pub.open-bio.org>


gss
Wed Jun 16 19:28:00 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv22519/S-MOBY/ref-impl/server/WebRoot

Removed Files:
	terms.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/server/WebRoot terms.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/terms.n3,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 19:29:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:29:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162329.i5GNTK4q022587@pub.open-bio.org>


gss
Wed Jun 16 19:29:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv22562/S-MOBY/ref-impl/core/src/org/smoby/parser

Modified Files:
	Parser.java 
Log Message:
Documentation

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/05/24 22:05:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/16 23:29:20	1.2
@@ -3,15 +3,17 @@
 import java.io.*;
 import java.net.*;
 import java.util.*;
-
 import org.smoby.graph.*;
 import org.smoby.graph.impl.*;
 import org.smoby.parser.*;
 import org.smoby.vocabulary.*;
-
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.vocabulary.*;
 
+/**
+ * This class is used to parse OWL models, stored as Jena2 models, into
+ * objects that implement interfaces from the org.smoby.graph package.
+ */
 public class Parser
 {
     /**
@@ -25,15 +27,17 @@
     public final static String LANGUAGE_N3 = "N3";
     
     /**
-     * The underlying Jena model on which the parsed graph is based
+     * Inference models containing inferred statements derived using
+     * rdfs:subClassOf relationships.
      */
-    private Model model;
+    private Map inferenceModels = new HashMap();
     
     /**
-     * An inference model containing inferred statements derived using
-     * rdfs:subClassOf relationships.
+     * Return the inference model associated with a given plain model
      */
-    private InfModel inferenceModel;
+    private InfModel getInferenceModel(Model model) {
+    	return (InfModel) inferenceModels.get(model);
+    }
 
     /**
      * Create and return a parser for parsing an N3 file
@@ -86,8 +90,8 @@
 	}
 
     /**
-     * Create and return a parser for parsing an input stream having
-     * the given format
+     * Create and return a parser for parsing an input stream containing
+     * the given language
      * @return a new instance of Parser
      * @throws IOException if reading the stream 
      * @throws UnparsableGraphException if the file doesn't contain a
@@ -105,6 +109,11 @@
         return new Parser(model);
     }
     
+    /**
+     * Create and return a parser for parsing a string in a given language
+     * @param graphString the string containing the graph
+     * @param language the language the model is expressed in
+     */
     public static Parser forString(String graphString, String language)
     	throws UnparsableGraphException
 	{
@@ -114,28 +123,71 @@
 	}
     
     /**
-     * Create an instance for parsing from the given model
+     * Create an instance for parsing the given model.
      */
     public Parser(Model model)
     {
-        this.model = model;
-        this.inferenceModel = ModelFactory.createRDFSModel(model);
-    }
-    
-    /**
-     * Return the underlying model
-     */
-    public Model getModel()
-    {
-        return model;
+    	
+        StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
+        while (it.hasNext())
+        {
+        	Statement stmt = it.nextStatement();
+        	Model subModel = ModelFactory.createDefaultModel();
+        	subModel.setNsPrefixes(model.getNsPrefixMap());
+        	Resource subject = stmt.getSubject();
+        	addReachableStmts(subModel, subject, subject.getURI());
+        	inferenceModels.put(subModel,
+        		ModelFactory.createRDFSModel(subModel));
+        }
     }
     
+	private void addReachableStmts(Model model, Resource subject, String uri)
+	{
+		// For each statement whose subject is the given resource
+		//
+		StmtIterator it = subject.getModel().listStatements(
+			subject, null, (RDFNode) null);
+		
+		while (it.hasNext())
+		{
+			Statement stmt = it.nextStatement();
+			
+			// The statement itself should be added
+			//
+			model.add(model.createStatement(
+				stmt.getSubject(), stmt.getPredicate(), stmt.getObject()));
+			
+			// If the object of the statement is a blank node or a
+			// resource whose URI starts with the provider URI, then
+			// recursively add the statements that are reachable
+			// from the object
+			//
+			if (stmt.getObject().canAs(Resource.class))
+			{
+				Resource object = (Resource) stmt.getObject().as(Resource.class);
+				if (object.isAnon() || object.getURI().startsWith(uri)) {
+					addReachableStmts(model, object, uri);
+				}
+			}
+		}
+	}
+
     /**
-     * Return the inference model
+     * Parse a provider from the model. If the model contains
+     * multiple providers, only one will be returned (at random). If
+     * the model is expected to contain multiple providers, then call
+     * parseProviders() instead to get all the providers in a
+     * MOBYCollection.
      */
-    public InfModel getInferenceModel()
+    public MOBYProvider parseProvider()
     {
-        return inferenceModel;
+    	MOBYUnorderedCollection providers = parseProviders();
+    	
+    	if (providers.size() == 0) {
+    		return null;
+    	} else {
+    		return (MOBYProvider) providers.iterator().next();
+    	}
     }
     
     /**
@@ -147,38 +199,28 @@
         
         // Find the statements that say something is of type Provider
         //
-        StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
+//        StmtIterator it = underlying.listStatements(null, RDF.type, MOBY.Provider);
+        
+        Iterator it = inferenceModels.keySet().iterator();
         
         // Parse each provider
         //
         while (it.hasNext())
         {
-            Statement stmt = it.nextStatement();
-            Resource provider = stmt.getSubject();
-            providers.add(parseProvider(provider));
+        	Model model = (Model) it.next();
+        	StmtIterator it2 = model.listStatements(null, RDF.type, MOBY.Provider);
+        	
+        	if (it2 != null)
+        	{
+        		Statement stmt = it2.nextStatement();
+	            Resource provider = stmt.getSubject();
+	            providers.add(parseProvider(provider));
+        	}
         }
         
         // Create and return an unordered collection of the parsed providers
         //
-        return MOBYObjectFactory.newUnorderedCollection(null, providers, model);
-    }
-
-    /**
-     * Parse a provider from the model. If the model contains
-     * multiple providers, only one will be parsed (at random). If
-     * the model is expected to contain multiple providers, then call
-     * parseProviders() instead to get all the providers in a
-     * MOBYCollection.
-     */
-    public MOBYProvider parseProvider()
-    {
-        StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
-        
-        if (it.hasNext()) {
-            return parseProvider(it.nextStatement().getSubject());
-        } else {
-            return null;
-        }
+        return MOBYObjectFactory.newUnorderedCollection(null, providers, null);
     }
     
     /**
@@ -187,6 +229,8 @@
      */
     public MOBYProvider parseProvider(Resource provider)
     {
+    	Model model = provider.getModel();
+    	
         // First parse the scalar properties name, oneLineDescription, and aboutURI
         //
         String name 	= getDataPropertyValue(provider, MOBY.name);
@@ -223,6 +267,8 @@
      */
     private MOBYGraphNode parseOperatesOn(Resource res)
     {
+    	Model model = res.getModel();
+    	
         if (isGraph(res))
         {
             // The resource is a MOBY Graph, so should have exactly one
@@ -263,6 +309,8 @@
      */
     private MOBYSubject parseHasMapping(Resource res)
     {
+    	Model model = res.getModel();
+    	
         // Collect the properties of this subject resource that are
         // subproperties of moby:Property, and create MOBY statements
         // for each.
@@ -354,6 +402,7 @@
         
         // Create and return a new MOBYObject
         //
+        Model model = res.getModel();
         return MOBYObjectFactory.newObject(res.getURI(),
             MOBYObjectFactory.newFixedCollection(null, statements, model),
             collectionFor(res, nested), model);
@@ -375,6 +424,9 @@
             Property p = stmt.getPredicate();
             RDFNode pval = stmt.getObject();
             
+            Model model = res.getModel();
+            Model inferenceModel = getInferenceModel(model);
+            
             if (model.contains(res, p, pval) &&
                 inferenceModel.contains(p, RDFS.subPropertyOf, MOBY.Property))
             {
@@ -409,13 +461,13 @@
     
     private String getDataPropertyValue(Resource subject, Property property)
     {
-        Statement s = model.getProperty(subject, property);
+        Statement s = subject.getModel().getProperty(subject, property);
         return (s == null) ? null : s.getObject().toString();
     }
     
     private Resource getResourcePropertyValue(Resource subject, Property property)
     {
-        Statement s = model.getProperty(subject, property);
+        Statement s = subject.getModel().getProperty(subject, property);
         return (s == null) ? null : (Resource) s.getObject();
     }
     
@@ -445,185 +497,100 @@
     private MOBYCollection collectionFor(Resource res, List elements)
     {
         if (isList(res)) {
-            return MOBYObjectFactory.newFixedCollection(null, elements, model);
+            return MOBYObjectFactory.newFixedCollection(null, elements, res.getModel());
         } else if (isBag(res)) {
-            return MOBYObjectFactory.newUnorderedCollection(null, elements, model);
+            return MOBYObjectFactory.newUnorderedCollection(null, elements, res.getModel());
         } else if (isSeq(res)) {
-            return MOBYObjectFactory.newOrderedCollection(null, elements, model);
+            return MOBYObjectFactory.newOrderedCollection(null, elements, res.getModel());
         } else if (isAlt(res)) {
-            return MOBYObjectFactory.newEnumeration(null, elements, model);
+            return MOBYObjectFactory.newEnumeration(null, elements, res.getModel());
         } else {
             return null;
         }
     }
     
-    private boolean isList(Resource res) { return res.canAs(RDFList.class); }
-    private boolean isBag (Resource res) { return isType(res, RDF.Bag);  }
-    private boolean isSeq (Resource res) { return isType(res, RDF.Seq);  }
-    private boolean isAlt (Resource res) { return isType(res, RDF.Alt);  }
-    
-    private boolean isDataStructure(Resource r) {
-        return isList(r) || isBag(r) || isSeq(r) || isAlt(r);
+    /**
+     * Return whether or not the given resource is an RDF List
+     */
+    private boolean isList(Resource res)
+    {
+    	return res.canAs(RDFList.class);
     }
-    
-    private boolean isGraph(Resource r) {
-        return isType(r, MOBY.Graph);
+
+    /**
+     * Return whether or not the given resource is an RDF Bag
+     */
+    private boolean isBag (Resource res)
+    {
+    	return isType(res, RDF.Bag);
     }
-    
-    private boolean isSubject(Resource res) {
-        return isType(res, MOBY.Subject);
+
+    /**
+     * Return whether or not the given resource is an RDF Seq
+     */
+    private boolean isSeq (Resource res)
+    {
+    	return isType(res, RDF.Seq);
     }
-    
-    private boolean isObject(Resource res) {
-        return isType(res, MOBY.Object);
+
+    /**
+     * Return whether or not the given resource is an RDF Alt
+     */
+    private boolean isAlt (Resource res)
+    {
+    	return isType(res, RDF.Alt);
     }
     
-    private boolean isType(Resource res, Resource type) {
-        return model.contains(res, RDF.type, type);
+    /**
+     * Return whether or not the given resource is an RDF data structure,
+     * i.e. a List, Bag, Seq, or Alt
+     */
+    private boolean isDataStructure(Resource r)
+    {
+        return isList(r) || isBag(r) || isSeq(r) || isAlt(r);
     }
     
-    public static String unparse(MOBYProvider provider) {
-        return Unparser.unparse(provider, 0);
+    /**
+     * Return whether or not the given resource is a MOBY Graph,
+     * i.e. the model contains a statement with the given resource
+     * as its subject, a predicate of rdf:type, and an object of
+     * moby:Graph
+     */
+    private boolean isGraph(Resource r)
+    {
+        return isType(r, MOBY.Graph);
     }
-    
-    public static String unparse(MOBYGraph graph) {
-        return Unparser.unparse(graph, 0);
+
+    /**
+     * Return whether or not the given resource is a MOBY Subject,
+     * i.e. the model contains a statement with the given resource
+     * as its subject, a predicate of rdf:type, and an object of
+     * moby:Subject
+     */
+    private boolean isSubject(Resource res)
+    {
+        return isType(res, MOBY.Subject);
     }
-    
-    public static String unparse(MOBYCollection collection) {
-        return Unparser.unparse(collection, 0);
+
+    /**
+     * Return whether or not the given resource is a MOBY Object,
+     * i.e. the model contains a statement with the given resource
+     * as its subject, a predicate of rdf:type, and an object of
+     * moby:Object
+     */
+    private boolean isObject(Resource res)
+    {
+        return isType(res, MOBY.Object);
     }
-    
-    private static class Unparser
+
+    /**
+     * Return whether or not the given resource is of the given type,
+     * i.e. the model contains a statement with the given resource
+     * as its subject, a predicate of rdf:type, and an object of the
+     * given type
+     */
+    private boolean isType(Resource res, Resource type)
     {
-        private static String unparse(MOBYProvider provider, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            
-            indent(sb, indent);
-            sb.append("Provider {");
-            newline(sb);
-            indent(sb, indent+4);
-            sb.append("name=\""); sb.append(provider.getName()); sb.append("\"");
-            newline(sb);
-            indent(sb, indent+4);
-            sb.append("oneLineDescription=\"");
-            sb.append(provider.getOneLineDescription()); sb.append("\"");
-            newline(sb);
-            indent(sb, indent+4);
-            sb.append("moreInfoURI=\"");
-            sb.append(provider.getMoreInfoURI().toString()); sb.append("\"");
-            
-            for (Iterator it = provider.getOperatesOn().iterator(); it.hasNext();)
-            {
-                MOBYGraphNode node = (MOBYGraphNode) it.next();
-                newline(sb);
-                indent(sb, indent+4);
-                sb.append("Operates on:");
-                newline(sb);
-                if (node.isSingular()) {
-                    sb.append(unparse((MOBYGraph) node, indent+8));
-                } else {
-                    sb.append(unparse((MOBYCollection) node, indent+8));
-                }
-            }
-            newline(sb);
-            indent(sb, indent);
-            sb.append("}");
-            
-            return sb.toString();
-        }
-        
-        private static String unparse(MOBYGraph graph, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            
-            indent(sb, indent);
-            sb.append("Graph {");
-            newline(sb);
-            MOBYGraphNode node = graph.gethasMapping();
-            if (node.isSingular()) {
-                sb.append(unparse((MOBYSubject) node, indent+4));
-            } else {
-                sb.append(unparse((MOBYCollection) node, indent+4));
-            }
-            indent(sb, indent);
-            sb.append("}");
-            
-            return sb.toString();
-        }
-        
-        private static String unparse(MOBYSubject subject, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            indent(sb, indent);
-            if (subject.isBlank()) {
-                sb.append("<bnode>");
-            } else {
-                sb.append("<"); sb.append(subject.getURI()); sb.append(">");
-            }
-            newline(sb);
-            
-            return sb.toString();
-        }
-        
-        private static String unparse(MOBYObject object, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            
-            return sb.toString();
-        }
-        
-        private static String unparse(MOBYCollection c, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            indent(sb, indent);
-            sb.append(descriptionOf(c));
-            sb.append(" {");
-            for (Iterator it = c.iterator(); it.hasNext();)
-            {
-                newline(sb);
-                Object element = it.next();
-                if (element instanceof MOBYProvider) {
-                    sb.append(unparse((MOBYProvider) element, indent+4));
-                } else if (element instanceof MOBYCollection) {
-                    sb.append(unparse((MOBYCollection) element, indent+4));
-                } else if (element instanceof MOBYGraph) {
-                    sb.append(unparse((MOBYGraph) element, indent+4));
-                } else if (element instanceof MOBYSubject) {
-                    sb.append(unparse((MOBYSubject) element, indent+4));
-                } else if (element instanceof MOBYObject) {
-                    sb.append(unparse((MOBYObject) element, indent+4));
-                } else {
-                    indent(sb, indent+4);
-                    sb.append(element.toString());
-                }
-            }
-            newline(sb);
-            indent(sb, indent);
-            sb.append("}");
-            return sb.toString();
-        }
-        
-        private static void newline(StringBuffer sb) {
-            sb.append("\n");
-        }
-        
-        private static void indent(StringBuffer sb, int count) {
-            for (int i = 0; i < count; i++) {
-                sb.append(' ');
-            }
-        }
-        
-        private static String descriptionOf(MOBYCollection c) {
-            
-            String name = "Collection";
-                 if (c instanceof MOBYFixedCollection)     name = "Fixed collection";
-            else if (c instanceof MOBYEnumeration)         name = "Choice collection";
-            else if (c instanceof MOBYOrderedCollection)   name = "Ordered collection";
-            else if (c instanceof MOBYUnorderedCollection) name = "Unordered collection";
-            
-            return name + " of " + c.size() + " elements";
-        }
+        return res.getModel().contains(res, RDF.type, type);
     }
 }
\ No newline at end of file



From gss at pub.open-bio.org  Wed Jun 16 19:29:32 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:29:32 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162329.i5GNTWJc022617@pub.open-bio.org>


gss
Wed Jun 16 19:29:32 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv22592/S-MOBY/ref-impl/core/src/org/smoby/parser/test

Modified Files:
	Test.java 
Log Message:
Documentation

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test Test.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java	2004/05/24 22:05:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java	2004/06/16 23:29:32	1.2
@@ -17,7 +17,5 @@
             "C|//Documents and Settings/gss/Desktop/citationSearch.n3");
         Parser parser = Parser.forN3File(inputFile);
         MOBYCollection coll = parser.parseProviders();
-        System.out.println("Providers:");
-        System.out.println(Parser.unparse(coll));
     }
 }



From gss at pub.open-bio.org  Wed Jun 16 19:30:14 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:30:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162330.i5GNUEaO022676@pub.open-bio.org>


gss
Wed Jun 16 19:30:13 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv22651/S-MOBY/ref-impl/core/src/org/smoby/vocabulary

Modified Files:
	MOBY.java 
Log Message:
No longer need registeredBy property

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/05/24 22:05:34	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/16 23:30:13	1.2
@@ -24,7 +24,6 @@
     public static final Property operatesOn			= property(getURI(), "operatesOn");
     public static final Property hasMapping			= property(getURI(), "hasMapping");
     public static final Property mapsTo				= property(getURI(), "mapsTo");
-    public static final Property registeredBy		= property(getURI(), "registeredBy");
     public static final Property lastModifiedDate	= property(getURI(), "lastModifiedDate");
     public static final Property Property			= property(getURI(), "Property");
 }
\ No newline at end of file



From gss at pub.open-bio.org  Wed Jun 16 19:30:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:30:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162330.i5GNUir3022714@pub.open-bio.org>


gss
Wed Jun 16 19:30:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev
In directory pub.open-bio.org:/tmp/cvs-serv22689/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev

Modified Files:
	RepositoryPrintServlet.java 
Log Message:
Print individual statements as N-triples

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev RepositoryPrintServlet.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java	2004/06/14 20:59:36	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java	2004/06/16 23:30:44	1.3
@@ -22,7 +22,10 @@
             if (model.isEmpty()) {
             	out.println("The repository is empty");
             } else {
-            	model.write(out, "RDF/XML-ABBREV");
+            	StmtIterator it = model.listStatements();
+            	while (it.hasNext()) {
+            		out.println(it.nextStatement());
+            	}
             }
             model.close();
         } catch (StorageException e) {



From gss at pub.open-bio.org  Wed Jun 16 19:31:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:31:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162331.i5GNVbrM022756@pub.open-bio.org>


gss
Wed Jun 16 19:31:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv22735/S-MOBY/ref-impl/server/src/org/smoby/ref/tools

Added Files:
	ProviderRemover.java 
Log Message:
Utility class to remove a provider's statements from a model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools ProviderRemover.java,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 19:33:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:33:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162333.i5GNX02f022802@pub.open-bio.org>


gss
Wed Jun 16 19:33:00 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db
In directory pub.open-bio.org:/tmp/cvs-serv22777/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db

Modified Files:
	StorageManager.java 
Log Message:
No longer cache separate model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/05/19 18:26:41	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/06/16 23:33:00	1.4
@@ -1,7 +1,7 @@
 package org.smoby.ref.tools.db;
 
 import org.smoby.graph.*;
-import org.smoby.graph.impl.MOBYProviderImpl;
+import org.smoby.graph.impl.*;
 import org.smoby.ref.tools.*;
 import org.smoby.vocabulary.*;
 import com.hp.hpl.jena.db.*;
@@ -17,19 +17,6 @@
 public class StorageManager
 {
     /**
-     * Return whether or not the database contains a provider with a
-     * given URI.
-     * @param providerURI URI of the provider in question
-     * @return boolean flag indicating if the database contains the provider in question
-     * @throws StorageException if unable to access the model in the database
-     */
-    public boolean containsProvider(String providerURI)
-        throws StorageException
-    {
-        return getModelMaker().hasModel(providerURI);
-    }
-    
-    /**
      * Return the date when a given provider was registered
      * @param providerURL URI of the provider
      * @return the registration date if the provider has been registered in
@@ -41,20 +28,19 @@
     {
         Date registrationDate = null;
         
-        ModelMaker maker = getModelMaker();
+        Model dbModel = openDBModel();
         
-        Model model = maker.openModel(providerURI);
+        Resource provider = dbModel.createResource(providerURI);
         
-        Resource provider = model.createResource(providerURI);
-        
-        NodeIterator it = model.listObjectsOfProperty(provider, MOBY.lastModifiedDate);
+        NodeIterator it = dbModel.listObjectsOfProperty(
+        	provider, MOBY.lastModifiedDate);
         
         if (it.hasNext()) {
             Literal lit = (Literal) it.nextNode().as(Literal.class);
             registrationDate = new Date(lit.getLong());
         }
         
-        model.close();
+        dbModel.close();
         
         return registrationDate;
     }
@@ -73,7 +59,8 @@
 	{
 	    Model model = ((MOBYProviderImpl) provider).getUnderlying();
         Model dbModel = null;
-        Resource uri = model.createResource(provider.getURI());
+        String uriString = provider.getURI();
+        Resource uri = model.createResource(uriString);
         
         try
         {
@@ -84,50 +71,32 @@
             // Open the database model
             //
             dbModel = openDBModel(maker);
-            
-            // First check if the database already has a graph registered under
-            // the URI of the new graph. If so, then throw an exception
-            //
-            if (dbModel.contains(null, MOBY.registeredBy, uri)) {
-                throw new StorageException("Graph already exists for " + uri);
-            }
 
             // Start a transaction on the database model
             //
             dbModel.begin();
             
-            // Add to the database the statements from providerGraph whose
-            // subjects are in the same namespace as the provider
+            // Add to the database all statements whose subjects are
+            // at the URI or deeper
             //
-            String providerNameSpace = uri.getNameSpace();
+            StmtIterator it = model.listStatements();
+            while (it.hasNext()) {
+            	Statement stmt = it.nextStatement();
+            	Resource subject = stmt.getSubject();
+            	if (subject.isAnon() || subject.getURI().startsWith(uriString)) {
+            		dbModel.add(stmt);
+            	}
+            }
             
-            for (StmtIterator it = model.listStatements(); it.hasNext();)
-            {
-                Statement stmt = it.nextStatement();
-                Resource subject = stmt.getSubject();
-                String nameSpace = subject.getNameSpace();
-                
-                if (subject.isAnon() || providerNameSpace.equals(nameSpace)) {
-                    dbModel.add(stmt);
-                }
+            // Add a statement asserting when the model was added
+            //
+            if (lastModifiedDate != null) {
+            	dbModel.add(uri, MOBY.lastModifiedDate, lastModifiedDate.getTime());
             }
             
             // Commit the transaction on the database model
             //
             dbModel.commit();
-            
-            // Add to the database another model, with the provider URL as its name
-            //
-            Model providerModel = maker.createModel(uri.getURI());
-            providerModel.add(model);
-            providerModel.setNsPrefixes(model.getNsPrefixMap());
-            
-            // Add a statement asserting when the model was added to the database
-            //
-            if (lastModifiedDate != null) {
-                providerModel.add(uri, MOBY.lastModifiedDate, lastModifiedDate.getTime());
-            }
-            providerModel.close();
         }
         catch (StorageException se) {
             throw se;
@@ -160,21 +129,16 @@
             Resource provider = dbModel.createResource(providerURI);
             String providerNameSpace = provider.getNameSpace();
             
-            Model modelToRemove = maker.openModel(providerURI);
-            
+            // Start a transaction on the database
+            //
             dbModel.begin();
-            for (StmtIterator it = modelToRemove.listStatements(); it.hasNext();)
-            {
-                Statement stmt = it.nextStatement();
-                Resource subject = stmt.getSubject();
-                String nameSpace = subject.getNameSpace();
-                
-                if (subject.isAnon() || providerNameSpace.equals(nameSpace)) {
-                	dbModel.remove(stmt);
-                }
-            }
-            modelToRemove.close();
-            maker.removeModel(providerURI);
+            
+            // Remove all statements that are reachable from the provider URI
+            //
+            ProviderRemover.remove(dbModel, providerURI);
+            
+            // Commit the transaction on the database
+            //
             dbModel.commit();
         }
         catch (StorageException se) {



From gss at pub.open-bio.org  Wed Jun 16 19:33:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:33:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162333.i5GNXPOW022832@pub.open-bio.org>


gss
Wed Jun 16 19:33:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv22807/S-MOBY/ref-impl/server/src/org/smoby/ref/tools

Modified Files:
	URIInvestigator.java 
Log Message:
Use new StorageManager protocol

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/05/19 18:26:40	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/06/16 23:33:25	1.4
@@ -131,33 +131,21 @@
         StorageManager manager = new StorageManager();
     
         // Find out if the provider is already registered, and if so, when
-        // was its graph last modified. If either operation fail, log a
-        // message and return.
+        // was its graph last modified.
         //
-        boolean alreadyRegistered = false;
         Date lastModifiedDate = null;
+        boolean alreadyRegistered = false;
         
         try {
-            alreadyRegistered = manager.containsProvider(providerURI);
+        	lastModifiedDate = manager.getLastModifiedDate(providerURI);
+            alreadyRegistered = (lastModifiedDate != null);
         }
         catch (StorageException e)
         {
-        	syncLog.error("Couldn't check if provider URL " + providerURI + " exists", e);
+        	syncLog.error("Couldn't check for last modified date of provider URL " + providerURI, e);
             return;
         }
         
-        if (alreadyRegistered)
-        {
-            try {
-            	lastModifiedDate = manager.getLastModifiedDate(providerURI);
-            }
-            catch (StorageException e)
-            {
-            	syncLog.error("Couldn't check for last modified date of provider URL " + providerURI, e);
-                return;
-            }
-        }
-        
         // Helper class for making the HTTP GET call
         //
         HTTPRequest request = HTTPRequest.newGetRequest(providerURI);



From gss at pub.open-bio.org  Thu Jun 17 13:34:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:34:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171734.i5HHYHoV025365@pub.open-bio.org>


gss
Thu Jun 17 13:34:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25340/S-MOBY/ref-impl/core/src/org/smoby/vocabulary

Modified Files:
	MOBY.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/16 23:30:13	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/17 17:34:17	1.3
@@ -10,7 +10,7 @@
 
     public static String getURI()
     {
-        return "http://www.s-moby.org:8080/terms#";
+        return "http://www.s-moby.org:8080/terms/";
     }
     
     public static final Resource Provider   		= resource(getURI(), "Provider");



From gss at pub.open-bio.org  Thu Jun 17 13:35:01 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:35:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171735.i5HHZ1eA025407@pub.open-bio.org>


gss
Thu Jun 17 13:35:01 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv25380/S-MOBY/ref-impl/core/src/org/smoby/parser

Modified Files:
	Parser.java 
Log Message:
Fixed typo

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/16 23:29:20	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/17 17:35:01	1.3
@@ -127,8 +127,7 @@
      */
     public Parser(Model model)
     {
-    	
-        StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
+    	StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
         while (it.hasNext())
         {
         	Statement stmt = it.nextStatement();



From gss at pub.open-bio.org  Thu Jun 17 13:35:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:35:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171735.i5HHZqHf025445@pub.open-bio.org>


gss
Thu Jun 17 13:35:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools
In directory pub.open-bio.org:/tmp/cvs-serv25420/S-MOBY/ref-impl/server/WebRoot/tools

Modified Files:
	developer.html 
Log Message:
Minor fixes

moby-live/S-MOBY/ref-impl/server/WebRoot/tools developer.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html	2004/06/16 22:27:14	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html	2004/06/17 17:35:52	1.4
@@ -40,7 +40,9 @@
       "Convert Graph"></p>
 
       <p><textarea name="graph" rows="15" cols="80">
-                                              
+                                                          
+                                                             
+                                                     
                                                
                                        
                                  
@@ -56,8 +58,7 @@
     <form method="get" action=
     "http://www.s-moby.org:8080/list-providers">
       &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; <input type="submit"
-      value="List Providers">&nbsp;&nbsp; <input type="checkbox" name=
-      "show-contents" value="true"> Show provider description graphs
+      value="List Providers">
     </form>
 
     <h4><u>List&nbsp;all statements&nbsp;in the S-MOBY metadata
@@ -79,7 +80,9 @@
       <p><input type="submit" value="Validate"></p>
 
       <p><textarea name="graph" rows="15" cols="80">
-                                              
+                                                          
+                                                             
+                                                     
                                                
                                        
                                  
@@ -99,7 +102,9 @@
       <p><input type="submit" value="Validate"></p>
 
       <p><textarea name="graph" rows="15" cols="80">
-                                              
+                                                          
+                                                             
+                                                     
                                                
                                        
                                  



From gss at pub.open-bio.org  Thu Jun 17 13:35:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:35:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171735.i5HHZqgT025464@pub.open-bio.org>


gss
Thu Jun 17 13:35:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv25420/S-MOBY/ref-impl/server/WebRoot

Modified Files:
	domains.html 
Log Message:
Minor fixes

moby-live/S-MOBY/ref-impl/server/WebRoot domains.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html	2004/04/01 00:34:23	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html	2004/06/17 17:35:52	1.4
@@ -1,178 +1,176 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
 <html>
-<head>
-  <title>Semantic MOBY Server - Hosted Pages</title>
-</head>
-<body>
-<table style="text-align: center; width: 100%;" border="1"
- cellpadding="0" cellspacing="0">
-  <tbody>
-    <tr>
-      <td
- style="vertical-align: top; background-color: rgb(204, 204, 204);"> <b>Semantic
-MOBY Server - Hosted Pages</b> </td>
-    </tr>
-  </tbody>
-</table>
-<p>
-The Semantic MOBY reference implementation server hosts the following
-pages:<br>
-<br>
-<table style="text-align: left; width: 100%;" border="1" cellpadding="2"
- cellspacing="0">
-  <tbody>
-    <tr>
-      <td style="vertical-align: top;"><span style="font-weight: bold;">Page</span><br>
-      </td>
-      <td style="vertical-align: top;"><span style="font-weight: bold;">Description</span><br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.acmepubs.com:8080">www.acmepubs.com</a></td>
-      <td style="vertical-align: top;">Home page of an
-acmepubs.com, a hypothetical citation search provider.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.acmepubs.com:8080/citationSearch">www.acmepubs.com/citationSearch</a></td>
-      <td style="vertical-align: top;">Provider description
-graph for acmepubs.com. Note that doing an HTTP GET on this URI (e.g.
-by clicking on the link at the left), by definition returns an RDF
-graph that describes the provider. Also note that in this reference
-implementation, the URI is implemented as a Java Servlet.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.megapubs.com:8080">www.megapubs.com</a></td>
-      <td style="vertical-align: top;">Home page of an
-megapubs.com, another example citation search provider.</td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.megapubs.com:8080/citationSearch">www.megapubs.com/citationSearch</a></td>
-      <td style="vertical-align: top;">Provider description
-graph for megapubs.com. The notes regarding the
-www.acmepubs.com/citationSearch also apply to this URI.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.pubs.org:8080">www.pubs.org</a></td>
-      <td style="vertical-align: top;">Home page of a
-hypothetical vocabulary provider, pubs.org.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.pubs.org:8080/terms">www.pubs.org/terms</a></td>
-      <td style="vertical-align: top;">The vocabulary of terms
-defined by pubs.org. Note that in this reference implementation, unlike
-the two citation search providers, this vocabulary is provided in a
-resource file (terms) delivered as is by the web server - no servlets
-are involved.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a href="http://www.go.org:8080">www.go.org</a></td>
-      <td style="vertical-align: top;">Home page of a
-hypothetical vocabulary provider, go.org. This provider is meant to be
-representative of the type of vocabulary information that the real Gene
-Ontology (GO) Consortium would need to provide in order to be a
-Semantic MOBY vocabulary provider.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.go.org:8080/terms">www.go.org/terms</a></td>
-      <td style="vertical-align: top;">The vocabulary of terms
-defined by go.org. The notes regarding www.pubs.org/terms apply
-here as well.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.sgd.org:8080/">www.sgd.org</a></td>
-      <td style="vertical-align: top;">Home page of a
-hypothetical vocabulary provider, sgd.org. This provider is meant to be
-representative of the type of vocabulary
-information that the real <i>Saccharomyces Gene Database </i>would
-need to
-provide in order to be a Semantic MOBY vocabulary provider.</td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.sgd.org:8080/terms">www.sgd.org/terms</a></td>
-      <td style="vertical-align: top;">The vocabulary of terms
-defined by go.org. The notes regarding www.pubs.org/terms apply
-here as well.</td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;">www.s-moby.org</td>
-      <td style="vertical-align: top;">This page you're
-currently viewing.</td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.s-moby.org:8080/terms">www.s-moby.org/terms</a></td>
-      <td style="vertical-align: top;">The Semantic MOBY
-vocabulary terms. The notes regarding www.pubs.org/terms
-apply here as well.</td>
-    </tr>
-  </tbody>
-</table>
-<span style="font-weight: bold;"></span><br>
-</p>
-<div style="margin-left: 40px;">
-<div style="margin-left: 40px;"></div>
-</div>
-Since these hosts are virtual, in order to access their pages by name,
-you will need to modify how hosts are looked up. This can most easily
-be
-done by adding
-entries to the <code>hosts</code> file, making the host names refer to
-the
-local host (<code>127.0.0.1</code>). The Tomcat web server / servlet
-container then resolves to a virtual host by name. The following
-entries
-should be added
-to the <code>hosts</code> file of the given operating system on which
-the
-test server is running:
-<p><u>Under Linux/Unix, add to <code>/etc/hosts</code></u>
-</p>
-<ul>
-  <code>
-127.0.0.1 www.acmepubs.com acmepubs.com<br>
-127.0.0.1 www.megapubs.com megapubs.com<br>
-127.0.0.1 www.pubs.org pubs.org<br>
-127.0.0.1 www.go.org go.org<br>
-127.0.0.1 www.sgd.org sgd.org<br>
-127.0.0.1 www.s-moby.org s-moby.org<br>
-127.0.0.1 www.smobydev.org smobydev.org<br>
-  </code>
-</ul>
-<p>
-<u>Under Windows NT/2000/XP, add to
-<code>&lt;WIN_DIR&gt;/system32/drivers/etc/hosts</code></u>
-</p>
-<ul>
-  <code>
-127.0.0.1 acmepubs.com<br>
-127.0.0.1 www.acmepubs.com<br>
-127.0.0.1 megapubs.com<br>
-127.0.0.1 www.megapubs.com<br>
-127.0.0.1 go.org<br>
-127.0.0.1 www.go.org<br>
-127.0.0.1 sgd.org<br>
-127.0.0.1 www.sgd.org<br>
-127.0.0.1 pubs.org<br>
-127.0.0.1 www.pubs.org<br>
-127.0.0.1 s-moby.org<br>
-127.0.0.1 www.s-moby.org<br>
-  </code>
-</ul>
-</body>
+  <head>
+    <meta name="generator" content="HTML Tidy, see www.w3.org">
+
+    <title>Semantic MOBY Server - Hosted Pages</title>
+  </head>
+
+  <body>
+    <table style="WIDTH: 100%; TEXT-ALIGN: center" border="1"
+    cellpadding="0" cellspacing="0">
+      <tbody>
+        <tr>
+          <td style=
+          "VERTICAL-ALIGN: top; BACKGROUND-COLOR: rgb(204,204,204)">
+          <b>Semantic MOBY Server - Hosted Pages</b></td>
+        </tr>
+      </tbody>
+    </table>
+
+    <p>The Semantic MOBY reference implementation server hosts the
+    following pages:<br>
+    <br>
+    </p>
+
+    <table style="WIDTH: 100%; TEXT-ALIGN: left" border="1"
+    cellpadding="2" cellspacing="0">
+      <tbody>
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><span style=
+          "FONT-WEIGHT: bold">Page</span><br>
+          </td>
+
+          <td style="VERTICAL-ALIGN: top"><span style=
+          "FONT-WEIGHT: bold">Description</span><br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.acmepubs.com:8080">www.acmepubs.com</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of an acmepubs.com,
+          a hypothetical citation search provider.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td><a href=
+          "http://www.acmepubs.com:8080/terms">http://www.acmepubs.com/terms</a></td>
+
+          <td>The vocabulary of terms defined by acmepubs.com.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.acmepubs.com:8080/citationSearch">www.acmepubs.com/citationSearch</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Provider description graph
+          for acmepubs.com. Note that doing an HTTP GET on this URI
+          (e.g. by clicking on the link at the left), by definition
+          returns an RDF graph that describes the provider. Also note
+          that in this reference implementation, the URI is implemented
+          as a Java Servlet.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.megapubs.com:8080">www.megapubs.com</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of an megapubs.com,
+          another example citation search provider.</td>
+        </tr>
+
+        <tr>
+          <td><a href=
+          "http://www.megapubs.com:8080/terms">www.megapubs.com/terms</a></td>
+
+          <td>The vocabulary of terms defined by megapubs.com.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.megapubs.com:8080/citationSearch">www.megapubs.com/citationSearch</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Provider description graph
+          for megapubs.com. The notes regarding the
+          www.acmepubs.com/citationSearch also apply to this URI.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.pubs.org:8080">www.pubs.org</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of a hypothetical
+          vocabulary provider, pubs.org.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.pubs.org:8080/terms">www.pubs.org/terms</a></td>
+
+          <td style="VERTICAL-ALIGN: top">The vocabulary of terms
+          defined by pubs.org. Note that in this reference
+          implementation, unlike the two citation search providers,
+          this vocabulary is provided in a resource file (terms)
+          delivered as is by the web server - no servlets are
+          involved.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.go.org:8080">www.go.org</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of a hypothetical
+          vocabulary provider, go.org. This provider is meant to be
+          representative of the type of vocabulary information that the
+          real Gene Ontology (GO) Consortium would need to provide in
+          order to be a Semantic MOBY vocabulary provider.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.go.org:8080/terms">www.go.org/terms</a></td>
+
+          <td style="VERTICAL-ALIGN: top">The vocabulary of terms
+          defined by go.org. The notes regarding www.pubs.org/terms
+          apply here as well.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.sgd.org:8080/">www.sgd.org</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of a hypothetical
+          vocabulary provider, sgd.org. This provider is meant to be
+          representative of the type of vocabulary information that the
+          real <i>Saccharomyces Gene Database</i> would need to provide
+          in order to be a Semantic MOBY vocabulary provider.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.sgd.org:8080/terms">www.sgd.org/terms</a></td>
+
+          <td style="VERTICAL-ALIGN: top">The vocabulary of terms
+          defined by go.org. The notes regarding www.pubs.org/terms
+          apply here as well.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top">www.s-moby.org</td>
+
+          <td style="VERTICAL-ALIGN: top">This page you're currently
+          viewing.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.s-moby.org:8080/terms">www.s-moby.org/terms</a></td>
+
+          <td style="VERTICAL-ALIGN: top">The Semantic MOBY vocabulary
+          terms. The notes regarding www.pubs.org/terms apply here as
+          well.</td>
+        </tr>
+      </tbody>
+    </table>
+  </body>
 </html>



From gss at pub.open-bio.org  Thu Jun 17 13:37:05 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:37:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171737.i5HHb5Mf025523@pub.open-bio.org>


gss
Thu Jun 17 13:37:05 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv25498/S-MOBY/ref-impl/server/src/org/smoby/ref/tools

Modified Files:
	URIInvestigator.java 
Log Message:
Cleanup

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/06/16 23:33:25	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/06/17 17:37:05	1.5
@@ -176,10 +176,30 @@
         
         switch (status)
         {
+            case HttpServletResponse.SC_NOT_MODIFIED:
+                
+                // The resource has not been modified since it was
+                // registered, so there is nothing to do but log a message.
+                //
+            	syncLog.info("IN-SYNC : " + providerURI);
+                break;
+            
+            case HttpServletResponse.SC_NOT_FOUND:
+                
+                // The resource is no longer accessible, so de-register it
+                // from the database.
+                //
+                if (alreadyRegistered) {
+                	deregisterProvider(manager, true);
+                } else {
+                	syncLog.info("IGNORED : " + providerURI + " doesn't exist");
+                }
+                break;
+                
             case HttpServletResponse.SC_OK:
                 
-                // The call succeeded, so graphString should contain a valid graph.
-                // Try to parse it.
+                // The call succeeded, so see if graphString contains
+            	// a valid graph by trying to parse it.
                 //
                 lastModifiedDate = null;
                 
@@ -226,61 +246,30 @@
                     Parser parser = Parser.forInputStream(in, Parser.LANGUAGE_RDF_XML);
                     provider = parser.parseProvider();
                 }
-                catch (UnparsableGraphException e)
-                {
-                	syncLog.warn("Unparsable graph found at " + providerURI +
-                        (alreadyRegistered ? "; deregistering" : "; ignoring"));
-                    if (alreadyRegistered) {
-                        deregisterProvider(manager);
-                    }
-                    return;
-                }
+                catch (Throwable t) {}
                 
-                if (alreadyRegistered) {
-                    deregisterProvider(manager);
-                }
-                
-                try
-                {
-                    manager.registerProvider(provider, lastModifiedDate);
-                    
-                    // Log a message about successfully registering the graph:
-                    //
-                    syncLog.info((alreadyRegistered ? "UPDATED : " : "ADDED   : ") + providerURI);
-                }
-                catch (StorageException e) {
-                	syncLog.error("Error storing graph for " + providerURI, e);
-                }
-                
-                break;
-                
-            case HttpServletResponse.SC_NOT_MODIFIED:
-                
-                // The resource has not been modified since it was
-                // registered, so there is nothing to do but log a message.
+                // De-register the provider, printing a removal message if
+                // a provider couldn't be parsed
                 //
-            	syncLog.info("IN-SYNC : " + providerURI);
-                break;
-            
-            case HttpServletResponse.SC_NOT_FOUND:
+                deregisterProvider(manager, provider==null);
                 
-                // The resource is no longer accessible, so de-register it
-                // from the database.
+                // If a provider was parsed, then register it
                 //
-                if (alreadyRegistered)
-                {    
-                    try
-                    {
-                    	manager.deregisterProvider(providerURI);
-                    	syncLog.info("REMOVED : " + providerURI);
-                    }
-                    catch (StorageException e) {
-                    	syncLog.error("Unable to de-register provider " + providerURI, e);
-                    }
-                }
-                else {
-                	syncLog.info("IGNORED : " + providerURI + " doesn't exist");
+                if (provider != null)
+                {
+	                try
+	                {
+	                    manager.registerProvider(provider, lastModifiedDate);
+	                    
+	                    // Log a message about successfully registering the graph:
+	                    //
+	                    syncLog.info((alreadyRegistered ? "UPDATED : " : "ADDED   : ") + providerURI);
+	                }
+	                catch (StorageException e) {
+	                	syncLog.error("Error storing graph for " + providerURI, e);
+	                }
                 }
+                
                 break;
             
             default:
@@ -293,10 +282,13 @@
         }
     }
     
-    private void deregisterProvider(StorageManager manager)
+    private void deregisterProvider(StorageManager manager, boolean removing)
     {
         try {
         	manager.deregisterProvider(providerURI);
+        	if (removing) {
+            	syncLog.info("REMOVED : " + providerURI);
+        	}
         }
         catch (StorageException e) {
         	syncLog.error("Unable to de-register provider " + providerURI, e);



From gss at pub.open-bio.org  Thu Jun 17 13:37:58 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:37:58 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171737.i5HHbwhw025564@pub.open-bio.org>


gss
Thu Jun 17 13:37:58 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev
In directory pub.open-bio.org:/tmp/cvs-serv25539/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev

Modified Files:
	ProviderListServlet.java 
Log Message:
Since only global model saved, iterate over its rdf:type moby:Provider statements

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev ProviderListServlet.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/06/14 20:59:36	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/06/17 17:37:57	1.4
@@ -1,12 +1,10 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.servlet.*;
-import org.smoby.tools.*;
-import org.smoby.ref.servlets.BaseServlet;
+import org.smoby.vocabulary.*;
+import org.smoby.ref.servlets.*;
 import org.smoby.ref.tools.db.*;
-import org.smoby.ref.tools.*;
-
 import com.hp.hpl.jena.rdf.model.*;
+import com.hp.hpl.jena.vocabulary.*;
 import java.io.*;
 import java.util.*;
 import javax.servlet.*;
@@ -22,23 +20,19 @@
         
         try
         {
-            boolean showContents = (request.getParameter("show-contents") != null);
-            String globalModelName = MOBYProperties.getProperty("DB_REPOSITORY_NAME", true);
-            ModelMaker maker = manager.getModelMaker();
+        	Model dbModel = manager.openDBModel();
             int count = 0;
-            for (Iterator it = maker.listModels(); it.hasNext();) {
-            	String modelName = it.next().toString();
-                if (! modelName.equals(globalModelName)) {
-                    count++;
-                    if (showContents) {
-                        Model model = maker.openModel(modelName);
-                        model.write(out, "RDF/XML-ABBREV");
-                        model.close();
-                    } else {
-                    	out.println(modelName);
-                    }
-                }
+            StmtIterator it = dbModel.listStatements(
+            	null, RDF.type, MOBY.Provider);
+            
+            while (it.hasNext()) {
+            	Statement stmt = it.nextStatement();
+            	out.println(stmt.getSubject().getURI());
+            	count++;
             }
+            
+            dbModel.close();
+            
             if (count < 1) {
             	out.println("No providers are defined");
             }
@@ -46,8 +40,5 @@
         catch (StorageException e) {
             throw new ServletException(e);
         }
-        catch (MissingPropertyException e) {
-            throw new ServletException(e);
-        }
     }
 }
\ No newline at end of file



From gss at pub.open-bio.org  Thu Jun 17 13:38:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:38:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171738.i5HHcx4E025602@pub.open-bio.org>


gss
Thu Jun 17 13:38:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary

Modified Files:
	MegaPubs.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary MegaPubs.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java	2004/05/19 18:26:48	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java	2004/06/17 17:38:59	1.4
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.megapubs.com:8080/";
+        return "http://www.megapubs.com:8080/terms/";
     }
     
     public static final Property geneSymbol  = property(getURI(), "geneSymbol");



From gss at pub.open-bio.org  Thu Jun 17 13:38:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:38:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171738.i5HHcxiZ025621@pub.open-bio.org>


gss
Thu Jun 17 13:38:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary

Modified Files:
	Go.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary Go.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java	2004/05/19 18:26:55	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java	2004/06/17 17:38:59	1.3
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.go.org:8080/";
+        return "http://www.go.org:8080/terms/";
     }
     
     public static final Resource GeneSymbol = resource(getURI(), "GeneSymbol");



From gss at pub.open-bio.org  Thu Jun 17 13:39:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:39:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171739.i5HHd0wp025641@pub.open-bio.org>


gss
Thu Jun 17 13:38:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary

Modified Files:
	SGD.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary SGD.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java	2004/05/19 18:26:22	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java	2004/06/17 17:38:59	1.3
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.sgd.org:8080/";
+        return "http://www.sgd.org:8080/terms/";
     }
     
     public static final Resource LiteratureGuide = resource(getURI(), "LiteratureGuide");



From gss at pub.open-bio.org  Thu Jun 17 13:39:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:39:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171739.i5HHd0Ft025663@pub.open-bio.org>


gss
Thu Jun 17 13:38:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary

Modified Files:
	AcmePubs.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary AcmePubs.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java	2004/05/19 18:26:52	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java	2004/06/17 17:38:59	1.5
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.acmepubs.com:8080/";
+        return "http://www.acmepubs.com:8080/terms/";
     }
     
     public static final Property geneSymbol  = property(getURI(), "geneSymbol");



From gss at pub.open-bio.org  Thu Jun 17 13:39:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:39:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171739.i5HHd0Fp025684@pub.open-bio.org>


gss
Thu Jun 17 13:39:00 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary

Modified Files:
	Pubs.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Pubs.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java	2004/05/19 18:26:25	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java	2004/06/17 17:39:00	1.4
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.pubs.org:8080/";
+        return "http://www.pubs.org:8080/terms/";
     }
     
     public static final Resource PubAbstract = resource(getURI(), "PubAbstract");



From gss at pub.open-bio.org  Fri Jun 18 17:37:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:37:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182137.i5ILbqHC029781@pub.open-bio.org>


gss
Fri Jun 18 17:37:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv29756/src/org/smoby/graph/impl

Modified Files:
	MOBYObjectFactory.java 
Added Files:
	MOBYProviderSetImpl.java 
Log Message:
New class to represent a set of providers

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl MOBYProviderSetImpl.java,NONE,1.1 MOBYObjectFactory.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java	2004/05/24 22:05:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java	2004/06/18 21:37:52	1.2
@@ -40,6 +40,11 @@
                 					underlying);
     }
     
+    public static MOBYProviderSet newProviderSet()
+    {
+    	return new MOBYProviderSetImpl();
+    }
+    
     public static MOBYGraph newGraph(String uri, MOBYGraphNode hasMapping, Model underlying)
     {
         return new MOBYGraphImpl(uri, hasMapping, underlying);



From gss at pub.open-bio.org  Fri Jun 18 17:37:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:37:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182137.i5ILbqEZ029796@pub.open-bio.org>


gss
Fri Jun 18 17:37:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv29756/src/org/smoby/graph

Added Files:
	MOBYProviderSet.java 
Log Message:
New class to represent a set of providers

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYProviderSet.java,NONE,1.1


From gss at pub.open-bio.org  Fri Jun 18 17:38:27 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:38:27 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182138.i5ILcRMk029838@pub.open-bio.org>


gss
Fri Jun 18 17:38:27 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv29813/src/org/smoby/parser

Modified Files:
	Parser.java 
Log Message:
Minor small fixes

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/17 17:35:01	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/18 21:38:27	1.4
@@ -6,6 +6,7 @@
 import org.smoby.graph.*;
 import org.smoby.graph.impl.*;
 import org.smoby.parser.*;
+import org.smoby.tools.Util;
 import org.smoby.vocabulary.*;
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.vocabulary.*;
@@ -100,7 +101,7 @@
     public static Parser forInputStream(InputStream is, String language)
 		throws UnparsableGraphException
     {
-        Model model = ModelFactory.createDefaultModel();
+        Model model = Util.newJenaModel();
         try {
             model.read(is, "", language);
         } catch (Throwable t) {
@@ -131,45 +132,14 @@
         while (it.hasNext())
         {
         	Statement stmt = it.nextStatement();
-        	Model subModel = ModelFactory.createDefaultModel();
+        	Model subModel = Util.newJenaModel();
         	subModel.setNsPrefixes(model.getNsPrefixMap());
         	Resource subject = stmt.getSubject();
-        	addReachableStmts(subModel, subject, subject.getURI());
+        	Util.addReachableStmts(model, subModel, subject, subject.getURI());
         	inferenceModels.put(subModel,
         		ModelFactory.createRDFSModel(subModel));
         }
     }
-    
-	private void addReachableStmts(Model model, Resource subject, String uri)
-	{
-		// For each statement whose subject is the given resource
-		//
-		StmtIterator it = subject.getModel().listStatements(
-			subject, null, (RDFNode) null);
-		
-		while (it.hasNext())
-		{
-			Statement stmt = it.nextStatement();
-			
-			// The statement itself should be added
-			//
-			model.add(model.createStatement(
-				stmt.getSubject(), stmt.getPredicate(), stmt.getObject()));
-			
-			// If the object of the statement is a blank node or a
-			// resource whose URI starts with the provider URI, then
-			// recursively add the statements that are reachable
-			// from the object
-			//
-			if (stmt.getObject().canAs(Resource.class))
-			{
-				Resource object = (Resource) stmt.getObject().as(Resource.class);
-				if (object.isAnon() || object.getURI().startsWith(uri)) {
-					addReachableStmts(model, object, uri);
-				}
-			}
-		}
-	}
 
     /**
      * Parse a provider from the model. If the model contains
@@ -196,14 +166,9 @@
     {
         ArrayList providers = new ArrayList();
         
-        // Find the statements that say something is of type Provider
-        //
-//        StmtIterator it = underlying.listStatements(null, RDF.type, MOBY.Provider);
-        
-        Iterator it = inferenceModels.keySet().iterator();
-        
         // Parse each provider
         //
+        Iterator it = inferenceModels.keySet().iterator();
         while (it.hasNext())
         {
         	Model model = (Model) it.next();



From gss at pub.open-bio.org  Fri Jun 18 17:38:46 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:38:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182138.i5ILckEJ029877@pub.open-bio.org>


gss
Fri Jun 18 17:38:46 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv29852/src/org/smoby/tools

Modified Files:
	Util.java 
Log Message:
New utility methods

moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools Util.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/Util.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/Util.java	2004/05/24 22:05:36	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/Util.java	2004/06/18 21:38:46	1.2
@@ -4,6 +4,15 @@
 import java.util.*;
 
 import org.apache.commons.httpclient.util.DateParser;
+import org.smoby.vocabulary.MOBY;
+
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.NsIterator;
+import com.hp.hpl.jena.rdf.model.RDFNode;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.rdf.model.StmtIterator;
 
 /**
  * This abstract class contains a miscellaneous set of useful static methods
@@ -26,4 +35,119 @@
     {
     	return HTTP_DATE_FORMAT.format(date);
     }
+    
+    public static Model newJenaModel()
+    {
+    	Model model = ModelFactory.createDefaultModel();
+    	MOBY.addNsPrefix(model);
+    	return model;
+    }
+    
+	public static void addReachableStmts(
+		Model source, Model dest, Resource subject, String uri)
+	{
+		// For each statement whose subject is the given resource
+		//
+		StmtIterator it = source.listStatements(
+			subject, null, (RDFNode) null);
+		
+		while (it.hasNext())
+		{
+			Statement stmt = it.nextStatement();
+			
+			// The statement itself should be added
+			//
+			dest.add(dest.createStatement(
+				stmt.getSubject(), stmt.getPredicate(), stmt.getObject()));
+			
+			// If the object of the statement is a blank node or a
+			// resource whose URI starts with the provider URI, then
+			// recursively add the statements that are reachable
+			// from the object
+			//
+			if (stmt.getObject().canAs(Resource.class))
+			{
+				Resource object = (Resource) stmt.getObject().as(Resource.class);
+				if (object.isAnon() || (uri != null && object.getURI().startsWith(uri))) {
+					addReachableStmts(source, dest, object, uri);
+				}
+			}
+		}
+	}
+	
+	/**
+	 * Add the namespace prefix mappings from a source model to a destination
+	 * model. A prefix mapping associates a qualified name (e.g. 'moby') with
+	 * a full URL (e.g. 'http://www.s-moby.org:8080/terms/'). In case a prefix
+	 * is already in the destination model, then use the next available prefix
+	 * formed by adding a number to the end of the prefix (e.g. if 'foo' is
+	 * taken, then add 'foo_1' if it is available, or 'foo_2' if not...).
+	 */
+	public static void addNsPrefixes(Model source, Model dest)
+	{
+		Map prefixes = source.getNsPrefixMap();
+		Iterator it = prefixes.keySet().iterator();
+		
+		while (it.hasNext())
+		{
+			// Prefix and associated URI to be added
+			//
+			String prefix = it.next().toString();
+			String uri = prefixes.get(prefix).toString();
+			
+			// Check to see if the prefix is already in the destination model
+			//
+			String prevURI = dest.getNsPrefixURI(prefix);
+			
+			if (prevURI == null)
+			{
+				// Not used, so just add it
+				//
+				dest.setNsPrefix(prefix, uri);
+			}
+			else if (! prevURI.equals(uri))
+			{
+				// Used and doesn't match previous, so add the next
+				// available prefix
+				//
+				boolean added = false;
+				for (int i = 1; (! added); i++)
+				{
+					String newPrefix = prefix + "_" + i;
+					if (dest.getNsPrefixURI(newPrefix) == null)
+					{
+						dest.setNsPrefix(newPrefix, uri);
+						added = true;
+					}
+				}
+			}
+		}
+	}
+	
+	/**
+	 * Remove unused namespace prefixes from the given model.
+	 */
+	public static void removeUnusedNsPrefixes(Model model)
+	{
+		Map newMap = new HashMap();
+		
+		for (NsIterator it = model.listNameSpaces(); it.hasNext();)
+		{
+			String uri = it.nextNs();
+			String prefix = model.getNsURIPrefix(uri);
+			newMap.put(prefix, uri);
+		}
+		
+		List toRemove = new ArrayList();
+		Iterator it = model.getNsPrefixMap().keySet().iterator();
+		while (it.hasNext()) {
+			toRemove.add(it.next());
+		}
+		it = toRemove.iterator();
+		while (it.hasNext()) {
+			model.removeNsPrefix(it.next().toString());
+		}
+		
+		model.setNsPrefixes(newMap);
+	}
 }



From gss at pub.open-bio.org  Fri Jun 18 17:39:42 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:39:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182139.i5ILdgl7029933@pub.open-bio.org>


gss
Fri Jun 18 17:39:42 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv29908/src/org/smoby/vocabulary

Modified Files:
	MOBY.java 
Log Message:
Added nsPrefix methods

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/17 17:34:17	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/18 21:39:42	1.4
@@ -13,6 +13,16 @@
         return "http://www.s-moby.org:8080/terms/";
     }
     
+    public static String getNsPrefix()
+    {
+    	return "moby";
+    }
+    
+    public static void addNsPrefix(Model model)
+    {
+    	model.setNsPrefix(getNsPrefix(), getURI()); 
+    }
+    
     public static final Resource Provider   		= resource(getURI(), "Provider");
     public static final Resource Graph      		= resource(getURI(), "Graph");
     public static final Resource Subject    		= resource(getURI(), "Subject");



From gss at pub.open-bio.org  Fri Jun 18 17:41:58 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:41:58 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182141.i5ILfwfr030037@pub.open-bio.org>


gss
Fri Jun 18 17:41:58 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools
In directory pub.open-bio.org:/tmp/cvs-serv30012/WebRoot/tools

Modified Files:
	client.html 
Log Message:
Minor small fixes

moby-live/S-MOBY/ref-impl/server/WebRoot/tools client.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html	2004/06/14 22:04:20	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html	2004/06/18 21:41:58	1.3
@@ -1,42 +1,53 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
 <html>
-<head>
-  <title>Semantic MOBY Client Tools</title>
-</head>
-<body>
-	<table style="text-align: center; width: 100%;" border="1"
+  <head>
+    <meta name="generator" content="HTML Tidy, see www.w3.org">
+
+    <title>Semantic MOBY Client Tools</title>
+  </head>
+
+  <body>
+    <table style="WIDTH: 100%; TEXT-ALIGN: center" border="1"
     cellspacing="0" cellpadding="0">
-    <tbody>
-      <tr>
-        <td style="vertical-align: top; background-color: rgb(204, 204, 204);">
-      	  <b>Semantic MOBY Client Tools</b>
-        </td>
-      </tr>
-    </tbody>
-  </table>
-
-<h4><u>Suggest a provider URL for S-MOBY to explore</u></h4>
-<form action="http://www.s-moby.org:8080/investigate" method="post">
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Provider URL:
-  <input size="60" name="provider-url">&nbsp;&nbsp;
-  <input value="Suggest" type="submit">
-</form>
-
-<h4><u>Discover matching graphs in the S-MOBY metadata repository</u></h4>
-<form action="http://www.s-moby.org:8080/find-providers" method="post">
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Paste a graph in RDF/XML format, select
-  statements to return, and press "Discover" to find matching graphs. &nbsp;&nbsp;
-  <p>
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-  Statements to return:&nbsp;&nbsp;
-  <input type="radio" name="statements" value="minimal">Minimal&nbsp;&nbsp;
-  <input type="radio" name="statements" value="query" CHECKED>Query only&nbsp;&nbsp;
-  <input type="radio" name="statements" value="cached">Cached&nbsp;&nbsp;
-  <input value="Discover" type="submit">
-  <p>
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-  <textarea cols="80" rows="15" name="query-graph"></textarea>
-</form>
+      <tbody>
+        <tr>
+          <td style=
+          "VERTICAL-ALIGN: top; BACKGROUND-COLOR: rgb(204,204,204)">
+          <b>Semantic MOBY Client Tools</b></td>
+        </tr>
+      </tbody>
+    </table>
+
+    <h4><u>Suggest a provider URL for S-MOBY to explore</u></h4>
+
+    <form action="http://www.s-moby.org:8080/investigate" method=
+    "post">
+      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Provider URL: <input size=
+      "60" name="provider-url">&nbsp;&nbsp; <input value="Suggest"
+      type="submit">
+    </form>
+
+    <h4><u>Discover matching graphs in the S-MOBY metadata
+    repository</u></h4>
+
+    <form action="http://www.s-moby.org:8080/find-providers" method=
+    "post">
+      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Paste a graph in RDF/XML
+      format, select statements to return, and press "Discover" to find
+      matching graphs. &nbsp;&nbsp; 
+
+      <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Statements to
+      return:&nbsp;&nbsp; <input type="radio" name="statements" value=
+      "minimal">Minimal&nbsp;&nbsp; <input type="radio" name=
+      "statements" value="query">Query only&nbsp;&nbsp; <input type=
+      "radio" name="statements" value="reachable" checked=
+      "">Reachable&nbsp; <input value="Discover" type="submit"></p>
 
-</body>
+      <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <textarea name=
+      "query-graph" rows="15" cols="80">
+          
+      </textarea></p>
+    </form>
+  </body>
 </html>



From gss at pub.open-bio.org  Fri Jun 18 17:42:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:42:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182142.i5ILgYdP030067@pub.open-bio.org>


gss
Fri Jun 18 17:42:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv30042/src/org/smoby/ref/tools

Modified Files:
	DiscoveryQuery.java 
Log Message:
Changes to utilize single model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/06/10 23:24:16	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/06/18 21:42:34	1.6
@@ -6,6 +6,7 @@
 
 import org.smoby.parser.*;
 import org.smoby.ref.tools.db.*;
+import org.smoby.tools.Util;
 import org.smoby.graph.*;
 import org.smoby.graph.impl.*;
 import org.smoby.vocabulary.*;
@@ -16,6 +17,7 @@
 import com.hp.hpl.jena.rdql.*;
 import com.hp.hpl.jena.shared.*;
 import com.hp.hpl.jena.util.iterator.*;
+import com.hp.hpl.jena.vocabulary.RDF;
 
 /**
  * This class finds graphs that match a query graph.
@@ -23,22 +25,24 @@
 public class DiscoveryQuery
 {
     /**
-     * Constant indicating that only the URI should be returned
-     * in each matching graph.
+     * Constant indicating that only the minimal statements should
+     * be returned in each matching graph.
      */
-    public final static int URI_ONLY = 0;
+    private final static int MINIMAL_STMTS = 0;
     
     /**
      * Constant indicating that only statements in the query should
      * be returned in each matching graph.
      */
-    public final static int QUERY_STMTS_ONLY = 1;
+    private final static int QUERY_STMTS = 1;
     
     /**
-     * Constants indicating that all statements (i.e. the ones found when
-     * the graph was registered) should be returned in each matching graph.
+     * Constant indicating that all reachable statements (i.e. the
+     * ones that can be traversed, starting with the provider node,
+     * without leaving the scope of the provider's URI) should be
+     * returned in each matching graph.
      */
-    public final static int ALL_STMTS = 2;
+    private final static int REACHABLE_STMTS = 2;
     
     /**
      * The graph that serves as a template for providers that match.
@@ -62,6 +66,21 @@
      */
     private int lastBnodeNumber;
     
+    public static DiscoveryQuery newMinimalStmtsQuery(MOBYProvider provider)
+    {
+    	return new DiscoveryQuery(provider, MINIMAL_STMTS);
+    }
+    
+    public static DiscoveryQuery newQueryStmtsQuery(MOBYProvider provider)
+    {
+    	return new DiscoveryQuery(provider, QUERY_STMTS);
+    }
+    
+    public static DiscoveryQuery newReachableStmtsQuery(MOBYProvider provider)
+    {
+    	return new DiscoveryQuery(provider, REACHABLE_STMTS);
+    }
+    
     /**
      * Create an instance for the given query graph and return statements
      * style.
@@ -69,7 +88,7 @@
      * @param statementsToReturn which statements should be returned: URI_ONLY,
      * QUERY_STMTS_ONLY, or ALL_STMTS (use the static constants on this class).
      */
-    public DiscoveryQuery(MOBYProvider queryProvider, int statementsToReturn)
+    private DiscoveryQuery(MOBYProvider queryProvider, int statementsToReturn)
     {
     	this.queryProvider = queryProvider;
         this.statementsToReturn = statementsToReturn;
@@ -85,21 +104,22 @@
         lastBnodeNumber = 0;
     }
     
-    public MOBYCollection findMatchingGraphs()
+    public MOBYProviderSet findMatchingGraphs()
 	{
         init();
         
+        Model dbModel = null;
 		try
 		{
 		    Model queryModel = ((MOBYProviderImpl) queryProvider).getUnderlying();
             String queryString = buildQueryString(queryModel);
             StorageManager manager = new StorageManager();
-            Model model = manager.openDBModel();
-            ((ModelRDB) model).setDoFastpath(false);
+            dbModel = manager.openDBModel();
+            ((ModelRDB) dbModel).setDoFastpath(false);
             
 			// Execute the query
 			//
-			QueryResults results = Query.exec(queryString, model);
+			QueryResults results = Query.exec(queryString, dbModel);
 			ArrayList matching = new ArrayList();
             
 			while (results.hasNext())
@@ -109,23 +129,27 @@
 			}
 			results.close();
 			
-			List returnList = new ArrayList();
+			MOBYProviderSet returnSet = MOBYObjectFactory.newProviderSet();
 			
 			for (Iterator it = matching.iterator(); it.hasNext();)
 			{
-				MOBYProvider mp = buildGraphModel(queryModel, (ResultBinding) it.next());
-				String uri = mp.getURI();
-				// YUCK!
-				Model providerModel = manager.openModel(uri);
-				Parser parser = new Parser(providerModel);
-				returnList.add(parser.parseProvider());
+				Object next = it.next();
+				MOBYProvider mp = buildGraphModel(dbModel,
+					queryModel, (ResultBinding) next);
+				returnSet.addProvider(mp);
 			}
 			
-			return MOBYObjectFactory.newUnorderedCollection(null, returnList, null);
+			return returnSet;
 			
 		} catch (Throwable t) {
 			return null;
 		}
+		finally
+		{
+			if (dbModel != null) {
+				dbModel.close();
+			}
+		}
 	}
 	
 	/**
@@ -221,11 +245,12 @@
 	 * @param binding bindings for variables
 	 * @return
 	 */
-	private MOBYProvider buildGraphModel(Model queryModel, ResultBinding binding)
+	private MOBYProvider buildGraphModel(
+		Model dbModel, Model queryModel, ResultBinding binding)
 	{
 		// Create a default model to return
 		//
-		Model model = ModelFactory.createDefaultModel();
+		Model model = Util.newJenaModel();
 		model.setNsPrefixes(queryModel.getNsPrefixMap());
 		
 		// For each statement in the query, create a new statement
@@ -244,10 +269,117 @@
 			Statement copy = model.createStatement(subject, property, object);
 			model.add(copy);
 		}
-		Parser parser = new Parser(model);
+		
+		// Add/remove statements based on the desired set, i.e.
+		// based on the value of statementsToReturn, and remove
+		// unused namespace prefixes from the model.
+		//
+		Model adjusted = adjustedModel(model, dbModel);
+		Util.removeUnusedNsPrefixes(adjusted);
+		
+		// Parse and return a MOBY provider using the adjusted model
+		//
+		Parser parser = new Parser(adjusted);
 		return parser.parseProvider();
 	}
 	
+	/**
+	 * Given a model built from the query template model, return a
+	 * model adjusted to include the statements to match the
+	 * statementsToReturn instance variable. The models that result
+	 * from performing a query consists of exactly the statements
+	 * that were in the query, with some blank nodes filled in. In
+	 * the case of QUERY_STMTS, that is the set that should be
+	 * returned. In the case of MINIMAL_STMTS, only the provider
+	 * type, name, one line description, and about URI statements
+	 * should be returned. In the case of REACHABLE_STMTS, all the
+	 * statements that are reachable from the provider URI, without
+	 * going outside the provider URI's scope, should be returned.
+	 */
+	private Model adjustedModel(Model original, Model dbModel)
+	{
+		switch (statementsToReturn)
+		{
+			case QUERY_STMTS	: return original;
+			case MINIMAL_STMTS	: return minimalModel(original, dbModel);
+			default				: return reachableModel(original, dbModel);
+		}
+	}
+	
+	/**
+	 * Return a model consisting of just the (rdf:type moby:Provider),
+	 * (moby:name <name>), (moby:oneLineDescription <description>), and
+	 * (moby:aboutURI <uri>) property statements for the provider.
+	 */
+	private Model minimalModel(Model original, Model dbModel)
+	{
+		Model minimal = Util.newJenaModel();
+		minimal.setNsPrefixes(dbModel.getNsPrefixMap());
+		
+		// Add the rdf:type MOBY:Provider statement
+		//
+		try {
+			Statement providerTypeStmt = original.listStatements(
+				null, RDF.type, MOBY.Provider).nextStatement();
+			minimal.add(providerTypeStmt);
+			
+			Resource subject = providerTypeStmt.getSubject();
+			
+			// Add a statement, if it exists in the repository, that
+			// says (<subject> moby:name <name>)
+			//
+			try {
+				minimal.add(dbModel.listStatements(subject,
+					MOBY.name, (RDFNode) null).nextStatement());
+			} catch (Throwable t) {} // There was no moby:name property
+
+			// Add a statement, if it exists in the repository, that
+			// says (<subject> moby:aboutURI <uri>)
+			//
+			try {
+				minimal.add(dbModel.listStatements(subject,
+					MOBY.aboutURI, (RDFNode) null).nextStatement());
+			} catch (Throwable t) {} // There was no moby:aboutURI property
+
+			// Add a statement, if it exists in the repository, that
+			// says <subject> moby:oneLineDescription <value>
+			//
+			try {
+				minimal.add(dbModel.listStatements(subject,
+					MOBY.oneLineDescription, (RDFNode) null).nextStatement());
+			} catch (Throwable t) {} // There was no moby:oneLineDescription
+		}
+		catch (Throwable t) {} // There was no (rdf:type moby:Provider)
+		
+		return minimal;
+	}
+	
+	/**
+	 * Return a model consisting of the statements in the original (query)
+	 * model, plus any statements not already in the model that are
+	 * reachable from the subject of the rdf:type moby:Provider statement.
+	 */
+	private Model reachableModel(Model original, Model dbModel)
+	{
+		// Start with a model consisting of the original statements
+		//
+		Model reachable = ModelFactory.createDefaultModel();
+		reachable.setNsPrefixes(dbModel.getNsPrefixMap());
+		reachable.add(original);
+		
+		// Find the subject of the (rdf:type MOBY:Provider) statement
+		//
+		try {
+			Statement providerTypeStmt = original.listStatements(
+				null, RDF.type, MOBY.Provider).nextStatement();
+			Resource subject = providerTypeStmt.getSubject();
+			Util.addReachableStmts(dbModel, reachable, subject, subject.getURI());
+		}
+		catch (Throwable t) {} // There was no (rdf:type moby:Provider)
+		
+		return reachable;
+	}
+	
 	private RDFNode getBinding(RDFNode node, ResultBinding binding)
 	{
 		// If the resource is not a blank node, then just return the
@@ -256,23 +388,16 @@
 		if (! node.asNode().isBlank()) {
 			return node;
 		}
-		//ResultBinding
 		ResultBindingIterator results = binding.iterator();
 		
 		while (results.hasNext())
 		{
-			Object object = results.next();
-			Value value = (Value) object;
+			results.next();
 			String varName = results.varName();
-//			Value value = results.value();
+			RDFNode value = (RDFNode) binding.get(varName);
 			Object cachedName = varNames.get(node.toString());
-			if (varName.equals(cachedName))
-			{
-//				if (value.isRDFLiteral()) {
-//					return value.getRDFLiteral();
-//				} else if (value.isRDFResource()) {
-//					return value.getRDFResource();
-//				}
+			if (varName.equals(cachedName)) {
+				return value;
 			}
 		}
 		return node;



From gss at pub.open-bio.org  Fri Jun 18 17:42:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:42:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182142.i5ILgYea030086@pub.open-bio.org>


gss
Fri Jun 18 17:42:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db
In directory pub.open-bio.org:/tmp/cvs-serv30042/src/org/smoby/ref/tools/db

Modified Files:
	StorageManager.java 
Log Message:
Changes to utilize single model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/06/16 23:33:00	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/06/18 21:42:34	1.5
@@ -3,6 +3,7 @@
 import org.smoby.graph.*;
 import org.smoby.graph.impl.*;
 import org.smoby.ref.tools.*;
+import org.smoby.tools.Util;
 import org.smoby.vocabulary.*;
 import com.hp.hpl.jena.db.*;
 import com.hp.hpl.jena.rdf.model.*;
@@ -83,11 +84,16 @@
             while (it.hasNext()) {
             	Statement stmt = it.nextStatement();
             	Resource subject = stmt.getSubject();
-            	if (subject.isAnon() || subject.getURI().startsWith(uriString)) {
+            	String subjectURI = subject.getURI();
+            	if (subject.isAnon() ||
+            		((subjectURI != null) &&
+            		  subjectURI.startsWith(uriString))) {
             		dbModel.add(stmt);
             	}
             }
             
+            Util.addNsPrefixes(model, dbModel);
+            
             // Add a statement asserting when the model was added
             //
             if (lastModifiedDate != null) {



From gss at pub.open-bio.org  Fri Jun 18 17:42:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:42:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182142.i5ILgYid030106@pub.open-bio.org>


gss
Fri Jun 18 17:42:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets
In directory pub.open-bio.org:/tmp/cvs-serv30042/src/org/smoby/ref/servlets

Modified Files:
	DiscoveryServlet.java 
Log Message:
Changes to utilize single model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets DiscoveryServlet.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/06/14 20:59:36	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/06/18 21:42:34	1.4
@@ -2,8 +2,7 @@
 
 import org.smoby.servlet.*;
 import org.smoby.graph.*;
-import org.smoby.parser.NonCanonicalException;
-import org.smoby.parser.Parser;
+import org.smoby.parser.*;
 import org.smoby.ref.tools.*;
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.rdql.*;
@@ -17,11 +16,15 @@
  * search the metadata repository for graphs that unify with a query graph
  * in the Prolog sense. The query graph should be sent via HTTP POST in a
  * parameter named "query-graph"; a set of matching graphs is returned in
- * the response body in either human-readable text format (the default),
- * or in an efficient, machine-readable binary format. To receive the
- * response in this binary format, the client should send a parameter
- * named "binary-return" in the request, with any value. The client can
- * obtain a Java object suitable for parsing either binary or text format
+ * the response body. The statements to be included in each matching graph
+ * is controlled by sending a parameter named "statements".  If the value
+ * of the parameter is "minimal", then only a small set of statements is
+ * returned, namely the statements that encode the name, one line
+ * description, and URI of the provider. If the value of the parameter is
+ * "reachable", then all statements reachable from the provider node are
+ * returned for each matching provider.
+ * 
+ * The client can obtain a Java object suitable for parsing the graph
  * into an array of ProviderDescriptionGraph objects, by calling the
  * GraphListTransceiverFactory.newReceiver() factory method.
  */
@@ -42,14 +45,30 @@
             //
 			Parser parser = Parser.forString(graphString, Parser.LANGUAGE_RDF_XML);
 			MOBYProvider provider = parser.parseProvider();
+			
+			// Find which statements the user wishes to have returned
+			//
+			String statements = ParamReader.getParameter(
+				"statements", request, false, new String[] {
+					"minimal", "query", "reachable"
+				});
             
             // Retrieve an array of provider description graphs that unify with
             // the query graph.
             //
-            DiscoveryQuery q = new DiscoveryQuery(provider, DiscoveryQuery.ALL_STMTS);
-			MOBYCollection matching = q.findMatchingGraphs();
+            DiscoveryQuery q = null;
+            
+            if (statements.equalsIgnoreCase("minimal")) {
+            	q = DiscoveryQuery.newMinimalStmtsQuery(provider);
+            } else if (statements.equalsIgnoreCase("query")) {
+            	q = DiscoveryQuery.newQueryStmtsQuery(provider);
+            } else {
+            	q = DiscoveryQuery.newReachableStmtsQuery(provider);
+            }
+            
+			MOBYProviderSet matching = q.findMatchingGraphs();
 			
-            if ((matching.size() == 0))
+            if ((matching == null) || (matching.size() == 0))
             {
                 // The client doesn't want the graphs sent in a binary
                 // format, so show a text message indicating that there
@@ -59,20 +78,10 @@
             }
             else
             {
-                for (Iterator it = matching.iterator(); it.hasNext();) {
-                    MOBYProvider p = (MOBYProvider) it.next();
-                    p.serialize(out);
-                }
+            	matching.serialize(out);
 			}
             
 		}
-//		catch (NonCanonicalException e)
-//		{
-//            // The query graph did not have the required canonical form
-//            //
-//			response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE,
-//				"Query graph is not canonical:\n" + e);
-//		}
 		catch (ParameterException e)
         {
             // The graph parameter was missing



From gss at pub.open-bio.org  Fri Jun 18 17:45:07 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:45:07 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182145.i5ILj7TR030161@pub.open-bio.org>


gss
Fri Jun 18 17:45:07 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery
In directory pub.open-bio.org:/tmp/cvs-serv30132/S-MOBY/ref-impl/queries/discovery

Modified Files:
	query.rdf query.n3 
Log Message:
Changed prefix mappings for go, sgd, and moby

moby-live/S-MOBY/ref-impl/queries/discovery query.rdf,1.2,1.3 query.n3,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf	2004/06/10 23:28:06	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf	2004/06/18 21:45:07	1.3
@@ -1,27 +1,27 @@
 <rdf:RDF
-    xmlns:go="http://www.go.org:8080/terms#"
+    xmlns:sgd="http://www.sgd.org:8080/terms/"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:moby="http://www.s-moby.org:8080/terms#"
-    xmlns:sgd="http://www.sgd.org:8080/terms#" >
+    xmlns:go="http://www.go.org:8080/terms/"
+    xmlns:moby="http://www.s-moby.org:8080/terms/" >
   <rdf:Description rdf:nodeID="A0">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <moby:hasMapping rdf:nodeID="A1"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-    <rdf:_1 rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Object"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms/LiteratureGuide"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A1">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <moby:mapsTo rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Provider"/>
+    <moby:operatesOn rdf:nodeID="A2"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A3">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Graph"/>
+    <moby:hasMapping rdf:nodeID="A4"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A2">
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A3"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A4">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <moby:operatesOn rdf:nodeID="A2"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms/GeneSymbol"/>
+    <moby:mapsTo rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Subject"/>
   </rdf:Description>
 </rdf:RDF>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3	2004/06/10 23:27:58	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3	2004/06/18 21:45:07	1.3
@@ -1,6 +1,6 @@
- at prefix go:       <http://www.go.org:8080/terms#> .
- at prefix sgd:      <http://www.sgd.org:8080/terms#> .
- at prefix moby:     <http://www.s-moby.org:8080/terms#> .
+ at prefix go:       <http://www.go.org:8080/terms/> .
+ at prefix sgd:      <http://www.sgd.org:8080/terms/> .
+ at prefix moby:     <http://www.s-moby.org:8080/terms/> .
 @prefix rdf:      <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 
 _:provider



From mwilkinson at pub.open-bio.org  Thu Jun 24 18:30:38 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 24 Jun 2004 18:30:38 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242230.i5OMUcqB032091@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:30:38 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor
In directory pub.open-bio.org:/tmp/cvs-serv32073/MOBY/Adaptor

Log Message:
Directory /home/repository/moby/moby-live/Perl/MOBY/Adaptor added to the repository

moby-live/Perl/MOBY/Adaptor - New directory
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/RCS/directory,v: No such file or directory



From mwilkinson at pub.open-bio.org  Thu Jun 24 18:30:52 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 24 Jun 2004 18:30:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242230.i5OMUqtw032135@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:30:52 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby
In directory pub.open-bio.org:/tmp/cvs-serv32117/MOBY/Adaptor/moby

Log Message:
Directory /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby added to the repository

moby-live/Perl/MOBY/Adaptor/moby - New directory
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/directory,v: No such file or directory



From mwilkinson at pub.open-bio.org  Thu Jun 24 18:31:00 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 24 Jun 2004 18:31:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242231.i5OMV0VT032179@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:31:00 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory pub.open-bio.org:/tmp/cvs-serv32161/MOBY/Adaptor/moby/queryapi

Log Message:
Directory /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi added to the repository

moby-live/Perl/MOBY/Adaptor/moby/queryapi - New directory
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/RCS/directory,v: No such file or directory



From mwilkinson at pub.open-bio.org  Thu Jun 24 18:32:38 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 24 Jun 2004 18:32:38 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242232.i5OMWcgc032293@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:32:38 EDT 2004
Update of /home/repository/moby/moby-live/Perl
In directory pub.open-bio.org:/tmp/cvs-serv32274

Modified Files:
	MANIFEST 
Log Message:
stratifying the SQL away from the MOBY Central module so that we can have a variety of underlying databases or SW-based data stores with teh MOBY Central API on top of them

moby-live/Perl MANIFEST,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MANIFEST,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MANIFEST	2004/06/15 00:37:55	1.10
+++ /home/repository/moby/moby-live/Perl/MANIFEST	2004/06/24 22:32:38	1.11
@@ -4,9 +4,9 @@
 Makefile.PL
 MOBY/authority.pm
 MOBY/central_db_connection.pm
-MOBY/mysql.pm
 MOBY/OntologyServer.pm
 MOBY/Config.pm
+MOBY/dbConfig.pm
 MOBY/CommonSubs.pm
 MOBY/CrossReference.pm
 MOBY/service_instance.pm
@@ -22,6 +22,8 @@
 MOBY/Client/ServiceInstance.pm
 MOBY/Client/SimpleArticle.pm
 MOBY/Client/Service.pm
+MOBY/Adaptor/moby/queryapi.pm
+MOBY/Adaptor/moby/queryapi/mysql.pm
 t/Client-Central.t
 scripts/debugYourService
 scripts/MOBY-Central.pl



From mwilkinson at pub.open-bio.org  Thu Jun 24 18:32:39 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 24 Jun 2004 18:32:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242232.i5OMWd8f032347@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:32:38 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv32274/MOBY

Modified Files:
	Central.pm Config.pm OntologyServer.pm 
	central_db_connection.pm collection_input.pm 
	collection_output.pm service_instance.pm simple_input.pm 
	simple_output.pm 
Added Files:
	dbConfig.pm 
Log Message:
stratifying the SQL away from the MOBY Central module so that we can have a variety of underlying databases or SW-based data stores with teh MOBY Central API on top of them

moby-live/Perl/MOBY dbConfig.pm,NONE,1.1 Central.pm,1.130,1.131 Config.pm,1.2,1.3 OntologyServer.pm,1.44,1.45 central_db_connection.pm,1.4,1.5 collection_input.pm,1.1,1.2 collection_output.pm,1.1,1.2 service_instance.pm,1.4,1.5 simple_input.pm,1.3,1.4 simple_output.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.130
retrieving revision 1.131
diff -u -r1.130 -r1.131
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/16 01:15:30	1.130
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/24 22:32:38	1.131
@@ -10,8 +10,6 @@
 use strict;
 use Carp;
 use vars qw($AUTOLOAD $WSDL_TEMPLATE);
-use DBI;
-use DBD::mysql;
 use XML::DOM;
 use MOBY::OntologyServer;
 use MOBY::service_type;
@@ -183,28 +181,6 @@
 	return 0;
 }
 
-sub _dbAccess {
-
-    my $conf = MOBY::Config->new;
-
-    my $username = $conf->{mobycentral}->{username};
-    my $password = $conf->{mobycentral}->{password};
-    my $port = $conf->{mobycentral}->{port};
-    my $dbname = $conf->{mobycentral}->{dbname};
-    my $url = $conf->{mobycentral}->{url};
-    
-	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
-	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
-	#my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
-	#my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
-	#my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
-	
-	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
-	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
-	
-	return ($dbh);
-}
-
 
 =head2 registerObjectClass
 
@@ -1264,7 +1240,7 @@
                     object_type_uri	=> $typeURI,
                     namespace_type_uris	=> $namespace_string,
                     article_name 	=> $article,
-                    collection_input_id 	=> 	$collid,
+                    collection_output_id 	=> 	$collid,
                     );
             unless ($soutput){
        			$SVC->DELETE_THYSELF; return (-1,"registration failed during registration of output object $typeURI.  Unknown reasons.");

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Config.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/Config.pm	2004/06/15 01:15:16	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/Config.pm	2004/06/24 22:32:38	1.3
@@ -6,8 +6,13 @@
 
 use strict;
 use Carp;
+use MOBY::dbConfig;
 use vars qw($AUTOLOAD);
 use Text::Shellwords;
+use vars '$VERSION','@ISA','@EXPORT','$CONFIG';
+
+ at ISA = qw(Exporter);
+ at EXPORT = ('$CONFIG');
 
 {
 	#Encapsulated class data
@@ -16,6 +21,11 @@
 	#ATTRIBUTES
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
+				   mobycentral	=> 	[undef,			'read/write'],
+				   mobyobject	=> 	[undef,			'read/write'],
+				   mobynamespace=> 	[undef,			'read/write'],
+				   mobyservice	=> 	[undef,			'read/write'],
+				   mobyrelationship	=> 	[undef,			'read/write'],
                     );
 
    #_____________________________________________________________
@@ -41,15 +51,14 @@
 
 }
 
-sub id {
-	my ($self, $val) =@_;
-	$self->registration_id($val) if defined $val;
-	return $self->registration_id;
-}
+# the expected sectionons (listed above) will have their dbCOnfig objects available
+# as methods.  The unexpected sections will have their dbConfig objects available
+# by $dbConfig = $CONFIG->{section_title}
 
 sub new {
 	my ($caller, %args) = @_;
 	
+#print STDERR "creating MOBY::Config\n";
 	my $caller_is_obj = ref($caller);
     my $class = $caller_is_obj || $caller;
 
@@ -65,32 +74,69 @@
     }
 
     my $file = $ENV{MOBY_CENTRAL_CONFIG};
-    chomp $file;
+	$file || die "can't open MOBY Configuration file $!\n";
+    
+	chomp $file;
     if ((-e $file) && (!(-d $file))){
         open IN, $file || die "can't open MOBY Configuration file $!\n";
     }
-    
-    while (my $l = <IN>){
-        chomp $l;
-        next if $l=~/\s*\#/;  # ignore comments
-        
-        if ($l=~/\[(\w+)\]/){
-            my $key = $1;
-            while (my $l2 = <IN>){
-                chomp $l2;
-                last unless ($l2 =~ /\S/);
-                my @terms = shellwords($l2);
-                last unless (scalar @terms > 2);
-                
-                $self->{$key}->{$terms[0]} = $terms[2];
-            }
-        }
-    }
+    my @sections = split /(\[\s*\S+\s*\][^\[]*)/s, join "", <IN>;
+#print STDERR "split into @sections\n";
+	foreach my $section (@sections){
+#print STDERR "calling MOBY::dbConfig\n";
+		my $dbConfig = MOBY::dbConfig->new(section => $section);  # this is an object full of strings, no actual connections.  It represents the information in the config file
+		next unless $dbConfig;
+		my $dbname = $dbConfig->section_title;
+		next unless $dbname;
+#print STDERR "setting the COnfig dbConfig for the title $dbname with object $dbConfig\n\n";
+		$self->{$dbname} = $dbConfig;
+	}
 
+	$CONFIG = $self;
     return $self;
 
 }
 
+sub getDataAdaptor {
+	my ($self, %args) = @_;
+	
+	my $source = $args{datasource};
+	$source ||= $args{source};
+	$source ||="mobycentral";
+	
+	if ($self->{"${source}Adaptor"}){return $self->{"${source}Adaptor"}};  # read from cache
+
+    my $username = $self->$source->{username};  # $self->source returns a MOBY::dbConfig object
+    my $password = $self->$source->{password};
+    my $port = $self->$source->{port};
+    my $dbname = $self->$source->{dbname};
+    my $url = $self->$source->{url};
+	my $adaptor = $self->$source->{adaptor};
+	my $sourcetype = $self->$source->{sourcetype};
+	
+	eval "require $adaptor";
+	return undef if $@;
+	eval "require $sourcetype";
+	return undef if $@;
+	
+	my $ADAPTOR = $adaptor->new(  # by default, this is queryapi
+								source => $source,
+								username => $username,
+								password => $password,
+								port => $port,
+								dbname => $dbname,
+								url => $url,
+								sourcetype => $sourcetype,
+							   );
+	if ($ADAPTOR){
+		$self->{"${source}Adaptor"} = $ADAPTOR;  # cache it
+		return $ADAPTOR;
+	} else {
+		return undef
+	}
+	
+}
+
 sub DESTROY {}
 
 sub AUTOLOAD {

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.44
retrieving revision 1.45
diff -u -r1.44 -r1.45
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 14:55:17	1.44
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/24 22:32:38	1.45
@@ -140,20 +140,23 @@
     $self->ontology eq 'service' && $self->database('mobyservice');
     $self->ontology eq 'relationship' && $self->database('mobyrelationship');
 
-	
-	my $conf = MOBY::Config->new;
-	$self->username($conf->{$self->database}->{username}) unless $self->username;
-    $self->password($conf->{$self->database}->{password}) unless $self->password;
-    $self->port($conf->{$self->database}->{port}) unless $self->port;
-    $self->host($conf->{$self->database}->{url}) unless $self->host;
+#print STDERR "\n\nCONFIG object is $CONFIG\n\n";
+	$CONFIG ||=MOBY::Config->new;
+#print STDERR "got username ",($CONFIG->{mobycentral}->{username})," for mobycentral\n";
+	$self->username($CONFIG->{$self->database}->{username}) unless $self->username;
+    $self->password($CONFIG->{$self->database}->{password}) unless $self->password;
+    $self->port($CONFIG->{$self->database}->{port}) unless $self->port;
+    $self->host($CONFIG->{$self->database}->{url}) unless $self->host;
  
 	my $host = $self->host?$self->host:$ENV{MOBY_CENTRAL_URL}; chomp $host;
 	my $username = $self->username?$self->username:$ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
 	my $password = $self->password?$self->password:$ENV{MOBY_CENTRAL_DBPASS}; chomp $password if $password; $password =~ s/\s//g if $password;
     my $port = $self->port?$self->port:$ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
     
-    my ($dsn) = "DBI:mysql:".($conf->{$self->database}->{dbname}).":".($host).":".($port);
+    my ($dsn) = "DBI:mysql:".($CONFIG->{$self->database}->{dbname}).":".($host).":".($port);
 
+#print STDERR "\n\nDSN was $dsn\n\n";
+	
     my $dbh;
 #	$debug && &_LOG("connecting to db with params ",$self->database, $self->username, $self->password,"\n");
     if (defined $password){

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/15 01:00:26	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/24 22:32:38	1.5
@@ -47,6 +47,7 @@
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
         db_connect_object => ["MOBY::mysql",        'read/write'],
+		datasource			=> ['mobycentral', 		'read/write'],
         #username => ["mobycentral",         'read/write'],
         #password => ["mobycentral",         'read/write'],        
         #dbname => ["mobycentral",       'read/write'],
@@ -108,25 +109,11 @@
     else {
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
-    #my $dbobj = $self->db_connect_object;
-    #my $dbh = &{$dbobj."::new"}(
-    #    $self->dbname,
-    #    $self->username,
-    #    $self->password,
-    #    $self->host,
-    #    $self->port);
-
-
-    my $conf = MOBY::Config->new;
-
-    my $username = $conf->{mobycentral}->{username};
-    my $password = $conf->{mobycentral}->{password};
-    my $port = $conf->{mobycentral}->{port};
-    my $dbname = $conf->{mobycentral}->{dbname};
-    my $url = $conf->{mobycentral}->{url};
-    	
-	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
-	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
+
+    $CONFIG ||= MOBY::Config->new;
+	
+	# getting the dbh is bad bad bad!!!
+	my $dbh = $CONFIG->getDataAdaptor(datasource => 'mobycentral')->dbh;
 	
     $self->dbh($dbh);
 	return $self;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/collection_input.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/collection_input.pm	2004/06/16 01:15:30	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/collection_input.pm	2004/06/24 22:32:38	1.2
@@ -1,9 +1,9 @@
-#!/usr/bin/perl -w
-
 package MOBY::collection_input;
 use strict;
 use Carp;
 use XML::DOM;
+use MOBY::Config;
+
 use vars qw($AUTOLOAD @ISA);
 
 
@@ -76,17 +76,6 @@
 
 }
 
-
-
-sub _dbh {
-    my ($self) = @_;
-    
-    my $central_connect = MOBY::central_db_connection->new();
-	$self->dbh($central_connect->dbh);
-	return $central_connect->dbh;
-	
-}
-
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -106,6 +95,7 @@
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
 
+
 	my $id = $self->WRITE;
 	$self->collection_input_id($id) if defined $id;
     return $self;
@@ -114,10 +104,13 @@
 
 sub WRITE {
 	my ($self) = @_;
-	my $dbh = $self->_dbh;
+	$CONFIG ||=MOBY::Config->new;  # exported by Config.pm
+	my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral');
+	my $id = $adaptor->insert_collection_input(
+									  service_instance => $self->service_instance_id,
+									  article_name	=> $self->article_name,
+									 );
 	
-	$dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($self->service_instance_id, $self->article_name));
-	my $id=$dbh->{mysql_insertid};
 	return $id;		
 }
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/collection_output.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/collection_output.pm	2004/06/16 01:15:30	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/collection_output.pm	2004/06/24 22:32:38	1.2
@@ -4,6 +4,8 @@
 use strict;
 use Carp;
 use XML::DOM;
+use MOBY::Config;
+
 use vars qw($AUTOLOAD @ISA);
 
 
@@ -76,17 +78,6 @@
 }
 
 
-
-sub _dbh {
-    my ($self) = @_;
-    
-    my $central_connect = MOBY::central_db_connection->new();
-	$self->dbh($central_connect->dbh);
-	return $central_connect->dbh;
-	
-}
-
-
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -115,10 +106,13 @@
 
 sub WRITE {
 	my ($self) = @_;
-	my $dbh = $self->_dbh;
+	$CONFIG ||=MOBY::Config->new;  # exported by Config.pm
+	my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral');
+	my $id = $adaptor->insert_collection_output(
+									  service_instance => $self->service_instance_id,
+									  article_name	=> $self->article_name,
+									 );
 	
-	$dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($self->service_instance_id, $self->article_name));
-	my $id=$dbh->{mysql_insertid};
 	return $id;		
 }
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm	2004/06/16 01:15:30	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm	2004/06/24 22:32:38	1.5
@@ -349,7 +349,7 @@
 				namespace_type_uris	=> $a{'namespace_type_uris'},
 				article_name 	=> $a{'article_name'},
 				service_instance_id	=> 	$self->service_instance_id,
-				collection_input_id 	=> 	$a{'collection_output_id'}
+				collection_output_id 	=> 	$a{'collection_output_id'}
 					   );
 
 	push @{$self->{outputs}}, $simple;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm	2004/06/16 01:15:30	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm	2004/06/24 22:32:38	1.4
@@ -4,6 +4,7 @@
 use strict;
 use Carp;
 use XML::DOM;
+use MOBY::Config;
 use vars qw($AUTOLOAD @ISA);
 
 
@@ -80,17 +81,6 @@
 
 }
 
-
-sub _dbh {
-    my ($self) = @_;
-    
-    my $central_connect = MOBY::central_db_connection->new();
-	$self->dbh($central_connect->dbh);
-	return $central_connect->dbh;
-	
-}
-
-
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -116,25 +106,20 @@
 
 }
 
+
 sub WRITE {
-	my ($self) = @_;	
-	my $dbh = $self->_dbh;
+	my ($self) = @_;
+	$CONFIG ||=MOBY::Config->new;  # exported by Config.pm
+	my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral');
+	my $id = $adaptor->insert_simple_input(
+		object_type_uri => $self->object_type_uri,
+		namespace_type_uris => $self->namespace_type_uris,
+		article_name => $self->article_name,
+		service_instance_id => $self->service_instance_id,
+		collection_input_id => $self->collection_input_id,
+									 );
 	
-	$dbh->do("insert into simple_input
-				 (object_type_uri,
-				  namespace_type_uris,
-				  article_name,
-				  service_instance_id,
-				  collection_input_id)
-				 values (?,?,?,?,?)",
-		undef,
-		($self->object_type_uri,
-		$self->namespace_type_uris,
-		$self->article_name,
-		$self->service_instance_id,
-		$self->collection_input_id));
-	my $id=$dbh->{mysql_insertid};
-	return $id;
+	return $id;		
 }
 
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm	2004/06/16 01:15:30	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm	2004/06/24 22:32:38	1.3
@@ -3,6 +3,7 @@
 package MOBY::simple_output;
 use strict;
 use Carp;
+use MOBY::Config;
 use XML::DOM;
 use vars qw($AUTOLOAD @ISA);
 
@@ -80,17 +81,6 @@
 }
 
 
-
-sub _dbh {
-    my ($self) = @_;
-    
-    my $central_connect = MOBY::central_db_connection->new();
-	$self->dbh($central_connect->dbh);
-	return $central_connect->dbh;
-	
-}
-
-
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -118,25 +108,20 @@
 
 sub WRITE {
 	my ($self) = @_;
-	my $dbh = $self->_dbh;	
-	$dbh->do("insert into simple_output
-				 (object_type_uri,
-				  namespace_type_uris,
-				  article_name,
-				  service_instance_id,
-				  collection_output_id)
-				 values (?,?,?,?,?)",
-		undef,
-		($self->object_type_uri,
-		$self->namespace_type_uris,
-		$self->article_name,
-		$self->service_instance_id,
-		$self->collection_output_id));
-	my $id=$dbh->{mysql_insertid};
+	$CONFIG ||=MOBY::Config->new;  # exported by Config.pm
+	my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral');
+	my $id = $adaptor->insert_simple_output(
+		object_type_uri => $self->object_type_uri,
+		namespace_type_uris => $self->namespace_type_uris,
+		article_name => $self->article_name,
+		service_instance_id => $self->service_instance_id,
+		collection_output_id => $self->collection_output_id,
+									 );
+	
 	return $id;		
-
 }
 
+
 sub AUTOLOAD {
     no strict "refs";
     my ($self, $newval) = @_;



From mwilkinson at pub.open-bio.org  Thu Jun 24 18:32:39 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 24 Jun 2004 18:32:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242232.i5OMWd2M032362@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:32:39 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby
In directory pub.open-bio.org:/tmp/cvs-serv32274/MOBY/Adaptor/moby

Added Files:
	queryapi.pm 
Log Message:
stratifying the SQL away from the MOBY Central module so that we can have a variety of underlying databases or SW-based data stores with teh MOBY Central API on top of them

moby-live/Perl/MOBY/Adaptor/moby queryapi.pm,NONE,1.1


From mwilkinson at pub.open-bio.org  Thu Jun 24 18:32:39 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 24 Jun 2004 18:32:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242232.i5OMWdAc032377@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:32:39 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory pub.open-bio.org:/tmp/cvs-serv32274/MOBY/Adaptor/moby/queryapi

Added Files:
	mysql.pm 
Log Message:
stratifying the SQL away from the MOBY Central module so that we can have a variety of underlying databases or SW-based data stores with teh MOBY Central API on top of them

moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,NONE,1.1


From mwilkinson at pub.open-bio.org  Tue Jun 29 12:24:00 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 29 Jun 2004 12:24:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406291624.i5TGO06q025875@pub.open-bio.org>


mwilkinson
Tue Jun 29 12:23:59 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv25852/MOBY

Modified Files:
	CommonSubs.pm dbConfig.pm 
Log Message:
CommonSubs now accepts HTML markup in the service provision block.  LocalServices (the example services that I run) now correctly credit the SeqHound project.

moby-live/Perl/MOBY CommonSubs.pm,1.52,1.53 dbConfig.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.52
retrieving revision 1.53
diff -u -r1.52 -r1.53
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/06/15 00:37:55	1.52
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/06/29 16:23:59	1.53
@@ -1425,7 +1425,8 @@
     foreach my $n(0..($responses->getLength - 1)){
         my $resp = $responses->item($n);
         foreach my $response_component($resp->getChildNodes){
-            $content .= $response_component->toString;
+#            $content .= $response_component->toString;
+            $content .= $response_component->getNodeValue if ($response_component->getNodeType == TEXT_NODE);
         }
     }
     return ($content);

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm	2004/06/24 22:32:38	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm	2004/06/29 16:23:59	1.2
@@ -78,6 +78,7 @@
     $key = $self->_readSections($self->section);
 	#if ($@){die "MOBY Configuration file is misconfigured: dbConfig line 71\n";}
 #print STDERR "I received the key $key\n";
+    return undef unless $key;
     return undef unless $key =~ /\S/;
 #print STDERR "returning the dbConfig object for database title $key\n";
     $self->section_title($key);



From mwilkinson at pub.open-bio.org  Tue Jun 29 12:24:00 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 29 Jun 2004 12:24:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406291624.i5TGO0OP025895@pub.open-bio.org>


mwilkinson
Tue Jun 29 12:24:00 EDT 2004
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv25852/scripts/Services

Modified Files:
	LocalServices.pm 
Log Message:
CommonSubs now accepts HTML markup in the service provision block.  LocalServices (the example services that I run) now correctly credit the SeqHound project.

moby-live/Perl/scripts/Services LocalServices.pm,1.62,1.63
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.62
retrieving revision 1.63
diff -u -r1.62 -r1.63
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2004/02/23 21:31:53	1.62
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2004/06/29 16:24:00	1.63
@@ -46,6 +46,8 @@
 
 my $debug = 1;
 
+my $SeqHoundCredit = "This data is provided by <a HREF='http://seqhound.blueprint.org'>SeqHound</a>; <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12401134&dopt=Abstract'>Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW.  SeqHound: biological sequence and structure database as a platform forbioinformatics research. BMC Bioinformatics. 2002 Oct 25;3(1):32</a>";
+
 use vars qw(@ISA);
 
 ##################################################
@@ -118,7 +120,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 
@@ -152,7 +154,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getSHoundProteinsFromOrganism {  # WORKS
@@ -185,7 +187,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 
@@ -219,7 +221,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 
@@ -253,7 +255,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getSHoundGODBGetParentOf {  # WORKS
@@ -290,7 +292,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getSHoundGODBGetChildrenOf {  # WORKS
@@ -327,7 +329,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getSHoundDNAFromOrganism {  # WORKS
@@ -360,7 +362,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getTaxChildNodes {  # WORKS
@@ -393,7 +395,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getTaxParent { # now it works.
@@ -419,7 +421,7 @@
 			$parent && ($MOBY_RESPONSE .= simpleResponse("<Object namespace='taxon' id='$parent'/>", "", $qID));
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 
@@ -449,7 +451,7 @@
 													   "</CrossReference>$name</String>", "", $qID));
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getGoTerm {
@@ -679,7 +681,7 @@
     }
 	$aa = SHoundFini();
 	#print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub _makeSeqObj {
@@ -778,7 +780,7 @@
     }
 	$aa = SHoundFini();
 #	print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub MOBYSHoundGetGenBankWhateverSequence {
@@ -865,7 +867,7 @@
     }
 	$aa = SHoundFini();
 #	print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub MOBYSHoundGetGenBankFasta {
@@ -927,7 +929,7 @@
     }
 	$aa = SHoundFini();
 	#print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 



From gss at pub.open-bio.org  Wed Jun 30 14:21:28 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 30 Jun 2004 14:21:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406301821.i5UILSfv031022@pub.open-bio.org>


gss
Wed Jun 30 14:21:28 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv30997/S-MOBY/ref-impl

Modified Files:
	INSTALL.html 
Log Message:
Fixed installation instructions to reflect problems that Ardavan K found.

moby-live/S-MOBY/ref-impl INSTALL.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/INSTALL.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/INSTALL.html	2004/06/10 23:10:44	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/INSTALL.html	2004/06/30 18:21:28	1.2
@@ -1,13 +1,14 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <html>
 <head>
+  <meta name="generator" content="HTML Tidy, see www.w3.org">
   <title>Building and Installing Semantic MOBY</title>
 </head>
 <body>
 <h2 style="text-align: center;">Building and Installing the Semantic
 MOBY<br>
 Reference Implementation</h2>
-<div style="text-align: justify;">This page contains step-by-step
+<div style="text-align: justify;"> This page contains step-by-step
 instructions on building and installing the complete reference
 implementation of Semantic MOBY. The complete installation includes a
 reference implementation of a discovery/registration server
@@ -23,7 +24,7 @@
 </div>
 <br>
 <h3>Prerequisites</h3>
-<div style="text-align: justify;">Before beginning to build the
+<div style="text-align: justify;"> Before beginning to build the
 reference implementation, certain software must be installed on the
 machine that is to host the installation. In the following list, the
 recommended software versions are the only ones that the author has
@@ -39,19 +40,15 @@
     <br>
   </li>
   <li>
-    <div style="text-align: justify;"><a href="http://ant.apache.org">Apache
+    <div style="text-align: justify;"> <a href="http://ant.apache.org">Apache
 Ant</a> (tested with version 1.6.1) should be installed and on the
-executable path. To check, type <code>'ant -version</code><code>' </code>(without
-the quotes) on a command line.<br>
-    </div>
-    <br>
-  </li>
-  <li style="text-align: justify;">One of the open source databases,
-either <a href="http://www.postgresql.org">PostgreSQL</a> (tested with
-version 7.4.1) or <a href="http://www.mysql.com">MySQL</a> (tested
-with version 4.0.18) should be installed and running, and a database
-named <code>smoby-dev</code> has been created.<br>
+executable path. To check, type <code>'ant -version</code><code>'</code>
+(without the quotes) on a command line.One of the open source
+databases, either <a href="http://www.postgresql.org">PostgreSQL</a>
+(tested with version 7.4.1) or <a href="http://www.mysql.com">MySQL</a>
+(tested with version 4.0.18) should be installed and running.<br>
     <br>
+    </div>
   </li>
   <li style="text-align: justify;">The Semantic MOBY distribution has
 been retrieved from CVS and saved locally. As of this writing, there
@@ -69,83 +66,108 @@
 <h3>Installation steps</h3>
 <ol type="1">
   <li>
-    <div style="text-align: justify;">Modify the <code>hosts</code>
+    <div style="text-align: justify;"> Modify the <code>hosts</code>
 file of the computer that is to host the reference implementation, as
-described in the <code>for-hosts-file </code>file located in the <code>ref-impl/config-files/</code>
+described in the <code>for-hosts-file</code> file located in the <code>ref-impl/config-files/</code>
 subdirectory of the reference implementation directory. Since one
 computer is to host several example domains (s-moby.org, acmepubs.com,
 etc.), this is the easiest way to make these virtual domain, hosted by
 Apache Tomcat (see the next step) resolve to the local host.<br>
-    </div>
     <br>
+    </div>
   </li>
   <li>
-    <div style="text-align: justify;">Install <a
+    <div style="text-align: justify;"> Install <a
  href="http://jakarta.apache.org/tomcat">Apache Tomcat 5.0</a> (tested
 with version 5.0.25) and start it. If all went well, you should be able
 to open <a href="http://localhost:8080">http://localhost:8080</a> in a
 browser. After making sure it is properly installed, shutdown Tomcat.<br>
+    <br>
     </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"> Modify Tomcat's main
+configuration file (<code>server.xml</code>), located in the <code>conf/</code>
+subdirectory of the Tomcat installation directory as instructed in the <code>for-tomcat-conf-server.xml</code>
+file, located in the <code>config-files/</code> subdirectory of the
+reference implementation directory. This modification sets up virtual
+hosts, accessible by name, that are all served by Tomcat 5.<br>
     <br>
+    </div>
   </li>
   <li>
-    <div style="text-align: justify;">Modify <tomcat-top-dir>Tomcat's
-main configuration file (<code>server.xml</code>), located in the <code>conf/</code>
-subdirectory of the Tomcat installation directory as instructed in the </tomcat-top-dir><code>for-tomcat-conf-server.xml
-    </code>file, located in the <code>config-files/</code>
-subdirectory of the reference implementation directory. This
-modification sets up virtual hosts, accessible by name, that are all
-served by Tomcat 5.<br>
-    </div>
-    <tomcat-top-dir><br>
-    </tomcat-top-dir></li>
-  <li>
-    <div style="text-align: justify;">Save a copy of the <ref-impl-top-dir><code>common.example.properties</code>
-file, located in the reference implementation<span
- style="font-family: monospace;"></span><code></code> directory, as <code>common.properties</code>
+    <div style="text-align: justify;"> Save a copy of the <code>common.example.properties</code>
+file, located in the reference implementation directory, as <code>common.properties</code>
 (in the same directory). This file is used by the Ant build scripts,
 and should be modified to reflect the system on which the reference
-implementation is being installed.</ref-impl-top-dir><br>
-    <ref-impl-top-dir></ref-impl-top-dir></div>
-    <ref-impl-top-dir><br>
-    </ref-impl-top-dir></li>
-  <li>
-    <div style="text-align: justify;">From the command line, change
-directory to the reference implementation directory and <ref-impl-top-dir>run
-    <code>'ant third-party' </code>(without the quotes). This
-retrieves third party components from CVS and builds them. Retrieving
-the components from CVS is admittedly less predictable than storing a
-version of the components with the Semantic MOBY distribution, but as
-the components (especially <a href="http://jena.sourceforge.net">Jena2</a>)
-are constantly being improved, it is considered more important to have
-the latest versions than to have stable versions. Currently, this step
-takes about three minutes on a 2GHz P4 machine with a broadband
-connection.</ref-impl-top-dir><br>
-    <ref-impl-top-dir></ref-impl-top-dir></div>
-    <br>
-    <ref-impl-top-dir></ref-impl-top-dir></li>
-  <li>
-    <div style="text-align: justify;">From the command line, while
-still in the reference implementation directory,&nbsp;<ref-impl-top-dir>
-run '<code>ant deploy-to-tomcat</code>' (without the quotes). This
-compiles the Semantic MOBY reference implementation and deploys the
-various parts to run as Java Servlets under Tomcat 5.</ref-impl-top-dir><br>
-    <ref-impl-top-dir></ref-impl-top-dir></div>
-    <ref-impl-top-dir><br>
-    </ref-impl-top-dir></li>
-  <li>
-    <div style="text-align: justify;">Copy the appropriate JDBC driver
-jar file into the <tomcat-top-dir><code>shared/lib</code>
-subdirectory of the Tomcat 5 installation. As of this writing, the
-latest PostgreSQL JDBC jar file
+implementation is being installed.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"> From the command line, change
+directory to the reference implementation directory and run <code>'ant
+third-party'</code> (without the quotes). This retrieves third party
+components from CVS and builds them. Retrieving the components from CVS
+is admittedly less predictable than storing a version of the components
+with the Semantic MOBY distribution, but as the components (especially <a
+ href="http://jena.sourceforge.net">Jena2</a>) are constantly being
+improved, it is considered more important to have the latest versions
+than to have stable versions. Currently, this step takes about three
+minutes on a 2GHz P4 machine with a broadband connection.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"> From the command line, while
+still in the reference implementation directory,&nbsp; run '<code>ant
+deploy-to-tomcat</code>' (without the quotes). This compiles the
+Semantic MOBY reference implementation and deploys the various parts to
+run as Java Servlets under Tomcat 5.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"> Copy the appropriate JDBC driver
+jar file into the <code>shared/lib</code> subdirectory of the Tomcat 5
+installation. As of this writing, the latest PostgreSQL JDBC jar file
 was named <span style="font-style: italic;">postgresql.jar</span> and
-the latest MySQL driver was named <span style="font-style: italic;">mysql-connector-java-3.0.11-stable-bin.jar</span>.</tomcat-top-dir><br>
-    <tomcat-top-dir></tomcat-top-dir></div>
-    <tomcat-top-dir><br>
-    </tomcat-top-dir></li>
+the latest MySQL driver was named <span style="font-style: italic;">mysql-connector-java-3.0.11-stable-bin.jar</span>.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"><!--StartFragment --> Using
+whatever tools are appropriate for your DBMS, create a database user
+(e.g. <code>joe</code>) with a password (e.g. <code>foobar</code>).
+For MySQL, the free MySQL Control Center works well, and for
+PostgreSQL, PGAdmin III works well.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"><!--StartFragment --> Create a
+database, and give it a name (e.g. <code>my-smoby-repository</code>).
+Make the owner of the database the user (e.g. <code>joe</code>)
+created in step&nbsp;8.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"><!--StartFragment --> Modify <code>smoby.properties</code>,
+located in the <code>webapps/s-moby.org</code> subdirectory of the
+Tomcat installation directory, setting <code>DB_USER_ID</code> to the
+user (e.g. <code>joe</code>) created in step 8, <code>DB_PASSWORD</code>
+to the password (e.g. <code>foobar</code>) of the user created in step
+8, and <code>DB_REPOSITORY_NAME</code> to the database name (e.g. <code>my-smoby-repository</code>)
+used in step 8.Also modify <code>DB_URL</code> to include the name of
+the database used in&nbsp;step 9&nbsp;(e.g. <code>jdbc:postgresql://localhost/my-smoby-repository</code>).<br>
+    <br>
+    </div>
+  </li>
   <li>Start Tomcat. If all went well, you should be able to open <a
- href="http://www.s-moby.org:8080">http://www.s-moby.org:8080</a>
-in a browser. </li>
+ href="http://www.s-moby.org:8080">http://www.s-moby.org:8080</a> in a
+browser.</li>
 </ol>
 </body>
 </html>



From gss at pub.open-bio.org  Wed Jun 30 14:21:28 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 30 Jun 2004 14:21:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406301821.i5UILSsL031041@pub.open-bio.org>


gss
Wed Jun 30 14:21:28 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv30997/S-MOBY/ref-impl/server/WebRoot

Modified Files:
	smoby.properties 
Log Message:
Fixed installation instructions to reflect problems that Ardavan K found.

moby-live/S-MOBY/ref-impl/server/WebRoot smoby.properties,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/smoby.properties,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/smoby.properties	2004/06/10 23:25:49	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/smoby.properties	2004/06/30 18:21:28	1.2
@@ -3,9 +3,9 @@
 
 # Common values for MySQL and PostgreSQL
 #
-DB_USER_ID            = smobydev
-DB_PASSWORD           = 
-DB_REPOSITORY_NAME    = smoby-dev
+DB_USER_ID            = <change-me>
+DB_PASSWORD           = <change-me>
+DB_REPOSITORY_NAME    = <change-me>
 
 # Uncomment if using MySQL
 #
@@ -17,4 +17,4 @@
 #
 DB_DRIVER_CLASS_NAME  = org.postgresql.Driver
 DB_TYPE               = PostgreSQL
-DB_URL                = jdbc:postgresql://localhost/smoby-dev
\ No newline at end of file
+DB_URL                = jdbc:postgresql://localhost/<change-me>
\ No newline at end of file



From simont at pub.open-bio.org  Tue Jun  1 16:51:27 2004
From: simont at pub.open-bio.org (Simon Twigger)
Date: Tue, 1 Jun 2004 12:51:27 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406011651.i51GpR7t003930@pub.open-bio.org>


simont
Tue Jun  1 12:51:26 EDT 2004
Update of /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege
In directory pub.open-bio.org:/tmp/cvs-serv3911

Modified Files:
	MOBY_Service_ontology.png 
Log Message:
update, no change to content

moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege MOBY_Service_ontology.png,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MOBY_Service_ontology.png,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
Binary files /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MOBY_Service_ontology.png	2004/04/28 18:48:41	1.2 and /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MOBY_Service_ontology.png	2004/06/01 16:51:26	1.3 differ
rcsdiff: /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MOBY_Service_ontology.png: diff failed



From gss at pub.open-bio.org  Thu Jun 10 18:47:42 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 14:47:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406101847.i5AIlger017252@pub.open-bio.org>


gss
Thu Jun 10 14:47:42 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files
In directory pub.open-bio.org:/tmp/cvs-serv17230/ref-impl/config-files

Removed Files:
	for-tomcat-conf-catalina.properties 
Log Message:
No longer needed

moby-live/S-MOBY/ref-impl/config-files for-tomcat-conf-catalina.properties,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files/RCS/for-tomcat-conf-catalina.properties,v: No such file or directory



From gss at pub.open-bio.org  Thu Jun 10 18:58:01 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 14:58:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406101858.i5AIw13A017320@pub.open-bio.org>


gss
Thu Jun 10 14:58:01 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files
In directory pub.open-bio.org:/tmp/cvs-serv17295/ref-impl/config-files

Modified Files:
	for-tomcat-conf-server.xml 
Added Files:
	for-hosts-file README 
Log Message:
Cleanup

moby-live/S-MOBY/ref-impl/config-files for-hosts-file,NONE,1.1 README,NONE,1.1 for-tomcat-conf-server.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files/for-tomcat-conf-server.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files/for-tomcat-conf-server.xml	2004/04/02 00:02:03	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/config-files/for-tomcat-conf-server.xml	2004/06/10 18:58:01	1.2
@@ -1,32 +1,32 @@
 <!-- Put the following just after the last </Host> closing element
      in <tomcat-home>/conf/server.xml -->
 
-      <Host appBase="webapps" name="acmepubs.com">
+      <Host appBase="webapps/acmepubs.com" name="acmepubs.com">
           <Alias>www.acmepubs.com</Alias>
-          <Context path="" docBase="acmepubs.com" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="megapubs.com">
+      <Host appBase="webapps/megapubs.com" name="megapubs.com">
           <Alias>www.megapubs.com</Alias>
-          <Context path="" docBase="megapubs.com" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="go.org">
+      <Host appBase="webapps/go.org" name="go.org">
           <Alias>www.go.org</Alias>
-          <Context path="" docBase="go.org" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="sgd.org">
+      <Host appBase="webapps/sgd.org" name="sgd.org">
           <Alias>www.sgd.org</Alias>
-          <Context path="" docBase="sgd.org" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="pubs.org">
+      <Host appBase="webapps/pubs.org" name="pubs.org">
           <Alias>www.pubs.org</Alias>
-          <Context path="" docBase="pubs.org" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>
 
-      <Host appBase="webapps" name="s-moby.org">
+      <Host appBase="webapps/s-moby.org" name="s-moby.org">
           <Alias>www.s-moby.org</Alias>
-          <Context path="" docBase="s-moby.org" debug="0" reloadable="true"/>
+          <Context path="" docBase="" debug="0" reloadable="true"/>
       </Host>



From gss at pub.open-bio.org  Thu Jun 10 23:06:55 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:06:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102306.i5AN6tGb017989@pub.open-bio.org>


gss
Thu Jun 10 19:06:55 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv17968/ref-impl

Added Files:
	.cvsignore 
Log Message:
Ignore products of building the reference implementation

moby-live/S-MOBY/ref-impl .cvsignore,NONE,1.1


From gss at pub.open-bio.org  Thu Jun 10 23:09:39 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:09:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102309.i5AN9dXo018072@pub.open-bio.org>


gss
Thu Jun 10 19:09:39 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv18051/ref-impl

Added Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl build.xml,NONE,1.1


From gss at pub.open-bio.org  Thu Jun 10 23:10:02 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:10:02 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102310.i5ANA2ta018104@pub.open-bio.org>


gss
Thu Jun 10 19:10:02 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv18083/ref-impl

Added Files:
	common.example.properties 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl common.example.properties,NONE,1.1


From gss at pub.open-bio.org  Thu Jun 10 23:10:31 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:10:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102310.i5ANAVTl018142@pub.open-bio.org>


gss
Thu Jun 10 19:10:31 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv18117/ref-impl

Modified Files:
	index.html 
Log Message:
Reference installation/deployment document

moby-live/S-MOBY/ref-impl index.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/index.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/index.html	2004/03/12 17:48:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/index.html	2004/06/10 23:10:30	1.2
@@ -65,7 +65,8 @@
 </div>
 <br>
 The above links provide more information about each part of the
-reference implementation.<br>
+reference implementation. See the file <a href="INSTALL.html">INSTALL.html</a>
+for information on building and installing the reference implementation.<br>
 <div style="margin-left: 40px;">
 <div style="margin-left: 40px;"></div>
 </div>



From gss at pub.open-bio.org  Thu Jun 10 23:10:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:10:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102310.i5ANAiop018168@pub.open-bio.org>


gss
Thu Jun 10 19:10:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv18147/ref-impl

Added Files:
	servlet.xml common.xml INSTALL.html 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl servlet.xml,NONE,1.1 common.xml,NONE,1.1 INSTALL.html,NONE,1.1


From gss at pub.open-bio.org  Thu Jun 10 23:11:02 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:11:02 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102311.i5ANB25b018206@pub.open-bio.org>


gss
Thu Jun 10 19:11:02 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv18181/ref-impl/core

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/core build.xml,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/05/27 15:54:44	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/06/10 23:11:02	1.4
@@ -3,24 +3,42 @@
 <project name="smoby-core" default="jar" basedir=".">
 
     <!-- Import shared stuff -->
-    <import file="../library.xml"/>
+    <import file="../common.xml"/>
 
-    <!-- Package the compiled source files into the main jar file -->
-    <target name="jar" depends="compile">
-        <jar destfile="${core-jar-file}" basedir="${classes-dir}"/>
-    </target>
+    <!-- Relative path for where to put stuff that gets built -->
+    <property name="build-dir" value="build"/>
     
+    <!-- Relative path for where javac should output class files -->
+    <property name="classes-dir" value="${build-dir}/classes"/>
+
     <!-- Compile all the source files that go into the library -->
     <target name="compile">
         <mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="core.classpath"/>
         </javac>
     </target>
     
+    <!-- Package the compiled source files into the main jar file -->
+    <target name="jar" depends="compile">
+        <jar destfile="${core-jar-file}" basedir="${classes-dir}"/>
+    </target>
+
     <!-- Deploy the jar file to the Tomcat shared library directory -->
     <target name="deploy-to-tomcat" depends="jar">
-        <copy file="${core-jar-file}" todir="${tomcat-shared-lib-dir}"/>
+        <copy file="${core-jar-file}"
+              todir="${tomcat-shared-lib-dir}"/>
+    </target>
+    
+	<!-- Remove the build directory and its contents -->
+	<target name="clean">
+		<delete dir="${build-dir}" includeEmptyDirs="true"/>
+        <delete file="${core-jar-file}"/>
+	</target>
+    
+    <!-- Un-deploy the jar file from the Tomcat shared library directory -->
+    <target name="undeploy-from-tomcat">
+        <delete file="${tomcat-shared-lib-dir}/${core-jar-file}"/>
     </target>
     
 </project>



From gss at pub.open-bio.org  Thu Jun 10 23:13:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:13:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDi92018265@pub.open-bio.org>


gss
Thu Jun 10 19:13:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF web.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/web.xml	2004/03/27 01:34:51	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.2
@@ -1,4 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE web-app PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN" "http://java.sun.com/dtd/web-app_2_3.dtd">
 <web-app>
+  <display-name>Example MOBY provider pubs.org</display-name>
 </web-app>



From gss at pub.open-bio.org  Thu Jun 10 23:13:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:13:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDiBN018284@pub.open-bio.org>


gss
Thu Jun 10 19:13:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF web.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml	2004/03/27 01:17:58	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.3
@@ -2,6 +2,8 @@
 <!DOCTYPE web-app PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN" "http://java.sun.com/dtd/web-app_2_3.dtd">
 <web-app>
   
+  <display-name>Example MOBY provider megapubs.com</display-name>
+
   <servlet>
     <servlet-name>CitationSearchServlet</servlet-name>
     <display-name>Publication Search</display-name>



From gss at pub.open-bio.org  Thu Jun 10 23:13:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:13:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDiOa018303@pub.open-bio.org>


gss
Thu Jun 10 19:13:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/server/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF web.xml,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml	2004/03/27 01:23:21	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.4
@@ -3,6 +3,8 @@
 
 <web-app>
 
+  <display-name>Semantic MOBY Server</display-name>
+
   <servlet>
     <servlet-name>GraphConversionServlet</servlet-name>
     <display-name>Graph Converter</display-name>



From gss at pub.open-bio.org  Thu Jun 10 23:13:45 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:13:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDjAt018322@pub.open-bio.org>


gss
Thu Jun 10 19:13:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF web.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml	2004/03/19 00:37:48	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.2
@@ -1,6 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE web-app PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN" "http://java.sun.com/dtd/web-app_2_3.dtd">
 <web-app>
+
+  <display-name>Example MOBY provider acmepubs.com</display-name>
   
   <servlet>
     <servlet-name>CitationSearchServlet</servlet-name>



From gss at pub.open-bio.org  Thu Jun 10 23:13:45 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:13:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102313.i5ANDjKv018344@pub.open-bio.org>


gss
Thu Jun 10 19:13:45 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv18240/ref-impl/example-providers/go.org/WebRoot/WEB-INF

Modified Files:
	web.xml 
Log Message:
Added display name

moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF web.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/web.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/web.xml	2004/04/01 00:30:50	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/WEB-INF/web.xml	2004/06/10 23:13:44	1.2
@@ -1,4 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE web-app PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN" "http://java.sun.com/dtd/web-app_2_3.dtd">
 <web-app>
+  <display-name>Example MOBY provider go.org</display-name>
 </web-app>



From gss at pub.open-bio.org  Thu Jun 10 23:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbSC018409@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-clients

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-clients build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/build.xml	2004/03/12 17:48:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/build.xml	2004/06/10 23:15:37	1.2
@@ -1,2 +1,11 @@
-<project name="example-clients" basedir=".">
+<project name="example-clients" default="all" basedir=".">
+
+    <target name="all">
+        <ant dir="SimpleEngager"/>
+    </target>
+
+    <target name="clean">
+        <ant dir="SimpleEngager" target="clean"/>
+    </target>
+
 </project>



From gss at pub.open-bio.org  Thu Jun 10 23:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbBK018428@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/server

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/server build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/05/27 15:54:12	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/06/10 23:15:37	1.3
@@ -1,29 +1,42 @@
-<!-- Apache Ant format build file for s-moby.org example provider -->
+<!-- Apache Ant format build file for s-moby.org server -->
 
-<project name="s-moby.org" default="war" basedir=".">
+<project name="s-moby.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="s-moby.org.war"/>
+    <!-- The web application name -->
+    <property name="webapp-name" value="s-moby.org"/>
 	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
-	
-	<!-- Compile all the source files that go into the library -->
+    <!-- Compile all the source files that go into the library, and copy any
+         properties files (i.e. smoby.properties and log4j.properties) into
+         the classes directory -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
+        <copy toDir="${classes-dir}">
+            <fileset dir="WebRoot">
+                <include name="*.properties"/>
+            </fileset>
+        </copy>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>



From gss at pub.open-bio.org  Thu Jun 10 23:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbfV018512@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-providers/megapubs.com

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml	2004/05/27 15:54:28	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml	2004/06/10 23:15:37	1.3
@@ -1,29 +1,35 @@
-<!-- Apache Ant format build file for acmepubs.com example provider -->
+<!-- Apache Ant format build file for megapubs.com server -->
 
-<project name="megapubs.com" default="war" basedir=".">
+<project name="s-moby.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="megapubs.com.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="megapubs.com"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>



From gss at pub.open-bio.org  Thu Jun 10 23:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbjJ018489@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-clients/SimpleEngager

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml	2004/05/28 21:35:17	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml	2004/06/10 23:15:37	1.3
@@ -3,22 +3,34 @@
 <project name="simple-engager" default="jar" basedir=".">
 
     <!-- Import shared stuff -->
-    <import file="../../library.xml"/>
+    <import file="../../common.xml"/>
+
+    <!-- Relative path for where to put stuff that gets built -->
+    <property name="build-dir" value="build"/>
+    
+    <!-- Relative path for where javac should output class files -->
+    <property name="classes-dir" value="${build-dir}/classes"/>
 
     <!-- The main jar file -->
-    <property name="jar-file" value="${build-dir}/engager.jar"/>
+    <property name="jar-file" value="simple-engager.jar"/>
 
-    <!-- Package the compiled source files into the main jar file -->
-    <target name="jar" depends="compile">
-        <jar destfile="${jar-file}" basedir="${classes-dir}"/>
-    </target>
-    
     <!-- Compile all the source files that go into the library -->
     <target name="compile">
         <mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
     </target>
     
+    <!-- Package the compiled source files into the main jar file -->
+    <target name="jar" depends="compile">
+        <jar destfile="${jar-file}" basedir="${classes-dir}"/>
+    </target>
+    
+	<!-- Remove the build directory and its contents -->
+	<target name="clean">
+		<delete dir="${build-dir}" includeEmptyDirs="true"/>
+        <delete file="${jar-file}"/>
+	</target>
+    
 </project>



From gss at pub.open-bio.org  Thu Jun 10 23:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbtN018470@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-providers/go.org

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/go.org build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/build.xml	2004/05/27 16:23:59	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/build.xml	2004/06/10 23:15:37	1.2
@@ -1,29 +1,35 @@
 <!-- Apache Ant format build file for go.org example provider -->
 
-<project name="go.org" default="war" basedir=".">
+<project name="go.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="go.org.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="go.org"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>



From gss at pub.open-bio.org  Thu Jun 10 23:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFbSU018534@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-providers/pubs.org

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/pubs.org build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/build.xml	2004/05/27 15:54:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/build.xml	2004/06/10 23:15:37	1.2
@@ -1,29 +1,35 @@
 <!-- Apache Ant format build file for pubs.org example provider -->
 
-<project name="pubs.org" default="war" basedir=".">
+<project name="s-moby.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="pubs.org.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="pubs.org"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>



From gss at pub.open-bio.org  Thu Jun 10 23:15:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102315.i5ANFb1V018448@pub.open-bio.org>


gss
Thu Jun 10 19:15:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com
In directory pub.open-bio.org:/tmp/cvs-serv18384/ref-impl/example-providers/acmepubs.com

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml	2004/05/27 15:54:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml	2004/06/10 23:15:37	1.3
@@ -1,29 +1,35 @@
 <!-- Apache Ant format build file for acmepubs.com example provider -->
 
-<project name="acmepubs.com" default="war" basedir=".">
+<project name="acmepubs.com" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="acmepubs.com.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="acmepubs.com"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>



From gss at pub.open-bio.org  Thu Jun 10 23:16:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:16:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102316.i5ANGmJn018573@pub.open-bio.org>


gss
Thu Jun 10 19:16:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data
In directory pub.open-bio.org:/tmp/cvs-serv18549/ref-impl/test-data

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data added to the repository

moby-live/S-MOBY/ref-impl/test-data - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Thu Jun 10 23:16:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:16:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102316.i5ANGmfG018591@pub.open-bio.org>


gss
Thu Jun 10 19:16:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser
In directory pub.open-bio.org:/tmp/cvs-serv18549/ref-impl/test-data/parser

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser added to the repository

moby-live/S-MOBY/ref-impl/test-data/parser - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Thu Jun 10 23:16:51 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:16:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102316.i5ANGpqR018636@pub.open-bio.org>


gss
Thu Jun 10 19:16:51 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/test-data/parser
In directory pub.open-bio.org:/tmp/cvs-serv18615/ref-impl/test-data/parser

Added Files:
	unparsable.n3 minimal.n3 three-providers.n3 README.txt 
Log Message:
Began writing JUnit test cases (feel free to help out, everyone :-)

moby-live/S-MOBY/ref-impl/test-data/parser unparsable.n3,NONE,1.1 minimal.n3,NONE,1.1 three-providers.n3,NONE,1.1 README.txt,NONE,1.1


From gss at pub.open-bio.org  Thu Jun 10 23:24:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:24:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102324.i5ANOGLl018745@pub.open-bio.org>


gss
Thu Jun 10 19:24:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv18720/ref-impl/server/src/org/smoby/ref/tools

Modified Files:
	DiscoveryQuery.java 
Log Message:
Commented out most functionality until I figure out the new
ResultBindingIterator protocol...

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/05/19 18:26:40	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/06/10 23:24:16	1.5
@@ -4,11 +4,10 @@
 import java.text.*;
 import java.util.*;
 
-import org.smoby.parser.Parser;
+import org.smoby.parser.*;
 import org.smoby.ref.tools.db.*;
 import org.smoby.graph.*;
-import org.smoby.graph.impl.MOBYObjectFactory;
-import org.smoby.graph.impl.MOBYProviderImpl;
+import org.smoby.graph.impl.*;
 import org.smoby.vocabulary.*;
 
 import com.hp.hpl.jena.db.*;
@@ -257,22 +256,23 @@
 		if (! node.asNode().isBlank()) {
 			return node;
 		}
-		
-		ResultBinding.ResultBindingIterator results = binding.iterator();
+		//ResultBinding
+		ResultBindingIterator results = binding.iterator();
 		
 		while (results.hasNext())
 		{
-			results.next();
+			Object object = results.next();
+			Value value = (Value) object;
 			String varName = results.varName();
-			Value value = results.value();
+//			Value value = results.value();
 			Object cachedName = varNames.get(node.toString());
 			if (varName.equals(cachedName))
 			{
-				if (value.isRDFLiteral()) {
-					return value.getRDFLiteral();
-				} else if (value.isRDFResource()) {
-					return value.getRDFResource();
-				}
+//				if (value.isRDFLiteral()) {
+//					return value.getRDFLiteral();
+//				} else if (value.isRDFResource()) {
+//					return value.getRDFResource();
+//				}
 			}
 		}
 		return node;



From gss at pub.open-bio.org  Thu Jun 10 23:25:49 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:25:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102325.i5ANPnGe018783@pub.open-bio.org>


gss
Thu Jun 10 19:25:49 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src
In directory pub.open-bio.org:/tmp/cvs-serv18760/ref-impl/server/src

Removed Files:
	log4j.properties smoby.properties 
Log Message:
Moved from src/ to WebRoot/

moby-live/S-MOBY/ref-impl/server/src log4j.properties,1.1,NONE smoby.properties,1.4,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/log4j.properties,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/RCS/smoby.properties,v: No such file or directory



From gss at pub.open-bio.org  Thu Jun 10 23:25:49 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:25:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102325.i5ANPn6V018798@pub.open-bio.org>


gss
Thu Jun 10 19:25:49 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv18760/ref-impl/server/WebRoot

Added Files:
	smoby.properties 
Log Message:
Moved from src/ to WebRoot/

moby-live/S-MOBY/ref-impl/server/WebRoot smoby.properties,NONE,1.1


From gss at pub.open-bio.org  Thu Jun 10 23:26:31 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:26:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102326.i5ANQV5p018845@pub.open-bio.org>


gss
Thu Jun 10 19:26:31 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage
In directory pub.open-bio.org:/tmp/cvs-serv18822/ref-impl/queries/engage

Removed Files:
	engage-megapubs-citationSearch.rdf 
	engage-megapubs-citationSearch.n3 
Log Message:
No longer needed

moby-live/S-MOBY/ref-impl/queries/engage engage-megapubs-citationSearch.rdf,1.1,NONE engage-megapubs-citationSearch.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/RCS/engage-megapubs-citationSearch.rdf,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/RCS/engage-megapubs-citationSearch.n3,v: No such file or directory



From gss at pub.open-bio.org  Thu Jun 10 23:27:12 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:27:12 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102327.i5ANRCR3018875@pub.open-bio.org>


gss
Thu Jun 10 19:27:12 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage
In directory pub.open-bio.org:/tmp/cvs-serv18850/ref-impl/queries/engage

Modified Files:
	engage-acmepubs-citationSearch.n3 
Log Message:
Simplified N3 by using un-named blank nodes

moby-live/S-MOBY/ref-impl/queries/engage engage-acmepubs-citationSearch.n3,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3	2004/04/02 00:05:16	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.n3	2004/06/10 23:27:12	1.2
@@ -10,28 +10,44 @@
 
 acmepubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
-    rdfs:comment "Industry standard search" ;
-    moby:operatesOn _:bnode1 .
-
-_:bnode1
-    a moby:Graph, rdf:Bag ;
-    moby:hasMapping _:bnode2 .
-
-_:bnode2
-    a moby:Subject, go:GeneSymbol ;
-    moby:mapsTo _:bnode3 ;
-    acmepubs:geneSymbol "REV7" .
-
-_:bnode3
-    a moby:Object, sgd:LiteratureGuide ;
-    acmepubs:literatureGuideURL _:bnode6 .
+    moby:name "AcmePubs Citation Search" ;
+    moby:oneLineDescription "Industry standard search" ;
+    moby:aboutURI "http://www.acmepubs.com/about/citationSearch" ;
+    moby:operatesOn [
+        a rdf:Bag ;
+        rdf:_1 [
+            a moby:Graph ;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                acmepubs:geneSymbol "REV5" ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide ;
+                    acmepubs:literatureGuideURL _:bnode1
+                ]
+            ]
+        ] ;
+        rdf:_2 [
+            a moby:Graph ;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                acmepubs:geneSymbol "REV7" ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide ;
+                    acmepubs:literatureGuideURL _:bnode2
+                ]
+            ]
+        ] ;
+    ] .
 
 acmepubs:geneSymbol
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain go:GeneSymbol ;
     rdfs:range xsd:string .
 
 acmepubs:literatureGuideURL
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain sgd:LiteratureGuide ;
     rdfs:range xsd:anyURI .
+



From gss at pub.open-bio.org  Thu Jun 10 23:27:41 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:27:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102327.i5ANRfwJ018915@pub.open-bio.org>


gss
Thu Jun 10 19:27:41 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage
In directory pub.open-bio.org:/tmp/cvs-serv18890/ref-impl/queries/engage

Modified Files:
	engage-acmepubs-citationSearch.rdf 
Log Message:
Use un-named blank nodes

moby-live/S-MOBY/ref-impl/queries/engage engage-acmepubs-citationSearch.rdf,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf	2004/04/02 00:05:16	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/engage/engage-acmepubs-citationSearch.rdf	2004/06/10 23:27:41	1.2
@@ -12,31 +12,54 @@
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A0">
     <moby:hasMapping rdf:nodeID="A1"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A1">
-    <moby:mapsTo rdf:nodeID="A2"/>
+  <rdf:Description rdf:nodeID="A2">
+    <moby:mapsTo rdf:nodeID="A3"/>
     <acmepubs:geneSymbol>REV7</acmepubs:geneSymbol>
     <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
   </rdf:Description>
+  <rdf:Description rdf:nodeID="A4">
+    <acmepubs:literatureGuideURL rdf:nodeID="A5"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A6">
+    <moby:hasMapping rdf:nodeID="A2"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <acmepubs:literatureGuideURL rdf:nodeID="A7"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A8">
+    <rdf:_2 rdf:nodeID="A6"/>
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A0"/>
+  </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <moby:oneLineDescription>Industry standard search</moby:oneLineDescription>
+    <moby:operatesOn rdf:nodeID="A8"/>
+    <moby:aboutURI>http://www.acmepubs.com/about/citationSearch</moby:aboutURI>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <rdfs:comment>Industry standard search</rdfs:comment>
-    <moby:operatesOn rdf:nodeID="A0"/>
+    <moby:name>AcmePubs Citation Search</moby:name>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <acmepubs:literatureGuideURL rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  <rdf:Description rdf:nodeID="A1">
+    <acmepubs:geneSymbol>REV5</acmepubs:geneSymbol>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <moby:mapsTo rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/literatureGuideURL">
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>



From gss at pub.open-bio.org  Thu Jun 10 23:27:58 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:27:58 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102327.i5ANRwYw018953@pub.open-bio.org>


gss
Thu Jun 10 19:27:58 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery
In directory pub.open-bio.org:/tmp/cvs-serv18928/ref-impl/queries/discovery

Modified Files:
	query.n3 
Log Message:
Simplified N3 by using un-named blank nodes

moby-live/S-MOBY/ref-impl/queries/discovery query.n3,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3	2004/04/02 00:05:16	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3	2004/06/10 23:27:58	1.2
@@ -5,15 +5,15 @@
 
 _:provider
     a moby:Provider ;
-    moby:operatesOn _:bnode1 .
-
-_:bnode1
-    a moby:Graph, rdf:Bag ;
-    moby:hasMapping _:bnode2 .
-
-_:bnode2
-    a moby:Subject, go:GeneSymbol ;
-    moby:mapsTo _:bnode3 .
-
-_:bnode3
-    a moby:Object, sgd:LiteratureGuide .
+    moby:operatesOn [
+        a rdf:Bag ;
+        rdf:_1 [
+            a moby:Graph;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide
+                ]
+            ]
+        ]
+    ] .



From gss at pub.open-bio.org  Thu Jun 10 23:28:06 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:28:06 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102328.i5ANS68x018983@pub.open-bio.org>


gss
Thu Jun 10 19:28:06 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery
In directory pub.open-bio.org:/tmp/cvs-serv18958/ref-impl/queries/discovery

Modified Files:
	query.rdf 
Log Message:
Use un-named blank nodes

moby-live/S-MOBY/ref-impl/queries/discovery query.rdf,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf	2004/04/02 00:05:16	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf	2004/06/10 23:28:06	1.2
@@ -4,21 +4,24 @@
     xmlns:moby="http://www.s-moby.org:8080/terms#"
     xmlns:sgd="http://www.sgd.org:8080/terms#" >
   <rdf:Description rdf:nodeID="A0">
-    <moby:mapsTo rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+    <moby:hasMapping rdf:nodeID="A1"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A2">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <moby:operatesOn rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A0"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A1">
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <moby:mapsTo rdf:nodeID="A3"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
     <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A3">
-    <moby:hasMapping rdf:nodeID="A0"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+  <rdf:Description rdf:nodeID="A4">
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
+    <moby:operatesOn rdf:nodeID="A2"/>
   </rdf:Description>
 </rdf:RDF>



From gss at pub.open-bio.org  Thu Jun 10 23:30:53 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:30:53 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102330.i5ANUr5l019096@pub.open-bio.org>


gss
Thu Jun 10 19:30:53 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv19071/ref-impl/example-providers/sgd.org

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers/sgd.org build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/build.xml	2004/05/27 15:54:20	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/build.xml	2004/06/10 23:30:53	1.2
@@ -1,29 +1,35 @@
 <!-- Apache Ant format build file for sgd.org example provider -->
 
-<project name="sgd.org" default="war" basedir=".">
+<project name="sgd.org" default="compile" basedir=".">
 
     <!-- Import shared stuff -->
     <import file="../../servlet.xml"/>
 
-	<!-- The full path of the web archive file to be built -->
-    <property name="war-file" value="sgd.org.war"/>
-	
-	<!-- Package the compiled source files into the main jar file -->
-	<target name="war" depends="compile">
-        <jar destfile="${war-file}" basedir="${web-root}"/>
-	</target>
+    <!-- The web application name -->
+    <property name="webapp-name" value="sgd.org"/>
 	
 	<!-- Compile all the source files that go into the library -->
 	<target name="compile">
 		<mkdir dir="${classes-dir}"/>
-        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+        <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
 	</target>
 
-    <!-- Clean the build directory and the war file -->
-    <target name="clean" depends="clean-build">
-        <delete file="${war-file}"/>
+    <!-- Deploy the application to Tomcat -->
+    <target name="deploy-to-tomcat" depends="compile">
+        <mkdir dir="${tomcat-webapps-dir}/${webapp-name}"/>
+        <copy todir="${tomcat-webapps-dir}/${webapp-name}">
+            <fileset dir="${web-root}"/>
+        </copy>
+    </target>
+	
+    <!-- Clean the build directory -->
+    <target name="clean" depends="clean-build"/>
+
+    <!-- Un-deploy the application from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <delete dir="${tomcat-webapps-dir}/${webapp-name}" includeEmptyDirs="true"/>
     </target>
 	
 </project>



From gss at pub.open-bio.org  Thu Jun 10 23:31:51 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:31:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102331.i5ANVp4D019169@pub.open-bio.org>


gss
Thu Jun 10 19:31:51 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv19144/ref-impl/example-providers/sgd.org

Modified Files:
	.cvsignore 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-providers/sgd.org .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore	2004/05/27 15:54:20	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore	2004/06/10 23:31:50	1.2
@@ -1 +1,5 @@
 *.war
+.classpath
+.encoding
+.mymetadata
+.project



From gss at pub.open-bio.org  Thu Jun 10 23:32:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 10 Jun 2004 19:32:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406102332.i5ANW9GK019207@pub.open-bio.org>


gss
Thu Jun 10 19:32:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers
In directory pub.open-bio.org:/tmp/cvs-serv19182/ref-impl/example-providers

Modified Files:
	build.xml 
Log Message:
Build and deploy process mostly worked out

moby-live/S-MOBY/ref-impl/example-providers build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/build.xml	2004/03/12 17:48:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/build.xml	2004/06/10 23:32:09	1.2
@@ -1,2 +1,39 @@
-<project name="example-providers" basedir=".">
+<project name="example-providers" basedir="." default="all">
+
+    <!-- Build all the example providers -->
+    <target name="all">
+        <ant dir="acmepubs.com"/>
+        <ant dir="go.org"/>
+        <ant dir="megapubs.com"/>
+        <ant dir="pubs.org"/>
+        <ant dir="sgd.org"/>
+    </target>
+
+    <!-- Clean all the example providers -->
+    <target name="clean">
+        <ant dir="acmepubs.com" target="clean"/>
+        <ant dir="go.org" target="clean"/>
+        <ant dir="megapubs.com" target="clean"/>
+        <ant dir="pubs.org" target="clean"/>
+        <ant dir="sgd.org" target="clean"/>
+    </target>
+
+    <!-- Deploy all the example providers to Tomcat -->
+    <target name="deploy-to-tomcat">
+        <ant dir="acmepubs.com" target="deploy-to-tomcat"/>
+        <ant dir="go.org" target="deploy-to-tomcat"/>
+        <ant dir="megapubs.com" target="deploy-to-tomcat"/>
+        <ant dir="pubs.org" target="deploy-to-tomcat"/>
+        <ant dir="sgd.org" target="deploy-to-tomcat"/>
+    </target>
+
+    <!-- Un-deploy all the example providers from Tomcat -->
+    <target name="undeploy-from-tomcat">
+        <ant dir="acmepubs.com" target="undeploy-from-tomcat"/>
+        <ant dir="go.org" target="undeploy-from-tomcat"/>
+        <ant dir="megapubs.com" target="undeploy-from-tomcat"/>
+        <ant dir="pubs.org" target="undeploy-from-tomcat"/>
+        <ant dir="sgd.org" target="undeploy-from-tomcat"/>
+    </target>
+
 </project>



From gss at pub.open-bio.org  Fri Jun 11 18:26:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:26:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111826.i5BIQQnt022787@pub.open-bio.org>


gss
Fri Jun 11 14:26:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv22758/S-MOBY/ref-impl

Modified Files:
	build.xml common.xml 
Log Message:
Needed to copy another jar file to Tomcat in deploy-to-tomcat target

moby-live/S-MOBY/ref-impl build.xml,1.1,1.2 common.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/build.xml	2004/06/10 23:09:39	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/build.xml	2004/06/11 18:26:25	1.2
@@ -72,9 +72,11 @@
         <!-- Copy jar files to the Tomcat shared library directory -->
         <copy toDir="${tomcat-shared-lib-dir}">
             <!-- Copy the HTTPClient jar files -->
+            <fileset dir="${http-client-lib-dir}">
+                <include name="*.jar"/>
+            </fileset>
             <fileset dir="${http-client-dist-dir}">
                 <include name="commons-httpclient.jar"/>
-                <include name="lib/*.jar"/>
             </fileset>
             <!-- Copy the jena jar files -->
             <fileset dir="${jena-lib-dir}">

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/common.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/common.xml	2004/06/10 23:10:44	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/common.xml	2004/06/11 18:26:25	1.2
@@ -25,6 +25,8 @@
         <property name="http-client-package" value="jakarta-commons/httpclient"/>
         <!-- Top level directory of the package -->
         <property name="http-client-top-dir" value="${third-party-dir}/${http-client-package}"/>
+        <!-- Library directory -->
+        <property name="http-client-lib-dir" value="${http-client-top-dir}/lib"/>
         <!-- Distribution directory -->
         <property name="http-client-dist-dir" value="${http-client-top-dir}/dist"/>
 



From gss at pub.open-bio.org  Fri Jun 11 18:43:15 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:43:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111843.i5BIhFkb022876@pub.open-bio.org>


gss
Fri Jun 11 14:43:15 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv22851/S-MOBY/ref-impl/core

Modified Files:
	.cvsignore 
Log Message:
Don't include smoby.jar in CVS

moby-live/S-MOBY/ref-impl/core .cvsignore,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/05/27 15:30:40	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/06/11 18:43:15	1.5
@@ -1,2 +1,2 @@
-classes
-build
\ No newline at end of file
+build
+smoby.jar
\ No newline at end of file



From gss at pub.open-bio.org  Fri Jun 11 18:44:07 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:44:07 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111844.i5BIi7jR022915@pub.open-bio.org>


gss
Fri Jun 11 14:44:07 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv22890/S-MOBY/ref-impl/example-clients/SimpleEngager

Modified Files:
	.cvsignore 
Log Message:
Don't include simple-engager.jar in CVS

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .cvsignore,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/05/27 19:37:10	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/11 18:44:07	1.3
@@ -1,2 +1,2 @@
-classes
 build
+simple-engager.jar
\ No newline at end of file



From gss at pub.open-bio.org  Fri Jun 11 18:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGtV022950@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-providers/acmepubs.com

Removed Files:
	.mymetadata .project .xdoclet .classpath 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .mymetadata,1.5,NONE .project,1.6,NONE .xdoclet,1.3,NONE .classpath,1.4,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.mymetadata,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.xdoclet,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/RCS/.classpath,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 18:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGHd022967@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/core

Removed Files:
	.classpath .project 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/core .classpath,1.4,NONE .project,1.4,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/.project,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 18:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGfc022986@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-providers/pubs.org

Removed Files:
	.mymetadata .classpath .project 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-providers/pubs.org .mymetadata,1.1,NONE .classpath,1.2,NONE .project,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/.mymetadata,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/RCS/.project,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 18:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGex023009@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/server

Removed Files:
	.project .classpath xdoclet-build.xml .xdoclet .mymetadata 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/server .project,1.2,NONE .classpath,1.4,NONE xdoclet-build.xml,1.1,NONE .xdoclet,1.1,NONE .mymetadata,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/xdoclet-build.xml,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/.xdoclet,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/RCS/.mymetadata,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 18:45:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjGmj023028@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY

Removed Files:
	.project 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY .project,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/RCS/.project,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 18:45:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjHcq023069@pub.open-bio.org>


gss
Fri Jun 11 14:45:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-clients/SimpleEngager

Removed Files:
	.classpath .project 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .classpath,1.2,NONE .project,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/.project,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 18:45:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjHnQ023049@pub.open-bio.org>


gss
Fri Jun 11 14:45:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-providers/go.org

Removed Files:
	.mymetadata .project .classpath 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-providers/go.org .mymetadata,1.1,NONE .project,1.1,NONE .classpath,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/.mymetadata,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/RCS/.classpath,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 18:45:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjHCS023090@pub.open-bio.org>


gss
Fri Jun 11 14:45:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/example-providers/megapubs.com

Removed Files:
	.project .classpath .mymetadata 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .project,1.2,NONE .classpath,1.2,NONE .mymetadata,1.3,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/.classpath,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/RCS/.mymetadata,v: No such file or directory



From gss at pub.open-bio.org  Fri Jun 11 18:45:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 11 Jun 2004 14:45:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406111845.i5BIjH6W023108@pub.open-bio.org>


gss
Fri Jun 11 14:45:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders
In directory pub.open-bio.org:/tmp/cvs-serv22925/S-MOBY/ref-impl/server/.externalToolBuilders

Removed Files:
	XDoclet Builder.launch 
Log Message:
Removed from CVS control stuff that an IDE had added

moby-live/S-MOBY/ref-impl/server/.externalToolBuilders XDoclet Builder.launch,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/XDoclet,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/Builder.launch,v: No such file or directory



From ambrose at pub.open-bio.org  Fri Jun 11 22:06:56 2004
From: ambrose at pub.open-bio.org (Ambrose Ng)
Date: Fri, 11 Jun 2004 18:06:56 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406112206.i5BM6uPZ023829@pub.open-bio.org>


ambrose
Fri Jun 11 18:06:56 EDT 2004
Update of /home/repository/moby/moby-live/Perl/Accessories
In directory pub.open-bio.org:/tmp/cvs-serv23807

Added Files:
	SearchDatabase.cgi 
Log Message:
adding Namespace Database search page

moby-live/Perl/Accessories SearchDatabase.cgi,NONE,1.1


From gss at pub.open-bio.org  Mon Jun 14 16:24:12 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:24:12 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141624.i5EGOCrf009597@pub.open-bio.org>


gss
Mon Jun 14 12:24:12 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv9572

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/core .cvsignore,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/06/11 18:43:15	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/06/14 16:24:12	1.6
@@ -1,2 +1,4 @@
 build
-smoby.jar
\ No newline at end of file
+smoby.jar
+.classpath
+.project



From gss at pub.open-bio.org  Mon Jun 14 16:30:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:30:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141630.i5EGUxLx009701@pub.open-bio.org>


gss
Mon Jun 14 12:30:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com
In directory pub.open-bio.org:/tmp/cvs-serv9676

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.cvsignore	2004/05/27 15:54:40	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.cvsignore	2004/06/14 16:30:58	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project



From gss at pub.open-bio.org  Mon Jun 14 16:35:27 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:35:27 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141635.i5EGZRma009780@pub.open-bio.org>


gss
Mon Jun 14 12:35:26 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com
In directory pub.open-bio.org:/tmp/cvs-serv9755

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.cvsignore	2004/05/27 15:54:28	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/.cvsignore	2004/06/14 16:35:26	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project



From gss at pub.open-bio.org  Mon Jun 14 16:44:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:44:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141644.i5EGiiFa010077@pub.open-bio.org>


gss
Mon Jun 14 12:44:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org
In directory pub.open-bio.org:/tmp/cvs-serv10052

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/pubs.org .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.cvsignore	2004/05/27 15:54:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/.cvsignore	2004/06/14 16:44:44	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project



From gss at pub.open-bio.org  Mon Jun 14 16:44:45 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:44:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141644.i5EGijjL010107@pub.open-bio.org>


gss
Mon Jun 14 12:44:45 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv10082

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .cvsignore,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/11 18:44:07	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/14 16:44:45	1.4
@@ -1,2 +1,4 @@
 build
-simple-engager.jar
\ No newline at end of file
+simple-engager.jar
+.classpath
+.project



From gss at pub.open-bio.org  Mon Jun 14 16:44:46 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:44:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141644.i5EGikoR010137@pub.open-bio.org>


gss
Mon Jun 14 12:44:46 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org
In directory pub.open-bio.org:/tmp/cvs-serv10112

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/go.org .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.cvsignore	2004/05/27 16:23:59	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/.cvsignore	2004/06/14 16:44:46	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project



From gss at pub.open-bio.org  Mon Jun 14 16:45:53 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:45:53 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141645.i5EGjrJs010177@pub.open-bio.org>


gss
Mon Jun 14 12:45:53 EDT 2004
Update of /home/repository/moby/moby-live
In directory pub.open-bio.org:/tmp/cvs-serv10156

Added Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live .cvsignore,NONE,1.1


From gss at pub.open-bio.org  Mon Jun 14 16:49:24 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:49:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141649.i5EGnOhi010210@pub.open-bio.org>


gss
Mon Jun 14 12:49:23 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv10185/S-MOBY/ref-impl/example-clients/SimpleEngager

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager .cvsignore,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/14 16:44:45	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/06/14 16:49:23	1.5
@@ -2,3 +2,4 @@
 simple-engager.jar
 .classpath
 .project
+classes



From gss at pub.open-bio.org  Mon Jun 14 16:52:32 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 12:52:32 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141652.i5EGqWqV010289@pub.open-bio.org>


gss
Mon Jun 14 12:52:32 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv10265/S-MOBY/ref-impl/example-providers/sgd.org

Removed Files:
	.project .mymetadata .classpath 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/sgd.org .project,1.1,NONE .mymetadata,1.1,NONE .classpath,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/.project,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/.mymetadata,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/RCS/.classpath,v: No such file or directory



From gss at pub.open-bio.org  Mon Jun 14 17:17:57 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 13:17:57 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406141717.i5EHHvJx010453@pub.open-bio.org>


gss
Mon Jun 14 13:17:56 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv10428

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/server .cvsignore,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore	2004/05/27 18:31:46	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore	2004/06/14 17:17:56	1.2
@@ -1 +1,4 @@
 *.war
+.classpath
+.mymetadata
+.project



From gss at pub.open-bio.org  Mon Jun 14 20:58:13 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 16:58:13 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142058.i5EKwD3K010951@pub.open-bio.org>


gss
Mon Jun 14 16:58:12 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv10926/src/org/smoby/ref/tools

Modified Files:
	MOBYProperties.java 
Log Message:
Use servlet context to find properties file

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools MOBYProperties.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/MOBYProperties.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/MOBYProperties.java	2004/03/20 00:36:48	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/MOBYProperties.java	2004/06/14 20:58:12	1.2
@@ -3,6 +3,8 @@
 import java.io.*;
 import java.util.*;
 
+import javax.servlet.ServletContext;
+
 
 /**
  * This abstract class contains a set of static methods for retrieving
@@ -32,25 +34,12 @@
     public static String getProperty(String propName, boolean required)
         throws MissingPropertyException
     {
-        try {
-            String value = getProps().getProperty(propName);
-            if (required && (value == null)) {
-                throw new MissingPropertyException(propName,
-                    "Property " + propName + " not found in " + PROP_FILE_NAME);
-            }
-            return value;
-        } catch (FileNotFoundException e) {
-            if (required) {
-                throw new MissingPropertyException(propName,
-                    "Properties file " + PROP_FILE_NAME + " not found on classpath", e);
-            }
-        } catch (IOException e) {
-            if (required) {
-            	throw new MissingPropertyException(propName,
-                    "Error while reading " + PROP_FILE_NAME, e);
-            }
+        String value = props.getProperty(propName);
+        if (required && (value == null)) {
+            throw new MissingPropertyException(propName,
+                "Property " + propName + " not found in " + PROP_FILE_NAME);
         }
-        return null;
+        return value;
     }
 
     /**
@@ -68,21 +57,22 @@
     }
     
     /**
-     * Use lazy evaluation to create a Properties object and load the
-     * properties file into it.
-     * @return the Properties object.
-     * @throws FileNotFoundException
-     * @throws IOException
+     * Read the properties file
+     * @throws FileNotFoundException if the file cannot be located
+     * @throws IOException if the file cannot be read
      */
-    private static Properties getProps()
-        throws FileNotFoundException, IOException
+    public static void initProps(ServletContext context)
+    	throws FileNotFoundException, IOException
     {
-        if (props == null) {
+        if (props == null) // Only try to read it once
+        {
         	props = new Properties();
-            InputStream is = MOBYProperties.class.getClassLoader().
-                getResourceAsStream(PROP_FILE_NAME);
-            props.load(is);
+            InputStream is = context.getResourceAsStream(PROP_FILE_NAME);
+            if (is == null) {
+            	throw new FileNotFoundException(
+            		"Properties file \"" + PROP_FILE_NAME + "\" not found");
+            }
+        	props.load(is);
         }
-        return props;
     }
 }



From gss at pub.open-bio.org  Mon Jun 14 20:58:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 16:58:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142058.i5EKwxLf010977@pub.open-bio.org>


gss
Mon Jun 14 16:58:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets
In directory pub.open-bio.org:/tmp/cvs-serv10956/src/org/smoby/ref/servlets

Added Files:
	BaseServlet.java 
Log Message:
Base class that does common initialization tasks

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets BaseServlet.java,NONE,1.1


From gss at pub.open-bio.org  Mon Jun 14 20:59:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 16:59:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142059.i5EKxae0011019@pub.open-bio.org>


gss
Mon Jun 14 16:59:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets
In directory pub.open-bio.org:/tmp/cvs-serv10990/src/org/smoby/ref/servlets

Modified Files:
	ProviderInvestigationServlet.java DiscoveryServlet.java 
Log Message:
Make subclass of new common superclass BaseServlet

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets ProviderInvestigationServlet.java,1.3,1.4 DiscoveryServlet.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java	2004/05/19 18:26:40	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java	2004/06/14 20:59:36	1.4
@@ -7,7 +7,7 @@
 import org.apache.commons.logging.*;
 import org.smoby.ref.tools.db.*;
 import org.smoby.graph.*;
-import org.smoby.ref.tools.URIInvestigator;
+import org.smoby.ref.tools.*;
 import org.smoby.servlet.*;
 
 /**
@@ -17,7 +17,7 @@
  * The only feedback given is that if the provider-url is missing, the response
  * status is set to 406 NOT ACCEPTABLE; otherwise, the status is set to 200 OK.
  */
-public class ProviderInvestigationServlet extends HttpServlet
+public class ProviderInvestigationServlet extends BaseServlet
 {
     private final static Log syncLog = LogFactory.getLog("SYNC");
     

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/06/14 20:59:36	1.3
@@ -25,7 +25,7 @@
  * into an array of ProviderDescriptionGraph objects, by calling the
  * GraphListTransceiverFactory.newReceiver() factory method.
  */
-public class DiscoveryServlet extends HttpServlet
+public class DiscoveryServlet extends BaseServlet
 {
 	public void doPost(HttpServletRequest request, HttpServletResponse response)
 		throws ServletException, IOException



From gss at pub.open-bio.org  Mon Jun 14 20:59:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 16:59:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142059.i5EKxaxO011055@pub.open-bio.org>


gss
Mon Jun 14 16:59:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev
In directory pub.open-bio.org:/tmp/cvs-serv10990/src/org/smoby/ref/servlets/dev

Modified Files:
	OWLValidationServlet.java MOBYGraphValidationServlet.java 
	GraphConversionServlet.java RepositoryPrintServlet.java 
	ProviderListServlet.java 
Log Message:
Make subclass of new common superclass BaseServlet

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev OWLValidationServlet.java,1.2,1.3 MOBYGraphValidationServlet.java,1.2,1.3 GraphConversionServlet.java,1.2,1.3 RepositoryPrintServlet.java,1.1,1.2 ProviderListServlet.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java	2004/06/14 20:59:36	1.3
@@ -1,5 +1,6 @@
 package org.smoby.ref.servlets.dev;
 
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.servlet.ParamReader;
 import org.smoby.servlet.ParameterException;
 
@@ -13,7 +14,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class OWLValidationServlet extends HttpServlet
+public class OWLValidationServlet extends BaseServlet
 {
 	public void doPost(HttpServletRequest request, HttpServletResponse response)
 		throws ServletException, IOException

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java	2004/06/14 20:59:36	1.3
@@ -1,6 +1,7 @@
 package org.smoby.ref.servlets.dev;
 
 import org.smoby.parser.Parser;
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.servlet.*;
 import org.smoby.graph.*;
 
@@ -11,7 +12,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class MOBYGraphValidationServlet extends HttpServlet
+public class MOBYGraphValidationServlet extends BaseServlet
 {
 	public void doPost(HttpServletRequest request, HttpServletResponse response)
 		throws ServletException, IOException

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java	2004/06/14 20:59:36	1.3
@@ -1,5 +1,6 @@
 package org.smoby.ref.servlets.dev;
 
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.servlet.ParamReader;
 import org.smoby.servlet.ParameterException;
 
@@ -9,7 +10,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class GraphConversionServlet extends HttpServlet
+public class GraphConversionServlet extends BaseServlet
 {
 	public void doPost(HttpServletRequest request, HttpServletResponse response)
 		throws ServletException, IOException

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java	2004/06/14 20:59:36	1.2
@@ -1,5 +1,6 @@
 package org.smoby.ref.servlets.dev;
 
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.ref.tools.db.*;
 
 import com.hp.hpl.jena.rdf.model.*;
@@ -8,7 +9,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class RepositoryPrintServlet extends HttpServlet
+public class RepositoryPrintServlet extends BaseServlet
 {
     public void doGet(HttpServletRequest request, HttpServletResponse response)
         throws ServletException, IOException

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/05/19 18:26:40	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/06/14 20:59:36	1.3
@@ -2,6 +2,7 @@
 
 import org.smoby.servlet.*;
 import org.smoby.tools.*;
+import org.smoby.ref.servlets.BaseServlet;
 import org.smoby.ref.tools.db.*;
 import org.smoby.ref.tools.*;
 
@@ -11,7 +12,7 @@
 import javax.servlet.*;
 import javax.servlet.http.*;
 
-public class ProviderListServlet extends HttpServlet
+public class ProviderListServlet extends BaseServlet
 {
     public void doGet(HttpServletRequest request, HttpServletResponse response)
         throws ServletException, IOException



From gss at pub.open-bio.org  Mon Jun 14 21:07:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 17:07:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142107.i5EL7ZId011109@pub.open-bio.org>


gss
Mon Jun 14 17:07:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv11084

Modified Files:
	build.xml 
Log Message:
No longer need to copy properties files to WEB-INF/classes

moby-live/S-MOBY/ref-impl/server build.xml,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/06/10 23:15:37	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/06/14 21:07:35	1.4
@@ -16,11 +16,6 @@
         <javac srcdir="src" destdir="${classes-dir}">
             <classpath refid="common.classpath"/>
         </javac>
-        <copy toDir="${classes-dir}">
-            <fileset dir="WebRoot">
-                <include name="*.properties"/>
-            </fileset>
-        </copy>
 	</target>
 
     <!-- Deploy the application to Tomcat -->



From gss at pub.open-bio.org  Mon Jun 14 22:04:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 14 Jun 2004 18:04:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406142204.i5EM4KjS011316@pub.open-bio.org>


gss
Mon Jun 14 18:04:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools
In directory pub.open-bio.org:/tmp/cvs-serv11291/WebRoot/tools

Modified Files:
	client.html 
Log Message:
Added radio buttons on Discover form

moby-live/S-MOBY/ref-impl/server/WebRoot/tools client.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html	2004/03/30 22:25:51	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html	2004/06/14 22:04:20	1.2
@@ -24,8 +24,14 @@
 
 <h4><u>Discover matching graphs in the S-MOBY metadata repository</u></h4>
 <form action="http://www.s-moby.org:8080/find-providers" method="post">
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Paste a graph in RDF/XML format
-  and press "Discover" to find matching graphs. &nbsp;&nbsp;
+  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Paste a graph in RDF/XML format, select
+  statements to return, and press "Discover" to find matching graphs. &nbsp;&nbsp;
+  <p>
+  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+  Statements to return:&nbsp;&nbsp;
+  <input type="radio" name="statements" value="minimal">Minimal&nbsp;&nbsp;
+  <input type="radio" name="statements" value="query" CHECKED>Query only&nbsp;&nbsp;
+  <input type="radio" name="statements" value="cached">Cached&nbsp;&nbsp;
   <input value="Discover" type="submit">
   <p>
   &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;



From mwilkinson at pub.open-bio.org  Tue Jun 15 00:08:14 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 20:08:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150008.i5F08EAc011629@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:08:14 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11614

Added Files:
	Config.pm 
Log Message:
added a configuration module.  MOBY Central will no longer use environment variables to get the database connection information

moby-live/Perl/MOBY Config.pm,NONE,1.1


From mwilkinson at pub.open-bio.org  Tue Jun 15 00:09:37 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 20:09:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150009.i5F09bw9011701@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:09:36 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11678

Modified Files:
	Central.pm Central.html 
Log Message:
modified the way Central gets its configuration.  Also fixed a bug that allowed object names to be registered with spaces

moby-live/Perl/MOBY Central.pm,1.127,1.128 Central.html,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.127
retrieving revision 1.128
diff -u -r1.127 -r1.128
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/04/20 23:24:25	1.127
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/15 00:09:36	1.128
@@ -18,6 +18,7 @@
 use MOBY::authority;
 use MOBY::service_instance;
 use MOBY::central_db_connection;
+use MOBY::Config;
 
 my $debug = 0;
 
@@ -72,6 +73,43 @@
 Servers/Services, or queryiong for available services given certain input/output
 or service type constraints.
 
+=cut
+
+
+=head1 CONFIGURATION
+
+This depends on a config file to get its database connection information.  At a minimum
+this config file must have the following clause:
+
+ [mobycentral]
+ url = some.url 
+ username = foo
+ password = bar
+ port = portnumber
+ dbname = mobycentral
+
+
+The space before and after the '=' is critical.
+
+The end of a clause is indicated by a blank line.
+
+Additional identically formatted clauses may be added for each of:
+
+  [mobyobject]
+  [mobynamespace]
+  [mobyservice]
+  [mobyrelationship]
+
+if these ontologies are being served from a local database (via the
+OntologyServer module).  These clauses will be read by the OntologyServer
+module if they are present, otherwise default connections will be made
+to the MOBY Central ontology server.
+
+The config file must be readable by the webserver, and the webserver
+environment should include the following ENV variable:
+
+$ENV{MOBY_CENTRAL_CONFIG} = /path/to/config/file.name
+
 
 =head1 AUTHORS
 
@@ -141,21 +179,20 @@
 }
 
 sub _dbAccess {
-	
-# this configuration system was stoopid and is now defunkt.
-	
-#    my $filename = "./MOBY/central.cfg";# $self->config;
-#	$debug && &_LOG("trying to open file $filename\n");
-#	open (IN, $filename) || die "can't open configuration file $filename:  $!";
-#	my $url = <IN>; chomp $url;
-#	my $dbname = <IN>; chomp $dbname;
-#	my $username = <IN>; chomp $username;
-#	my $password = <IN>; chomp $password;
-	my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
-	my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
-	my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
-	my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
-	my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
+
+    my $conf = MOBY::Config->new;
+
+    $username = $conf->{mobycentral}->{username};
+    $password = $conf->{mobycentral}->{password};
+    $port = $conf->{mobycentral}->{port};
+    $dbname = $conf->{mobycentral}->{dbname};
+    $url = $conf->{mobycentral}->{url};
+    
+	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
+	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
+	#my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
+	#my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
+	#my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
 	
 	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
 	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
@@ -237,6 +274,10 @@
 	return &_error("Malformed authURI - must not have an http:// prefix","") if $auth =~ '[/:]';
 	return &_error("Malformed authURI - must take the form NNN.NNN.NNN","") unless $auth =~ /\./;
 	return &_error("Malformed email - must be a valid email address of the form name\@organization.foo","") unless $email =~ /\S\@\S+\.\S+/;
+	return &_error("Object name may not contain spaces or other characters invalid in a URN","") if $term =~ /\s\"\&\<\>\[\]\^\`\{\|\}\~/;
+	if ($term =~ m"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?"){  # matches a URI
+        return &_error("Object name may not be an URN or URI","") if $1;
+    }
 
 	# validate that the final ontology will be valid by testing against existing relationships and such
 	while (my ($reltype, $obj) = each %{$relationships}){

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.html,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOBY/Central.html	2004/04/15 14:38:22	1.13
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.html	2004/06/15 00:09:36	1.14
@@ -15,6 +15,7 @@
 	<li><a href="#name">NAME</a></li>
 	<li><a href="#synopsis">SYNOPSIS</a></li>
 	<li><a href="#description">DESCRIPTION</a></li>
+	<li><a href="#configuration">CONFIGURATION</a></li>
 	<li><a href="#authors">AUTHORS</a></li>
 	<li><a href="#registration_xml_object">Registration XML Object</a></li>
 	<li><a href="#methods">METHODS</a></li>
@@ -107,6 +108,34 @@
 <p>
 </p>
 <hr />
+<h1><a name="configuration">CONFIGURATION</a></h1>
+<p>This depends on a config file to get its database connection information.  At a minimum
+this config file must have the following clause:</p>
+<pre>
+ [mobycentral]
+ url = some.url 
+ username = foo
+ password = bar
+ port = portnumber
+ dbname = mobycentral</pre>
+<p>The space before and after the '=' is critical.</p>
+<p>The end of a clause is indicated by a blank line.</p>
+<p>Additional identically formatted clauses may be added for each of:</p>
+<pre>
+  [mobyobject]
+  [mobynamespace]
+  [mobyservice]
+  [mobyrelationship]</pre>
+<p>if these ontologies are being served from a local database (via the
+OntologyServer module).  These clauses will be read by the OntologyServer
+module if they are present, otherwise default connections will be made
+to the MOBY Central ontology server.</p>
+<p>The config file must be readable by the webserver, and the webserver
+environment should include the following ENV variable:</p>
+<p>$ENV{MOBY_CENTRAL_CONFIG} = /path/to/config/file.name</p>
+<p>
+</p>
+<hr />
 <h1><a name="authors">AUTHORS</a></h1>
 <p>Mark Wilkinson (<a href="mailto:markw at illuminae.com">markw at illuminae.com</a>)</p>
 <p>BioMOBY Project:  <a href="http://www.biomoby.org">http://www.biomoby.org</a></p>



From mwilkinson at pub.open-bio.org  Tue Jun 15 00:22:05 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 20:22:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150022.i5F0M5db011857@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:22:05 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11838

Modified Files:
	OntologyServer.pm 
Log Message:
OntologyServer now reads the config file as well

moby-live/Perl/MOBY OntologyServer.pm,1.41,1.42
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.41
retrieving revision 1.42
diff -u -r1.41 -r1.42
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/05/11 15:48:45	1.41
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 00:22:05	1.42
@@ -74,6 +74,7 @@
 use vars qw($AUTOLOAD);
 use DBI;
 use DBD::mysql;
+use MOBY::Config;
 
 my $debug = 0;
 
@@ -139,6 +140,14 @@
     $self->ontology eq 'service' && $self->database('mobyservice');
     $self->ontology eq 'relationship' && $self->database('mobyrelationship');
 
+	
+	my $conf = MOBY::Config->new;
+	$self->username = $conf->{$self->database}->{username} unless $self->username;
+    $self->password = $conf->{$self->database}->{password} unless $self->password;
+    $self->port = $conf->{$self->database}->{port} unless $self->port;
+    $self->dbname = $self->database unless $self->dbname;
+    $self->host = $conf->{$self->database}->{url} unless $self->host;
+ 
 	my $host = $self->host?$self->host:$ENV{MOBY_CENTRAL_URL}; chomp $host;
 	my $username = $self->username?$self->username:$ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
 	my $password = $self->password?$self->password:$ENV{MOBY_CENTRAL_DBPASS}; chomp $password if $password; $password =~ s/\s//g if $password;



From mwilkinson at pub.open-bio.org  Tue Jun 15 00:37:55 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 20:37:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150037.i5F0btA2011994@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:37:55 EDT 2004
Update of /home/repository/moby/moby-live/Perl
In directory pub.open-bio.org:/tmp/cvs-serv11975

Modified Files:
	MANIFEST 
Log Message:
using config file here too

moby-live/Perl MANIFEST,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MANIFEST,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MANIFEST	2004/03/18 23:10:34	1.9
+++ /home/repository/moby/moby-live/Perl/MANIFEST	2004/06/15 00:37:55	1.10
@@ -6,6 +6,7 @@
 MOBY/central_db_connection.pm
 MOBY/mysql.pm
 MOBY/OntologyServer.pm
+MOBY/Config.pm
 MOBY/CommonSubs.pm
 MOBY/CrossReference.pm
 MOBY/service_instance.pm



From mwilkinson at pub.open-bio.org  Tue Jun 15 00:37:55 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 20:37:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150037.i5F0btjl012018@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:37:55 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11975/MOBY

Modified Files:
	CommonSubs.pm central_db_connection.pm 
Log Message:
using config file here too

moby-live/Perl/MOBY CommonSubs.pm,1.51,1.52 central_db_connection.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.51
retrieving revision 1.52
diff -u -r1.51 -r1.52
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/04 23:54:16	1.51
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/06/15 00:37:55	1.52
@@ -200,6 +200,7 @@
     getResponseArticles
     getCrossReferences
     genericServiceInputParser
+    genericServiceInputParserAsObject
     complexServiceInputParser
     whichDeepestParentObject
     getServiceNotes
@@ -233,6 +234,7 @@
     getResponseArticles
     getCrossReferences
     genericServiceInputParser
+    genericServiceInputParserAsObject
     complexServiceInputParser
     whichDeepestParentObject
     getServiceNotes
@@ -327,6 +329,48 @@
 
 
 
+=head2 serviceInputParser
+
+ name     : DO NOT USE!!
+ function : to take a MOBY message and break the objects out of it.  This is identical
+            to the genericServiceInputParser method above, except that it returns the data as
+            Objects rather than XML::DOM nodes.  This is an improvement!
+ usage    : my @inputs = serviceInputParser($MOBY_mssage));
+ args     : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message
+ returns  : @inputs - the structure of @inputs is a list of listrefs.
+            Each listref has three components:
+                1. COLLECTION|SIMPLE|SECONDARY (i.e. constants 1, 2, 3)
+                2. queryID (undef for Secondary parameters)
+                3. $data - either MOBY::Client::SimpleArticle, CollectionArticle, or SecondaryArticle
+
+=cut
+
+
+sub serviceInputParser {
+    my ($message) = @_;  # get the incoming MOBY query XML
+    my @inputs;           # set empty response
+    my @queries = getInputs($message);  # returns XML::DOM nodes <mobyData>...</mobyData>
+
+
+# mark, this doesn't work for complex services.  We need to allow more than one input per invocation
+    foreach my $query(@queries){
+        my $queryID = getInputID($query);  # get the queryID attribute of the mobyData
+        my @input_articles = getArticlesAsObjects($query); # get the Simple/Collection articles making up this query <Simple>...</Simple> or <Collection>...</Collection> or <Parameter>...</Parameter
+        foreach my $article(@input_articles){       # input is a listref
+            if ($article->isCollection){
+                my @simples = getCollectedSimples($article->XML);
+                push @inputs, [COLLECTION,$queryID, \@simples];
+            } elsif ($article->isSimple){
+                push @inputs, [SIMPLE,$queryID,$article];
+            } elsif ($article->isSecondary){
+                push @inputs, [SECONDARY,$queryID,$article];
+            }
+        }
+    }
+    return @inputs;
+}
+
+
 =head2 complexServiceInputParser
 
  name     : complexServiceInputParser
@@ -487,46 +531,6 @@
 
 
 
-=head2 genericServiceInputParserAsObject
-
- name     : DO NOT USE!
- function : to take a MOBY message and break the objects out of it.  This is identical
-            to the subroutine above, except that it returns the data as
-            Objects rather than XML::DOM nodes
- usage    : my @inputs = genericServiceInputParser($MOBY_mssage));
- args     : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message
- returns  : @inputs - the structure of @inputs is a list of listrefs.
-            Each listref has three components:
-                1. COLLECTION|SIMPLE|SECONDARY (i.e. constants 1, 2, 3)
-                2. queryID (undef for Secondary parameters)
-                3. $data - either MOBY::Client::SimpleArticle, CollectionArticle, or SecondaryArticle
-
-=cut
-
-
-sub genericServiceInputParserAsObject {
-    my ($message) = @_;  # get the incoming MOBY query XML
-    my @inputs;           # set empty response
-    my @queries = getInputs($message);  # returns XML::DOM nodes <mobyData>...</mobyData>
-
-    foreach my $query(@queries){
-        my $queryID = getInputID($query);  # get the queryID attribute of the mobyData
-        my @input_articles = getArticlesAsObjects($query); # get the Simple/Collection articles making up this query <Simple>...</Simple> or <Collection>...</Collection> or <Parameter>...</Parameter
-        foreach my $article(@input_articles){       # input is a listref
-            if ($article->isCollection){
-                my @simples = getCollectedSimples($article->XML);
-                push @inputs, [COLLECTION,$queryID, \@simples];
-            } elsif ($article->isSimple){
-                push @inputs, [SIMPLE,$queryID,$article];
-            } elsif ($article->isSecondary){
-                push @inputs, [SECONDARY,$queryID,$article];
-            }
-        }
-    }
-    return @inputs;
-}
-
-
 #################################################
 					 ##################################
 					 ##################################

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2003/06/10 17:12:52	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/15 00:37:55	1.3
@@ -3,7 +3,7 @@
 use Carp;
 use XML::DOM;
 use vars qw($AUTOLOAD @ISA);
-
+use MOBY::Config;
 
 =head1 NAME
 
@@ -116,6 +116,26 @@
     #    $self->host,
     #    $self->port);
 
+
+    my $conf = MOBY::Config->new;
+
+    $username = $conf->{mobycentral}->{username};
+    $password = $conf->{mobycentral}->{password};
+    $port = $conf->{mobycentral}->{port};
+    $dbname = $conf->{mobycentral}->{dbname};
+    $url = $conf->{mobycentral}->{url};
+    
+	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
+	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
+	#my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
+	#my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
+	#my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
+	
+	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
+	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
+	
+	return ($dbh);
+
 	my $host = $ENV{MOBY_CENTRAL_URL}; chomp $host;
 	my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
 	my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;



From mwilkinson at pub.open-bio.org  Tue Jun 15 00:37:55 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 20:37:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150037.i5F0btFP012043@pub.open-bio.org>


mwilkinson
Mon Jun 14 20:37:55 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv11975/MOBY/Client

Modified Files:
	CollectionArticle.pm SimpleArticle.pm 
Log Message:
using config file here too

moby-live/Perl/MOBY/Client CollectionArticle.pm,1.7,1.8 SimpleArticle.pm,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm	2004/04/14 19:56:59	1.7
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/CollectionArticle.pm	2004/06/15 00:37:55	1.8
@@ -9,12 +9,39 @@
 
 =head1 NAME
 
-MOBY::Client::CollectionArticle - a small object describing the Collection articles from the findService Response message of MOBY Central
+MOBY::Client::CollectionArticle - a small object describing the Collection articles from the findService Response message of MOBY Central or representing the collection part of a MOBY invocation or response block
 
 =head1 SYNOPSIS
 
-experimental - please do not use in your code
+This module can be used in two ways.  One is to represent the Collection
+portion of a findService response.  The other is to represent the Collecion
+portion of a MOBY service invocation or response message.
+
+Parsing a MOBY Service Invocation
+
+ use MOBY::CommonSubs qw(:all);
+ 
+ sub myService {
+    my ($caller, $data) = @_;
+	
+    my (@inputs)= serviceInputParser($data);
+
+    foreach (@inputs){
+        my ($articleType, $qID, $OBJECT) = @{$_};
+        if ($articleType == COLLECTION){
+            $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;  # send back a blank response for this queryID
+            next;
+        } elsif ($articleType == SIMPLE) {
+        
+        } elsif ($articleType == SECONDARY){
+        
+        }
+    }
+ }
 
+ 
+ 
+ 
 =cut
 
 =head1 DESCRIPTION

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm	2004/04/14 19:56:59	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/SimpleArticle.pm	2004/06/15 00:37:55	1.5
@@ -328,6 +328,11 @@
     return $self;
 }
 
+sub value {
+    my ($self) = @_;
+    # ?????  what to do here ????
+    
+}
 sub AUTOLOAD {
     no strict "refs";
     my ($self, $newval) = @_;



From mwilkinson at pub.open-bio.org  Tue Jun 15 01:00:26 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 21:00:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150100.i5F10QMf012399@pub.open-bio.org>


mwilkinson
Mon Jun 14 21:00:26 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv12372/MOBY

Modified Files:
	Central.pm OntologyServer.pm central_db_connection.pm 
Log Message:
a few bugfixes for undeclared variables etc

moby-live/Perl/MOBY Central.pm,1.128,1.129 OntologyServer.pm,1.42,1.43 central_db_connection.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.128
retrieving revision 1.129
diff -u -r1.128 -r1.129
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/15 00:09:36	1.128
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/15 01:00:26	1.129
@@ -182,11 +182,11 @@
 
     my $conf = MOBY::Config->new;
 
-    $username = $conf->{mobycentral}->{username};
-    $password = $conf->{mobycentral}->{password};
-    $port = $conf->{mobycentral}->{port};
-    $dbname = $conf->{mobycentral}->{dbname};
-    $url = $conf->{mobycentral}->{url};
+    my $username = $conf->{mobycentral}->{username};
+    my $password = $conf->{mobycentral}->{password};
+    my $port = $conf->{mobycentral}->{port};
+    my $dbname = $conf->{mobycentral}->{dbname};
+    my $url = $conf->{mobycentral}->{url};
     
 	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
 	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.42
retrieving revision 1.43
diff -u -r1.42 -r1.43
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 00:22:05	1.42
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 01:00:26	1.43
@@ -142,11 +142,10 @@
 
 	
 	my $conf = MOBY::Config->new;
-	$self->username = $conf->{$self->database}->{username} unless $self->username;
-    $self->password = $conf->{$self->database}->{password} unless $self->password;
-    $self->port = $conf->{$self->database}->{port} unless $self->port;
-    $self->dbname = $self->database unless $self->dbname;
-    $self->host = $conf->{$self->database}->{url} unless $self->host;
+	$self->username($conf->{$self->database}->{username}) unless $self->username;
+    $self->password($conf->{$self->database}->{password}) unless $self->password;
+    $self->port($conf->{$self->database}->{port}) unless $self->port;
+    $self->host($conf->{$self->database}->{url}) unless $self->host;
  
 	my $host = $self->host?$self->host:$ENV{MOBY_CENTRAL_URL}; chomp $host;
 	my $username = $self->username?$self->username:$ENV{MOBY_CENTRAL_DBUSER}; chomp $username;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/15 00:37:55	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/15 01:00:26	1.4
@@ -119,40 +119,17 @@
 
     my $conf = MOBY::Config->new;
 
-    $username = $conf->{mobycentral}->{username};
-    $password = $conf->{mobycentral}->{password};
-    $port = $conf->{mobycentral}->{port};
-    $dbname = $conf->{mobycentral}->{dbname};
-    $url = $conf->{mobycentral}->{url};
-    
-	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
-	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
-	#my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
-	#my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
-	#my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
-	
+    my $username = $conf->{mobycentral}->{username};
+    my $password = $conf->{mobycentral}->{password};
+    my $port = $conf->{mobycentral}->{port};
+    my $dbname = $conf->{mobycentral}->{dbname};
+    my $url = $conf->{mobycentral}->{url};
+    	
 	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
 	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
 	
-	return ($dbh);
-
-	my $host = $ENV{MOBY_CENTRAL_URL}; chomp $host;
-	my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
-	my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
-	my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
-    my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
-    
-    #my $dbname = $self->dbname;
-    #my $host = $self->host;
-    #my $port = $self->port;
-    #my $username = $self->username;
-    #my $password = $self->password;
-    my ($dsn) = "DBI:mysql:$dbname:$host:$port";
-
-    my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
-
     $self->dbh($dbh);
-    return $self;
+	return $self;
 
 }
 



From mwilkinson at pub.open-bio.org  Tue Jun 15 01:15:16 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 14 Jun 2004 21:15:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406150115.i5F1FGWS012533@pub.open-bio.org>


mwilkinson
Mon Jun 14 21:15:16 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv12514/MOBY

Modified Files:
	Config.pm 
Log Message:
Doh.  I hard-coded a testing path in there.

moby-live/Perl/MOBY Config.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Config.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/Config.pm	2004/06/15 00:08:14	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/Config.pm	2004/06/15 01:15:16	1.2
@@ -65,7 +65,6 @@
     }
 
     my $file = $ENV{MOBY_CENTRAL_CONFIG};
-    $file = "/home/markw/conf.conf";
     chomp $file;
     if ((-e $file) && (!(-d $file))){
         open IN, $file || die "can't open MOBY Configuration file $!\n";



From mwilkinson at pub.open-bio.org  Tue Jun 15 14:55:17 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 15 Jun 2004 10:55:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406151455.i5FEtHJL014835@pub.open-bio.org>


mwilkinson
Tue Jun 15 10:55:17 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv14816/MOBY

Modified Files:
	OntologyServer.pm 
Log Message:
be sure to extract the database name from the config file in the case of a non-standard installation of the registry

moby-live/Perl/MOBY OntologyServer.pm,1.43,1.44
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.43
retrieving revision 1.44
diff -u -r1.43 -r1.44
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 01:00:26	1.43
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 14:55:17	1.44
@@ -152,7 +152,7 @@
 	my $password = $self->password?$self->password:$ENV{MOBY_CENTRAL_DBPASS}; chomp $password if $password; $password =~ s/\s//g if $password;
     my $port = $self->port?$self->port:$ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
     
-    my ($dsn) = "DBI:mysql:".($self->database).":".($host).":".($port);
+    my ($dsn) = "DBI:mysql:".($conf->{$self->database}->{dbname}).":".($host).":".($port);
 
     my $dbh;
 #	$debug && &_LOG("connecting to db with params ",$self->database, $self->username, $self->password,"\n");



From mwilkinson at pub.open-bio.org  Wed Jun 16 01:15:30 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 15 Jun 2004 21:15:30 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406160115.i5G1FU0T016502@pub.open-bio.org>


mwilkinson
Tue Jun 15 21:15:30 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv16447/MOBY/Client

Modified Files:
	Central.pm SecondaryArticle.pm 
Added Files:
	SimpleInput.pm 
Log Message:
all sorts of additions and changes.  Secondary parameters now work for me on two systems, so that problem should now be solved.  I am starting to rip out the SQL that is in MOBY Central into other modules, and it will eventually end up in a single mysql-specific module with an API to make it easier to code MOBY onto other data back-ends.  Various bug fixes here and there as well.

moby-live/Perl/MOBY/Client SimpleInput.pm,NONE,1.1 Central.pm,1.75,1.76 SecondaryArticle.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.75
retrieving revision 1.76
diff -u -r1.75 -r1.76
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/05/03 19:49:18	1.75
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/06/16 01:15:30	1.76
@@ -10,6 +10,7 @@
 use MOBY::Client::Registration;
 use MOBY::Client::SimpleArticle;
 use MOBY::Client::CollectionArticle;
+use MOBY::Client::SecondaryArticle;
 use MOBY::Client::OntologyServer;
 
 use vars qw($AUTOLOAD @ISA $MOBY_server $MOBY_uri);
@@ -722,8 +723,8 @@
 
 	if ($Category eq "moby" || $Category eq 'soap') {
 		my %SEC;
-		if ($a{'secondary'} && ref($a{'secondary'} =~ /hash/i)){
-			%SEC = %{$a{secondary}}
+		if ($a{'secondary'} && (ref($a{'secondary'}) =~ /hash/i)){
+			%SEC = %{$a{secondary}};
 		} elsif ($a{'secondary'} && !(ref($a{'secondary'}) =~ /hash/i)){
 			return $self->errorRegXML("invalid structure of secondary parameters.  Expected hashref.")
 		}
@@ -799,13 +800,14 @@
 			my $min = $data{min};
 			my $datatype = $data{datatype};
 			unless ($datatype){return $self->errorRegXML("a secondaryArticle must contain at least a datatype value in secondary article $param");}
+			unless (($datatype =~ /Integer/) || ($datatype =~ /Float/) || ($datatype =~ /String/) || ($datatype =~ /DateTime/)){return $self->errorRegXML("a secondaryArticle must have a datatype of Integer, Float, String, or DateTime");}
 			unless ((ref($data{enum})) =~ /array/i){return $self->errorRegXML("invalid structure of enum limits in secondary article $param; expected arrayref")}
 			my @enums = @{$data{enum}};
 			$message .="<Parameter articleName='$param'>\n";
 			$message .="<default>$default</default>\n";
 			$message .="<datatype>$datatype</datatype>\n";
-			$message .="<max></max>\n";
-			$message .="<min></min>\n";
+			$message .="<max>$max</max>\n";
+			$message .="<min>$min</min>\n";
 			foreach (@enums){
 				$message .="<enum>$_</enum>\n";
 			}

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm	2004/05/03 19:49:18	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm	2004/06/16 01:15:30	1.2
@@ -185,7 +185,7 @@
 
     sub addEnum {
         my ($self, $enum) = @_;
-        return $self->{enum} unless $enum;
+        return $self->{enum} unless defined($enum);
         push @{$self->{enum}}, $enum;
         return $self->{enum};
     }
@@ -265,36 +265,46 @@
 
     my $objects = $dom->getElementsByTagName("datatype");
     if ($objects->item(0)){
+        my $data;
         foreach my $child($objects->item(0)->getChildNodes){ 
             next unless $child->getNodeType == TEXT_NODE;
-            $self->datatype($self->datatype . $child->toString);
+            $data .= $child->toString;
+            $data =~ s/\s//g;
         }
+        $self->datatype($data);
     }
-    $self->datatype($self->datatype =~ s/^\s//);
-    $self->datatype($self->datatype =~ s/\s$//);
     
     $objects = $dom->getElementsByTagName("default");
     if ($objects->item(0)){
+        my $def;
         foreach my $child($objects->item(0)->getChildNodes){ 
             next unless $child->getNodeType == TEXT_NODE;
-            $self->default($self->default . $child->toString);
+            $def .= $child->toString;
+            $def =~ s/\s//g;
         }
+        $self->default($def);
     }
     
     $objects = $dom->getElementsByTagName("max");
     if ($objects->item(0)){
+        my $max;
         foreach my $child($objects->item(0)->getChildNodes){ 
             next unless $child->getNodeType == TEXT_NODE;
-            $self->max($self->max . $child->toString);
+            $max .= $child->toString;
+            $max =~ s/\s//g;
         }
+        $self->max($max);
     }
     
     $objects = $dom->getElementsByTagName("min");
     if ($objects->item(0)){
+        my $min;
         foreach my $child($objects->item(0)->getChildNodes){ 
             next unless $child->getNodeType == TEXT_NODE;
-            $self->min($self->min . $child->toString);
+            $min .= $child->toString;
+            $min =~ s/\s//g;
         }
+        $self->min($min);
     }
     
     $objects = $dom->getElementsByTagName("enum");
@@ -303,7 +313,8 @@
             foreach my $child($objects->item($_)->getChildNodes){
                 my $val;
                 next unless $child->getNodeType == TEXT_NODE;
-                next unless $val = $child->toString;
+                $val = $child->toString;
+                next unless defined($val);
                 $val =~ s/^\s//; $val =~ s/\s$//;
                 $self->addEnum($val);
             }



From mwilkinson at pub.open-bio.org  Wed Jun 16 01:15:30 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 15 Jun 2004 21:15:30 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406160115.i5G1FURZ016478@pub.open-bio.org>


mwilkinson
Tue Jun 15 21:15:30 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv16447/MOBY

Modified Files:
	Central.pm service_instance.pm simple_input.pm 
	simple_output.pm 
Added Files:
	collection_input.pm collection_output.pm secondary_input.pm 
Log Message:
all sorts of additions and changes.  Secondary parameters now work for me on two systems, so that problem should now be solved.  I am starting to rip out the SQL that is in MOBY Central into other modules, and it will eventually end up in a single mysql-specific module with an API to make it easier to code MOBY onto other data back-ends.  Various bug fixes here and there as well.

moby-live/Perl/MOBY collection_input.pm,NONE,1.1 collection_output.pm,NONE,1.1 secondary_input.pm,NONE,1.1 Central.pm,1.129,1.130 service_instance.pm,1.3,1.4 simple_input.pm,1.2,1.3 simple_output.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.129
retrieving revision 1.130
diff -u -r1.129 -r1.130
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/15 01:00:26	1.129
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/16 01:15:30	1.130
@@ -17,6 +17,11 @@
 use MOBY::service_type;
 use MOBY::authority;
 use MOBY::service_instance;
+use MOBY::simple_input;
+use MOBY::simple_output;
+use MOBY::collection_input;
+use MOBY::collection_output;
+use MOBY::secondary_input;
 use MOBY::central_db_connection;
 use MOBY::Config;
 
@@ -1150,7 +1155,7 @@
 	return &_error("Service with this authority/servicename already exists","") if ($SVC == -1);
 
 	$debug && &_LOG("new service instance created\n");
-	
+    
 	foreach my $IN(@IN){
 		my ($success,$msg) = &_registerArticles($SVC, "input", $IN, undef); 
 		return &_error("Registration Failed During INPUT Article Registration: $msg","") unless ($success==1);
@@ -1160,7 +1165,7 @@
 		return &_error("Registration Failed During OUTPUT Article Registration: $msg","") unless ($success==1);
 	}
 	foreach my $SEC(@SECS){
-		my ($success,$msg) = &_registerArticles($SVC, "secondary", $SEC, undef); 
+    	my ($success,$msg) = &_registerArticles($SVC, "secondary", $SEC, undef); 
 		return &_error("Registration Failed During SECONDARY Article Registration: $msg","") unless ($success==1);
 	}
 	
@@ -1172,7 +1177,7 @@
     my $dbh = $SVC->dbh;
     return  (-1,'Bad node') unless $node->getNodeType == ELEMENT_NODE;
 
-    # this is a Simple or a Collection object
+    # this is a Simple, Collection, or Parameter object
     my $simp_coll = $node->getTagName;
 	$debug && &_LOG("TAGNAME in $inout _registerArticle is $simp_coll");
 	
@@ -1183,9 +1188,20 @@
     my ($object_type, @namespaces);
 
     if ($simp_coll eq "Collection"){
-		$debug && &_LOG("Collection!\n");  # the following SQl belongs in the service_instance object, but screw it, I'm running out of time!
-		$dbh->do("insert into collection_$inout (service_instance_id, article_name) values (?,?)", undef, ($SVC->service_instance_id, $article));
-		my $collection_id=$dbh->{mysql_insertid};
+		$debug && &_LOG("Collection!\n");
+        my $collection_id;
+        if ($inout eq 'input'){
+            $collection_id = $SVC->add_collection_input(article_name => $article);
+        } elsif ($inout eq 'output') {
+            $collection_id = $SVC->add_collection_output(article_name => $article);            
+        } else {
+            $SVC->DELETE_THYSELF; return (-1,"found article that was neither input nor output");
+        }
+        
+        # the following SQl belongs in the service_instance object, but screw it, I'm running out of time!
+		#$dbh->do("insert into collection_$inout (service_instance_id, article_name) values (?,?)", undef, ($SVC->service_instance_id, $article));
+		#my $collection_id=$dbh->{mysql_insertid};
+        
 		my $Simples = $node->getElementsByTagName('Simple');
 		my $length = $Simples->getLength;
 		for (my $x=0; $x<$length; ++$x){
@@ -1227,67 +1243,88 @@
 		chop($namespace_string);  # remove trailing comma
 		my $dbh = $SVC->dbh;
 		my $service_instance_id;
-		unless ($collid) {
+		unless ($collid) {  # this SIMPLE is either alone, or is part of a COLLECTION ($collid > 0)
+                            # therefore we want either its service instance ID, or its Collection ID.
 			$service_instance_id = $SVC->service_instance_id;
 		}				# one or the other, but not both
-		$dbh->do("insert into simple_".$inout."
-				 (object_type_uri,
-				  namespace_type_uris,
-				  article_name,
-				  service_instance_id,
-				  collection_".$inout."_id)
-				 values (?,?,?,?,?)",
-		undef,
-		($typeURI,
-		$namespace_string,
-		$article,
-		$service_instance_id,
-		$collid));
-
+        
+        if ($inout eq 'input'){
+            my $sinput = $SVC->add_simple_input(
+                    object_type_uri	=> $typeURI,
+                    namespace_type_uris	=> $namespace_string,
+                    article_name 	=> $article,
+                    collection_input_id 	=> 	$collid,
+                    );
+            unless ($sinput){
+       			$SVC->DELETE_THYSELF; return (-1,"registration failed during registration of input object $typeURI.  Unknown reasons.");
+            }
+
+        } elsif ($inout eq 'output'){
+            my $soutput = $SVC->add_simple_output(
+                    object_type_uri	=> $typeURI,
+                    namespace_type_uris	=> $namespace_string,
+                    article_name 	=> $article,
+                    collection_input_id 	=> 	$collid,
+                    );
+            unless ($soutput){
+       			$SVC->DELETE_THYSELF; return (-1,"registration failed during registration of output object $typeURI.  Unknown reasons.");
+            }
+        }
+        
     } elsif ($simp_coll eq "Parameter"){
-	    my $article = $node->getAttributeNode("articleName");
-		$article = $article->getValue() if $article;
-        my $types =  $node->getElementsByTagName('datatype');
-	    my ($datatype, $def, $max, $min, @enums);
+        my $parameter = $node;
+        my $article = $parameter->getAttributeNode("articleName");
+        $article = $article->getValue() if $article;
+        my ($datatype, $def, $max, $min, @enums);
+        my $types =  $parameter->getElementsByTagName('datatype');
         if ($types->item(0)){
-			foreach ($types->item(0)->getChildNodes){ # should only ever be one!
+            foreach ($types->item(0)->getChildNodes){ # should only ever be one!
             ($_->getNodeType == TEXT_NODE) && ($datatype = $_->toString);
-	        }
-		}
-        my $defs =  $node->getElementsByTagName('default');
+            }
+        }
+        my $defs =  $parameter->getElementsByTagName('default');
         if ($defs->item(0)){
-			foreach ($defs->item(0)->getChildNodes){ # should only ever be one!
-				($_->getNodeType == TEXT_NODE) && ($def = $_->toString);
-			}
-		}
-        my $maxs =  $node->getElementsByTagName('max');
+            foreach ($defs->item(0)->getChildNodes){ # should only ever be one!
+                ($_->getNodeType == TEXT_NODE) && ($def = $_->toString);
+            }
+        }
+        my $maxs =  $parameter->getElementsByTagName('max');
         if ($maxs->item(0)){
-			foreach ($maxs->item(0)->getChildNodes){ # should only ever be one!
-				($_->getNodeType == TEXT_NODE) && ($max = $_->toString);
-			}
-		}
-        my $mins =  $node->getElementsByTagName('min');
+            foreach ($maxs->item(0)->getChildNodes){ # should only ever be one!
+                ($_->getNodeType == TEXT_NODE) && ($max = $_->toString);
+            }
+        }
+        my $mins =  $parameter->getElementsByTagName('min');
         if ($mins->item(0)){
-			foreach ($mins->item(0)->getChildNodes){ # should only ever be one!
-				($_->getNodeType == TEXT_NODE) && ($min = $_->toString);
-			}
-		}
-        my $enums =  $node->getElementsByTagName('enum');
-		my $numenums = $enums->getLength;
-		for (my $n=0;$n<$numenums;++$n){
-			foreach ($enums->item($n)->getChildNodes){ # should only ever be one!
-				($_->getNodeType == TEXT_NODE) && (push @enums, $_->toString);
-			}
-		}
-		my $enum_string = join "",(map {$_.","} @enums);
-		chop $enum_string; # get rid of trailing comma
-		my $dbh = $SVC->dbh;
-		$dbh->do(q{insert into secondary_input (default_value,maximum_value,minimum_value,enum_value,datatype,article_name,service_instance_id) values (?,?,?,?,?,?,?)},
-				 undef,
-				 ($def, $max, $min, $enum_string, $datatype, $article, $SVC->service_instance_id));		
+            foreach ($mins->item(0)->getChildNodes){ # should only ever be one!
+                ($_->getNodeType == TEXT_NODE) && ($min = $_->toString);
+            }
+        }
+        my $enums =  $parameter->getElementsByTagName('enum');
+        my $numenums = $enums->getLength;
+        for (my $n=0;$n<$numenums;++$n){
+            foreach ($enums->item($n)->getChildNodes){ # should only ever be one!
+                ($_->getNodeType == TEXT_NODE) && (push @enums, $_->toString);
+            }
+        }
+        my $enum_string = join "",(map {$_.","} @enums);
+        chop $enum_string; # get rid of trailing comma
+        my $sec = $SVC->add_secondary_input(
+                    default_value => $def,
+                    maximum_value => $max,
+                    minimum_value => $min,
+                    enum_value   => $enum_string,
+                    datatype     => $datatype,
+                    article_name => $article,
+                                            );
+        unless ($sec){
+            $SVC->DELETE_THYSELF; return (-1,"registration failed during registration of parameter $article.  Must be of type Integer, String, DateTime, or Float.");
+        }       
 	}
 	return 1;
 }
+
+
 sub _registerServicePayload {
 	my ($payload) = @_;
 	my $Parser = new XML::DOM::Parser;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm	2003/12/02 00:23:23	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm	2004/06/16 01:15:30	1.4
@@ -43,7 +43,7 @@
 
 =head1 AUTHORS
 
-Mark Wilkinson (mwilkinson at gene.pbi.nrc.ca)
+Mark Wilkinson (mwilkinson at mrl.ubc.ca)
 
 
 =cut
@@ -321,6 +321,94 @@
     return $authority;
 }
 
+sub add_simple_input {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $simple = MOBY::simple_input->new(
+				object_type_uri	=> $a{'object_type_uri'},
+				namespace_type_uris	=> $a{'namespace_type_uris'},
+				article_name 	=> $a{'article_name'},
+				service_instance_id	=> 	$self->service_instance_id,
+				collection_input_id 	=> 	$a{'collection_input_id'}
+					   );
+
+	push @{$self->{inputs}}, $simple;
+	return $simple->simple_input_id;
+}
+
+
+sub add_simple_output {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $simple = MOBY::simple_output->new(
+				object_type_uri	=> $a{'object_type_uri'},
+				namespace_type_uris	=> $a{'namespace_type_uris'},
+				article_name 	=> $a{'article_name'},
+				service_instance_id	=> 	$self->service_instance_id,
+				collection_input_id 	=> 	$a{'collection_output_id'}
+					   );
+
+	push @{$self->{outputs}}, $simple;
+	return $simple->simple_output_id;
+}
+
+
+sub add_collection_input {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $coll = MOBY::collection_input->new(
+				article_name 	=> $a{'article_name'},
+				service_instance_id	=> 	$self->service_instance_id,
+					   );
+
+	push @{$self->{inputs}}, $coll;
+	return $coll->collection_input_id;
+}
+
+
+sub add_collection_output {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $coll = MOBY::collection_output->new(
+				article_name 	=> $a{'article_name'},
+				service_instance_id	=> 	$self->service_instance_id,
+					   );
+
+	push @{$self->{outputs}}, $coll;
+	return $coll->collection_output_id;
+}
+
+
+sub add_secondary_input {
+	my ($self, %a) = @_;
+
+# validate here... one day...
+
+	my $sec = MOBY::secondary_input->new(
+		default_value => $a{'default_value'},
+		maximum_value => $a{'maximum_value'},
+		minimum_value => $a{'minimum_value'},
+		enum_value   => $a{'enum_value'},
+		datatype     => $a{'datatype'},
+		article_name => $a{'article_name'},
+		service_instance_id => $self->service_instance_id,
+					   );
+
+	push @{$self->{inputs}}, $sec;
+	return $sec->secondary_input_id;	
+
+}
+
+
+
 sub AUTOLOAD {
     no strict "refs";
     my ($self, $newval) = @_;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm	2003/12/28 20:41:59	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm	2004/06/16 01:15:30	1.3
@@ -9,11 +9,13 @@
 
 =head1 NAME
 
-MOBY::authority - a lightweight connection to the
+MOBY::simple_input - a lightweight connection to the
 simple_input table in the database
 
 =head1 SYNOPSIS
 
+NON FUNCTIONAL AT THIS TIME
+
  use MOBY::simple_input;
  my $Instance = MOBY::simple_input->new(
           object_type => "Sequence",
@@ -28,7 +30,7 @@
 
 =head1 DESCRIPTION
 
-representation of the authority table.  Can write to the database
+representation of the simple_input table.  Can write to the database
 
 =head1 AUTHORS
 
@@ -46,11 +48,13 @@
 	#ATTRIBUTES
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
-                    object_type          => [undef,        'read/write'],
-                    namespaces => [undef,        'read/write'],
-                    article_name         => [undef,       'read/write'],
-                    simple_input_id         => [undef,       'read/write'],
-                    service_instance_id         => [undef,       'read/write'],
+				simple_input_id	=> 	[undef, 		'read/write'],
+				object_type_uri	=> 	[undef, 		'read/write'],
+				namespace_type_uris	=> 	[undef, 		'read/write'],
+				article_name 	=> 	[undef, 		'read/write'],
+				service_instance_id	=> 	[undef, 		'read/write'],
+				collection_input_id 	=> 	[undef, 		'read/write'],
+				dbh 	=> 	[undef, 		'read/write'],
 				);
 
    #_____________________________________________________________
@@ -76,6 +80,17 @@
 
 }
 
+
+sub _dbh {
+    my ($self) = @_;
+    
+    my $central_connect = MOBY::central_db_connection->new();
+	$self->dbh($central_connect->dbh);
+	return $central_connect->dbh;
+	
+}
+
+
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -95,10 +110,33 @@
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
 
+	my $id = $self->WRITE;
+	$self->simple_input_id($id) if defined $id;
     return $self;
 
 }
 
+sub WRITE {
+	my ($self) = @_;	
+	my $dbh = $self->_dbh;
+	
+	$dbh->do("insert into simple_input
+				 (object_type_uri,
+				  namespace_type_uris,
+				  article_name,
+				  service_instance_id,
+				  collection_input_id)
+				 values (?,?,?,?,?)",
+		undef,
+		($self->object_type_uri,
+		$self->namespace_type_uris,
+		$self->article_name,
+		$self->service_instance_id,
+		$self->collection_input_id));
+	my $id=$dbh->{mysql_insertid};
+	return $id;
+}
+
 
 sub AUTOLOAD {
     no strict "refs";

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm	2003/05/07 19:20:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm	2004/06/16 01:15:30	1.2
@@ -14,6 +14,7 @@
 
 =head1 SYNOPSIS
 
+NON FUNCTIONAL AT THIS TIME
  use MOBY::simple_output;
  my $Instance = MOBY::simple_output->new(
           object_type => "Sequence",
@@ -28,7 +29,7 @@
 
 =head1 DESCRIPTION
 
-representation of the authority table.  Can write to the database
+representation of the simple_output table.  Can write to the database
 
 =head1 AUTHORS
 
@@ -46,11 +47,13 @@
 	#ATTRIBUTES
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
-                    object_type          => [undef,        'read/write'],
-                    namespaces => [undef,        'read/write'],
-                    article_name         => [undef,       'read/write'],
-                    simple_output_id         => [undef,       'read/write'],
-                    service_instance_id         => [undef,       'read/write'],
+				simple_output_id	=> 	[undef, 		'read/write'],
+				object_type_uri	=> 	[undef, 		'read/write'],
+				namespace_type_uris	=> 	[undef, 		'read/write'],
+				article_name 	=> 	[undef, 		'read/write'],
+				service_instance_id	=> 	[undef, 		'read/write'],
+				collection_output_id 	=> 	[undef, 		'read/write'],
+				dbh 	=> 	[undef, 		'read/write'],
 				);
 
    #_____________________________________________________________
@@ -76,6 +79,18 @@
 
 }
 
+
+
+sub _dbh {
+    my ($self) = @_;
+    
+    my $central_connect = MOBY::central_db_connection->new();
+	$self->dbh($central_connect->dbh);
+	return $central_connect->dbh;
+	
+}
+
+
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -95,15 +110,31 @@
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
 
+	my $id = $self->WRITE;
+	$self->simple_output_id($id) if defined $id;
     return $self;
 
 }
 
-sub object_type
 sub WRITE {
-    my ($caller, $dbh) = @_;
-    my $sth = $dbh->prepare("insert into simple_input (object_type_id, namespace_type_ids, article_name, service_instance_id) values (?,?,?,?)");
-    
+	my ($self) = @_;
+	my $dbh = $self->_dbh;	
+	$dbh->do("insert into simple_output
+				 (object_type_uri,
+				  namespace_type_uris,
+				  article_name,
+				  service_instance_id,
+				  collection_output_id)
+				 values (?,?,?,?,?)",
+		undef,
+		($self->object_type_uri,
+		$self->namespace_type_uris,
+		$self->article_name,
+		$self->service_instance_id,
+		$self->collection_output_id));
+	my $id=$dbh->{mysql_insertid};
+	return $id;		
+
 }
 
 sub AUTOLOAD {



From mwilkinson at pub.open-bio.org  Wed Jun 16 01:15:30 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 15 Jun 2004 21:15:30 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406160115.i5G1FUai016521@pub.open-bio.org>


mwilkinson
Tue Jun 15 21:15:30 EDT 2004
Update of /home/repository/moby/moby-live/Perl/scripts
In directory pub.open-bio.org:/tmp/cvs-serv16447/scripts

Modified Files:
	testMOBYClientCentral_v05.pl 
Log Message:
all sorts of additions and changes.  Secondary parameters now work for me on two systems, so that problem should now be solved.  I am starting to rip out the SQL that is in MOBY Central into other modules, and it will eventually end up in a single mysql-specific module with an API to make it easier to code MOBY onto other data back-ends.  Various bug fixes here and there as well.

moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.15,1.16
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl	2004/04/20 23:24:25	1.15
+++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl	2004/06/16 01:15:30	1.16
@@ -24,10 +24,10 @@
 }
 
 my $C = MOBY::Client::Central->new(
-#Registries => {
-#	mobycentral => {URL => 'http://localhost/cgi-bin/MOBY-Central.pl',
-#                       URI => 'http://localhost/MOBY/Central'}
-#		}
+Registries => {
+  mobycentral => {URL => $ENV{MOBY_SERVER}?$ENV{MOBY_SERVER}:'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl',
+		  URI => $ENV{MOBY_URI}?$ENV{MOBY_URI}:'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'}
+						}
 );
 
 



From mwilkinson at pub.open-bio.org  Wed Jun 16 01:15:30 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 15 Jun 2004 21:15:30 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406160115.i5G1FU7Y016541@pub.open-bio.org>


mwilkinson
Tue Jun 15 21:15:30 EDT 2004
Update of /home/repository/moby/moby-live/Perl/t
In directory pub.open-bio.org:/tmp/cvs-serv16447/t

Modified Files:
	Client-Central.t 
Log Message:
all sorts of additions and changes.  Secondary parameters now work for me on two systems, so that problem should now be solved.  I am starting to rip out the SQL that is in MOBY Central into other modules, and it will eventually end up in a single mysql-specific module with an API to make it easier to code MOBY onto other data back-ends.  Various bug fixes here and there as well.

moby-live/Perl/t Client-Central.t,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/t/Client-Central.t,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/t/Client-Central.t	2004/01/08 19:05:58	1.3
+++ /home/repository/moby/moby-live/Perl/t/Client-Central.t	2004/06/16 01:15:30	1.4
@@ -12,9 +12,11 @@
 
 # Test 2
 my $C = MOBY::Client::Central->new(
-    #MOBY_server => "http://localhost/cgi-bin/MOBY-Central.pl",
-    #MOBY_uri  => "http://localhost/MOBY/Central"
-    );
+		Registries => {
+						mobycentral => {	URL => 'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl',
+											URI => 'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'}
+						}
+                                  );
 
 isa_ok( $C,'MOBY::Client::Central',"Connected to test MOBY Central") or
     die("Cannot Connect to MOBY Central... cannot continue?");



From gss at pub.open-bio.org  Wed Jun 16 18:37:19 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:37:19 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161837.i5GIbJHC020447@pub.open-bio.org>


gss
Wed Jun 16 14:37:19 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20422/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 18:49:45 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:49:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161849.i5GInjsF020496@pub.open-bio.org>


gss
Wed Jun 16 14:49:45 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20472/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 18:50:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:50:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161850.i5GIoxcl020538@pub.open-bio.org>


gss
Wed Jun 16 14:50:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20517/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms

Added Files:
	literatureGuideURI.n3 literatureGuideURI geneSymbol 
	geneSymbol.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms literatureGuideURI.n3,NONE,1.1 literatureGuideURI,NONE,1.1 geneSymbol,NONE,1.1 geneSymbol.n3,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 18:50:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:50:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161850.i5GIox5V020562@pub.open-bio.org>


gss
Wed Jun 16 14:50:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv20517/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot

Modified Files:
	citationSearch.rdf citationSearch.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.6,1.7 citationSearch.n3,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/05/19 20:42:37	1.6
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/06/16 18:50:59	1.7
@@ -1,50 +1,37 @@
 <rdf:RDF
-    xmlns:go="http://www.go.org:8080/terms#"
+    xmlns:sgd="http://www.sgd.org:8080/terms/"
     xmlns:acmepubs="http://www.acmepubs.com:8080/"
+    xmlns:pubs="http://www.pubs.org:8080/terms/"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+    xmlns:acmeterms="http://www.acmepubs.com:8080/terms/"
+    xmlns:go="http://www.go.org:8080/terms/"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
-    xmlns:pubs="http://www.pubs.org:8081/terms#"
-    xmlns:moby="http://www.s-moby.org:8080/terms#"
-    xmlns:sgd="http://www.sgd.org:8080/terms#" >
-  <rdf:Description rdf:about="http://www.acmepubs.com:8080/geneSymbol">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
-  </rdf:Description>
+    xmlns:moby="http://www.s-moby.org:8080/terms/" >
   <rdf:Description rdf:nodeID="A0">
-    <moby:hasMapping rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A1">
-    <acmepubs:geneSymbol rdf:nodeID="A2"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <moby:mapsTo rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms/GeneSymbol"/>
+    <acmeterms:geneSymbol rdf:nodeID="A1"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Subject"/>
+    <moby:mapsTo rdf:nodeID="A2"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A2">
+    <acmeterms:literatureGuideURI rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms/LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Object"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A4">
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-    <rdf:_1 rdf:nodeID="A0"/>
+    <moby:hasMapping rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Graph"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/citationSearch">
-    <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
-    <moby:operatesOn rdf:nodeID="A4"/>
-    <moby:oneLineDescription>Industry standard search</moby:oneLineDescription>
-    <moby:aboutURI>http://www.acmepubs.com/about/citationSearch</moby:aboutURI>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
     <moby:name>AcmePubs Citation Search</moby:name>
+    <moby:oneLineDescription>Industry standard search</moby:oneLineDescription>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Provider"/>
+    <moby:operatesOn rdf:nodeID="A5"/>
+    <rdf:type rdf:resource="http://www.pubs.org:8080/terms/citationSearch"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A3">
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <acmepubs:literatureGuideURL rdf:nodeID="A5"/>
-  </rdf:Description>
-  <rdf:Description rdf:about="http://www.acmepubs.com:8080/literatureGuideURL">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
-    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  <rdf:Description rdf:nodeID="A5">
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A4"/>
   </rdf:Description>
 </rdf:RDF>
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3	2004/05/19 20:42:37	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3	2004/06/16 18:50:59	1.6
@@ -1,41 +1,28 @@
- at prefix pubs:     <http://www.pubs.org:8081/terms#> .
- at prefix xsd:      <http://www.w3.org/2001/XMLSchema#> .
- at prefix acmepubs: <http://www.acmepubs.com:8080/> .
- at prefix go:       <http://www.go.org:8080/terms#> .
- at prefix sgd:      <http://www.sgd.org:8080/terms#> .
- at prefix moby:     <http://www.s-moby.org:8080/terms#> .
- at prefix rdfs:     <http://www.w3.org/2000/01/rdf-schema#> .
- at prefix rdf:      <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
- at prefix owl:      <http://www.w3.org/2002/07/owl#> .
+ at prefix acmepubs:   <http://www.acmepubs.com:8080/> .
+ at prefix acmeterms:  <http://www.acmepubs.com:8080/terms/> .
+ at prefix pubs:       <http://www.pubs.org:8080/terms/> .
+ at prefix go:         <http://www.go.org:8080/terms/> .
+ at prefix sgd:        <http://www.sgd.org:8080/terms/> .
+ at prefix moby:       <http://www.s-moby.org:8080/terms/> .
+ at prefix rdfs:       <http://www.w3.org/2000/01/rdf-schema#> .
+ at prefix rdf:        <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+ at prefix owl:        <http://www.w3.org/2002/07/owl#> .
 
 acmepubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
     moby:name "AcmePubs Citation Search" ;
     moby:oneLineDescription "Industry standard search" ;
-    moby:aboutURI "http://www.acmepubs.com/about/citationSearch" ;
     moby:operatesOn [
         a rdf:Bag ;
         rdf:_1 [
             a moby:Graph ;
             moby:hasMapping [
                 a moby:Subject, go:GeneSymbol ;
-                acmepubs:geneSymbol _:bnode1 ;
+                acmeterms:geneSymbol _:bnode1 ;
                 moby:mapsTo [
                     a moby:Object, sgd:LiteratureGuide ;
-                    acmepubs:literatureGuideURL _:bnode2
+                    acmeterms:literatureGuideURI _:bnode2
                 ]
             ]
         ]
-    ] .
-
-acmepubs:geneSymbol
-    a owl:DataTypeProperty ;
-    rdfs:subPropertyOf moby:Property ;
-    rdfs:domain go:GeneSymbol ;
-    rdfs:range xsd:string .
-
-acmepubs:literatureGuideURL
-    a owl:DataTypeProperty ;
-    rdfs:subPropertyOf moby:Property ;
-    rdfs:domain sgd:LiteratureGuide ;
-    rdfs:range xsd:anyURI .
\ No newline at end of file
+    ] .
\ No newline at end of file



From gss at pub.open-bio.org  Wed Jun 16 18:51:13 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:51:13 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161851.i5GIpDk0020600@pub.open-bio.org>


gss
Wed Jun 16 14:51:13 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20579/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms

Added Files:
	literatureGuideURI.n3 geneSymbol geneSymbol.n3 
	literatureGuideURI 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms literatureGuideURI.n3,NONE,1.1 geneSymbol,NONE,1.1 geneSymbol.n3,NONE,1.1 literatureGuideURI,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 18:51:13 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:51:13 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161851.i5GIpDCp020624@pub.open-bio.org>


gss
Wed Jun 16 14:51:13 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv20579/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot

Modified Files:
	citationSearch.n3 citationSearch.rdf 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.5,1.6 citationSearch.rdf,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3	2004/05/19 20:42:33	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3	2004/06/16 18:51:13	1.6
@@ -1,41 +1,28 @@
- at prefix pubs:     <http://www.pubs.org:8081/terms#> .
- at prefix xsd:      <http://www.w3.org/2001/XMLSchema#> .
- at prefix megapubs: <http://www.megapubs.com:8080/> .
- at prefix go:       <http://www.go.org:8080/terms#> .
- at prefix sgd:      <http://www.sgd.org:8080/terms#> .
- at prefix moby:     <http://www.s-moby.org:8080/terms#> .
- at prefix rdfs:     <http://www.w3.org/2000/01/rdf-schema#> .
- at prefix rdf:      <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
- at prefix owl:      <http://www.w3.org/2002/07/owl#> .
+ at prefix megapubs:   <http://www.megapubs.com:8080/> .
+ at prefix megaterms:  <http://www.megapubs.com:8080/terms/> .
+ at prefix pubs:       <http://www.pubs.org:8080/terms/> .
+ at prefix go:         <http://www.go.org:8080/terms/> .
+ at prefix sgd:        <http://www.sgd.org:8080/terms/> .
+ at prefix moby:       <http://www.s-moby.org:8080/terms/> .
+ at prefix rdfs:       <http://www.w3.org/2000/01/rdf-schema#> .
+ at prefix rdf:        <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+ at prefix owl:        <http://www.w3.org/2002/07/owl#> .
 
 megapubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
     moby:name "MegaPubs Citation Search" ;
     moby:oneLineDescription "Cool new search" ;
-    moby:aboutURI "http://www.megapubs.com/about/citationSearch" ;
     moby:operatesOn [
         a rdf:Bag ;
         rdf:_1 [
             a moby:Graph ;
             moby:hasMapping [
                 a moby:Subject, go:GeneSymbol ;
-                megapubs:geneSymbol _:bnode1 ;
+                megaterms:geneSymbol _:bnode1 ;
                 moby:mapsTo [
                     a moby:Object, sgd:LiteratureGuide ;
-                    megapubs:literatureGuideURL _:bnode2
+                    megaterms:literatureGuideURI _:bnode2
                 ]
             ]
         ]
-    ] .
-
-megapubs:geneSymbol
-    a owl:DataTypeProperty ;
-    rdfs:subPropertyOf moby:Property ;
-    rdfs:domain go:GeneSymbol ;
-    rdfs:range xsd:string .
-
-megapubs:literatureGuideURL
-    a owl:DataTypeProperty ;
-    rdfs:subPropertyOf moby:Property ;
-    rdfs:domain sgd:LiteratureGuide ;
-    rdfs:range xsd:anyURI .
\ No newline at end of file
+    ] .
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/05/19 20:42:34	1.6
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/06/16 18:51:13	1.7
@@ -1,50 +1,37 @@
 <rdf:RDF
-    xmlns:go="http://www.go.org:8080/terms#"
+    xmlns:sgd="http://www.sgd.org:8080/terms/"
+    xmlns:pubs="http://www.pubs.org:8080/terms/"
     xmlns:megapubs="http://www.megapubs.com:8080/"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+    xmlns:go="http://www.go.org:8080/terms/"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
-    xmlns:pubs="http://www.pubs.org:8081/terms#"
-    xmlns:moby="http://www.s-moby.org:8080/terms#"
-    xmlns:sgd="http://www.sgd.org:8080/terms#" >
+    xmlns:moby="http://www.s-moby.org:8080/terms/"
+    xmlns:megaterms="http://www.megapubs.com:8080/terms/" >
   <rdf:Description rdf:nodeID="A0">
-    <moby:hasMapping rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-  </rdf:Description>
-  <rdf:Description rdf:about="http://www.megapubs.com:8080/literatureGuideURL">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
-    <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <megaterms:geneSymbol rdf:nodeID="A1"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Subject"/>
+    <moby:mapsTo rdf:nodeID="A2"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms/GeneSymbol"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/citationSearch">
-    <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Provider"/>
+    <moby:operatesOn rdf:nodeID="A3"/>
     <moby:oneLineDescription>Cool new search</moby:oneLineDescription>
-    <moby:operatesOn rdf:nodeID="A2"/>
-    <moby:aboutURI>http://www.megapubs.com/about/citationSearch</moby:aboutURI>
+    <rdf:type rdf:resource="http://www.pubs.org:8080/terms/citationSearch"/>
     <moby:name>MegaPubs Citation Search</moby:name>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <rdf:_1 rdf:nodeID="A0"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A1">
-    <moby:mapsTo rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <megapubs:geneSymbol rdf:nodeID="A4"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A3">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <megapubs:literatureGuideURL rdf:nodeID="A5"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:_1 rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
-  <rdf:Description rdf:about="http://www.megapubs.com:8080/geneSymbol">
-    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
-    <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
+  <rdf:Description rdf:nodeID="A2">
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms/LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Object"/>
+    <megaterms:literatureGuideURI rdf:nodeID="A5"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A4">
+    <moby:hasMapping rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Graph"/>
   </rdf:Description>
 </rdf:RDF>



From gss at pub.open-bio.org  Wed Jun 16 18:52:04 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:52:04 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161852.i5GIq4QV020656@pub.open-bio.org>


gss
Wed Jun 16 14:52:04 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv20631/S-MOBY/ref-impl/example-providers/sgd.org

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/example-providers/sgd.org .cvsignore,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore	2004/06/10 23:31:50	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/.cvsignore	2004/06/16 18:52:04	1.3
@@ -3,3 +3,4 @@
 .encoding
 .mymetadata
 .project
+.settings



From gss at pub.open-bio.org  Wed Jun 16 18:55:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:55:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161855.i5GItaBd020712@pub.open-bio.org>


gss
Wed Jun 16 14:55:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv20690/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot

Removed Files:
	terms 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot terms,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/RCS/terms,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 18:57:56 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 14:57:56 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161857.i5GIvutQ020758@pub.open-bio.org>


gss
Wed Jun 16 14:57:56 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv20736/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot

Removed Files:
	terms.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot terms.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/RCS/terms.n3,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 19:00:29 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 15:00:29 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161900.i5GJ0Tdc020857@pub.open-bio.org>


gss
Wed Jun 16 15:00:29 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20833/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 19:00:31 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 15:00:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161900.i5GJ0VRJ020891@pub.open-bio.org>


gss
Wed Jun 16 15:00:31 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv20870/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms

Added Files:
	LiteratureGuide LiteratureGuide.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms LiteratureGuide,NONE,1.1 LiteratureGuide.n3,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 19:01:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 15:01:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161901.i5GJ1K3b020933@pub.open-bio.org>


gss
Wed Jun 16 15:01:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv20908/S-MOBY/ref-impl/server

Modified Files:
	.cvsignore 
Log Message:
Ignore IDE files

moby-live/S-MOBY/ref-impl/server .cvsignore,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore	2004/06/14 17:17:56	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.cvsignore	2004/06/16 19:01:20	1.3
@@ -2,3 +2,4 @@
 .classpath
 .mymetadata
 .project
+.settings



From mwilkinson at pub.open-bio.org  Wed Jun 16 19:07:34 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed, 16 Jun 2004 15:07:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161907.i5GJ7Y7o021017@pub.open-bio.org>


mwilkinson
Wed Jun 16 15:07:34 EDT 2004
Update of /home/repository/moby/moby-live/Perl/scripts
In directory pub.open-bio.org:/tmp/cvs-serv20998/scripts

Modified Files:
	testMOBYClientCentral_v05.pl 
Log Message:
fixed test script

moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.16,1.17
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl	2004/06/16 01:15:30	1.16
+++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl	2004/06/16 19:07:34	1.17
@@ -148,7 +148,7 @@
 	         ],
 	secondary => {
         parametername1 => {
-            datatype => 'Int',
+            datatype => 'Integer',
     		default => 0,
 			max => 10,
 			min => -10,



From mwilkinson at pub.open-bio.org  Wed Jun 16 19:08:05 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed, 16 Jun 2004 15:08:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161908.i5GJ85Qi021064@pub.open-bio.org>


mwilkinson
Wed Jun 16 15:08:05 EDT 2004
Update of /home/repository/moby/moby-live/Perl/t
In directory pub.open-bio.org:/tmp/cvs-serv21045/t

Modified Files:
	Client-Central.t 
Log Message:
fixing an incorrect test in the test suite

moby-live/Perl/t Client-Central.t,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/t/Client-Central.t,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/t/Client-Central.t	2004/06/16 01:15:30	1.4
+++ /home/repository/moby/moby-live/Perl/t/Client-Central.t	2004/06/16 19:08:05	1.5
@@ -100,7 +100,7 @@
 	         ],
 	secondary => {
         parametername1 => {
-            datatype => 'Int',
+            datatype => 'Integer',
     		default => 0,
 			max => 10,
 			min => -10,



From gss at pub.open-bio.org  Wed Jun 16 19:19:54 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 15:19:54 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161919.i5GJJsei021114@pub.open-bio.org>


gss
Wed Jun 16 15:19:54 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv21093/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms

Added Files:
	index.html 
Log Message:
Index of OWL terms

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/terms index.html,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 19:21:57 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 15:21:57 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406161921.i5GJLvAF021170@pub.open-bio.org>


gss
Wed Jun 16 15:21:57 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv21149/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms

Added Files:
	index.html 
Log Message:
Index of OWL terms

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/terms index.html,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 22:07:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:07:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162207.i5GM70mA021799@pub.open-bio.org>


gss
Wed Jun 16 18:07:00 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir
In directory pub.open-bio.org:/tmp/cvs-serv21775/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir added to the repository

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 22:07:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:07:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162207.i5GM73iE021841@pub.open-bio.org>


gss
Wed Jun 16 18:07:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir
In directory pub.open-bio.org:/tmp/cvs-serv21820/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir

Added Files:
	CitationSearch CitationSearch.n3 index.html PubAbstract 
	PubAbstract.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir CitationSearch,NONE,1.1 CitationSearch.n3,NONE,1.1 index.html,NONE,1.1 PubAbstract,NONE,1.1 PubAbstract.n3,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 22:08:53 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:08:53 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162208.i5GM8rkW021880@pub.open-bio.org>


gss
Wed Jun 16 18:08:53 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv21857/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot

Removed Files:
	terms terms.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot terms,1.1,NONE terms.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/terms,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/RCS/terms.n3,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 22:11:54 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:11:54 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162211.i5GMBsNP021939@pub.open-bio.org>


gss
Wed Jun 16 18:11:54 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv21915/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 22:13:13 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:13:13 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162213.i5GMDDUL021984@pub.open-bio.org>


gss
Wed Jun 16 18:13:13 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv21963/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms

Added Files:
	index.html PubAbstract CitationSearch PubAbstract.n3 
	CitationSearch.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms index.html,NONE,1.1 PubAbstract,NONE,1.1 CitationSearch,NONE,1.1 PubAbstract.n3,NONE,1.1 CitationSearch.n3,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 22:14:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:14:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162214.i5GMEIpb022021@pub.open-bio.org>


gss
Wed Jun 16 18:14:18 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir
In directory pub.open-bio.org:/tmp/cvs-serv21995/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir

Removed Files:
	CitationSearch CitationSearch.n3 index.html PubAbstract 
	PubAbstract.n3 
Log Message:
Moved to terms/ directory

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir CitationSearch,1.1,NONE CitationSearch.n3,1.1,NONE index.html,1.1,NONE PubAbstract,1.1,NONE PubAbstract.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/CitationSearch,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/CitationSearch.n3,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/index.html,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/PubAbstract,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/WebRoot/terms-dir/RCS/PubAbstract.n3,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 22:18:50 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:18:50 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162218.i5GMIoag022108@pub.open-bio.org>


gss
Wed Jun 16 18:18:50 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22079/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms

Modified Files:
	LiteratureGuide LiteratureGuide.n3 
Added Files:
	index.html 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms index.html,NONE,1.1 LiteratureGuide,1.1,1.2 LiteratureGuide.n3,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide	2004/06/16 19:00:30	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide	2004/06/16 22:18:50	1.2
@@ -1,8 +1,8 @@
 <rdf:RDF
+    xmlns:sgd="http://www.sgd.org:8080/terms/"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:owl="http://www.w3.org/2002/07/owl#"
-    xmlns:sgd="http://www.sgd.org:8080/terms#" >
-  <rdf:Description rdf:about="http://www.sgd.org:8080/terms#LiteratureGuide">
+    xmlns:owl="http://www.w3.org/2002/07/owl#" >
+  <rdf:Description rdf:about="http://www.sgd.org:8080/terms/LiteratureGuide">
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
   </rdf:Description>
 </rdf:RDF>
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide.n3,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide.n3	2004/06/16 19:00:30	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/terms/LiteratureGuide.n3	2004/06/16 22:18:50	1.2
@@ -1,4 +1,4 @@
- at prefix sgd: <http://www.sgd.org:8080/terms#> .
+ at prefix sgd: <http://www.sgd.org:8080/terms/> .
 @prefix owl: <http://www.w3.org/2002/07/owl#> .
 
 sgd:LiteratureGuide



From gss at pub.open-bio.org  Wed Jun 16 22:23:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:23:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162223.i5GMNxai022173@pub.open-bio.org>


gss
Wed Jun 16 18:23:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv22150/S-MOBY/ref-impl/example-providers/go.org/WebRoot

Removed Files:
	terms terms.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot terms,1.1,NONE terms.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/RCS/terms,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/RCS/terms.n3,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 22:25:14 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:25:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162225.i5GMPEj3022216@pub.open-bio.org>


gss
Wed Jun 16 18:25:14 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22192/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 22:25:16 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:25:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162225.i5GMPGCH022258@pub.open-bio.org>


gss
Wed Jun 16 18:25:16 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22237/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms

Added Files:
	index.html GeneSymbol GeneSymbol.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/example-providers/go.org/WebRoot/terms index.html,NONE,1.1 GeneSymbol,NONE,1.1 GeneSymbol.n3,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 22:27:14 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:27:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162227.i5GMRExb022299@pub.open-bio.org>


gss
Wed Jun 16 18:27:14 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools
In directory pub.open-bio.org:/tmp/cvs-serv22274/S-MOBY/ref-impl/server/WebRoot/tools

Modified Files:
	developer.html 
Log Message:
Added developer tool to list statements in metadata repository

moby-live/S-MOBY/ref-impl/server/WebRoot/tools developer.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html	2004/03/30 23:54:34	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html	2004/06/16 22:27:14	1.3
@@ -1,67 +1,112 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
 <html>
-<head>
-  <title>Semantic MOBY Developer Tools</title>
-</head>
-<body>
-	<table style="text-align: center; width: 100%;" border="1"
+  <head>
+    <meta name="generator" content="HTML Tidy, see www.w3.org">
+
+    <title>Semantic MOBY Developer Tools</title>
+  </head>
+
+  <body>
+    <table style="WIDTH: 100%; TEXT-ALIGN: center" border="1"
     cellspacing="0" cellpadding="0">
-    <tbody>
-      <tr>
-        <td style="vertical-align: top; background-color: rgb(204, 204, 204);">
-      	  <b>Semantic MOBY Developer Tools</b>
-        </td>
-      </tr>
-    </tbody>
-  </table>
-  <br>
-  <h4><u>Convert a graph to a different format</u></h4>
-<form method="POST" action="http://www.s-moby.org:8080/convert-graph">
-  Paste a graph, select its input format,
-  and press "Convert Graph" to convert to the other format
-  <p>
-  Input format:&nbsp;&nbsp;&nbsp;
-  <input type="radio" name="input-format" value="N3" CHECKED>N3&nbsp;&nbsp;
-  <input type="radio" name="input-format" value="RDF/XML">RDF/XML
-  <input type="radio" name="input-format" value="N-TRIPLE">N-Triples&nbsp;&nbsp;
-  <br>
-  Output format:
-  <input type="radio" name="output-format" value="N3">N3&nbsp;&nbsp;
-  <input type="radio" name="output-format" value="RDF/XML" CHECKED>RDF/XML
-  <input type="radio" name="output-format" value="N-TRIPLE">N-Triples&nbsp;&nbsp;
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-  <input type="submit" value="Convert Graph">
-  <p>
-  <textarea name="graph" rows="15" cols="80"></textarea>
-  &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;
-
-</form>
-<H4><U>List the providers in the S-MOBY metadata repository</U></H4>
-<FORM method="GET" action="http://www.s-moby.org:8080/list-providers">
-  &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;
-  <INPUT type="submit" value="List Providers">&nbsp;&nbsp;
-  <INPUT type="checkbox" name="show-contents" value=true>
-  Show provider description graphs
-</FORM>
-<h4><u>Validate an OWL Graph using Jena</u></h4>
-<form method="POST" action="http://www.s-moby.org:8080/validate-owl-graph">
-  Paste a graph in RDF/XML format and press "Validate" to see what type of
-  OWL the graph represents
-  <p>
-  <input type="submit" value="Validate">
-  <p>
-  <textarea name="graph" rows="15" cols="80"></textarea>
-</form>
-
-<h4><u>Validate that a graph is MOBY canonical form</u></h4>
-<form method="POST" action="http://www.s-moby.org:8080/validate-canonical-graph">
-  Paste a graph in RDF/XML format and press "Validate" to see if it is
-  MOBY canonical form
-  <p>
-  <input type="submit" value="Validate">
-  <p>
-  <textarea name="graph" rows="15" cols="80"></textarea>
-</form>
-  
-</body>
+      <tbody>
+        <tr>
+          <td style=
+          "VERTICAL-ALIGN: top; BACKGROUND-COLOR: rgb(204,204,204)">
+          <b>Semantic MOBY Developer Tools</b></td>
+        </tr>
+      </tbody>
+    </table><br>
+     
+
+    <h4><u>Convert a graph to a different format</u></h4>
+
+    <form method="post" action=
+    "http://www.s-moby.org:8080/convert-graph">
+      Paste a graph, select its input format, and press "Convert Graph"
+      to convert to the other format 
+
+      <p>Input format:&nbsp;&nbsp;&nbsp; <input type="radio" name=
+      "input-format" value="N3" checked>N3&nbsp;&nbsp; <input type=
+      "radio" name="input-format" value="RDF/XML">RDF/XML <input type=
+      "radio" name="input-format" value=
+      "N-TRIPLE">N-Triples&nbsp;&nbsp;<br>
+       Output format: <input type="radio" name="output-format" value=
+      "N3">N3&nbsp;&nbsp; <input type="radio" name="output-format"
+      value="RDF/XML" checked>RDF/XML <input type="radio" name=
+      "output-format" value="N-TRIPLE">N-Triples&nbsp;&nbsp;
+      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <input type="submit" value=
+      "Convert Graph"></p>
+
+      <p><textarea name="graph" rows="15" cols="80">
+                                              
+                                               
+                                       
+                                 
+                         
+                   
+           
+      </textarea> &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;</p>
+    </form>
+
+    <h4><u>List the providers in the S-MOBY metadata
+    repository</u></h4>
+
+    <form method="get" action=
+    "http://www.s-moby.org:8080/list-providers">
+      &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; <input type="submit"
+      value="List Providers">&nbsp;&nbsp; <input type="checkbox" name=
+      "show-contents" value="true"> Show provider description graphs
+    </form>
+
+    <h4><u>List&nbsp;all statements&nbsp;in the S-MOBY metadata
+    repository</u></h4>
+
+    <form name="List statements" action=
+    "http://www.s-moby.org:8080/print-repository" method="get">
+      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;<input type=
+      "submit" value="List Statements in Repository">
+    </form>
+
+    <h4><u>Validate an OWL Graph using Jena</u></h4>
+
+    <form method="post" action=
+    "http://www.s-moby.org:8080/validate-owl-graph">
+      Paste a graph in RDF/XML format and press "Validate" to see what
+      type of OWL the graph represents 
+
+      <p><input type="submit" value="Validate"></p>
+
+      <p><textarea name="graph" rows="15" cols="80">
+                                              
+                                               
+                                       
+                                 
+                         
+                   
+           
+      </textarea></p>
+    </form>
+
+    <h4><u>Validate that a graph is MOBY canonical form</u></h4>
+
+    <form method="post" action=
+    "http://www.s-moby.org:8080/validate-canonical-graph">
+      Paste a graph in RDF/XML format and press "Validate" to see if it
+      is MOBY canonical form 
+
+      <p><input type="submit" value="Validate"></p>
+
+      <p><textarea name="graph" rows="15" cols="80">
+                                              
+                                               
+                                       
+                                 
+                         
+                   
+           
+      </textarea></p>
+    </form>
+  </body>
 </html>



From gss at pub.open-bio.org  Wed Jun 16 22:27:47 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 18:27:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162227.i5GMRln5022326@pub.open-bio.org>


gss
Wed Jun 16 18:27:47 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv22304/S-MOBY/ref-impl/server/WebRoot

Removed Files:
	terms 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/server/WebRoot terms,1.2,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/terms,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 23:27:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:27:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162327.i5GNRQwk022472@pub.open-bio.org>


gss
Wed Jun 16 19:27:26 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22448/S-MOBY/ref-impl/server/WebRoot/terms

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms added to the repository

moby-live/S-MOBY/ref-impl/server/WebRoot/terms - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 23:27:29 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:27:29 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162327.i5GNRTDB022514@pub.open-bio.org>


gss
Wed Jun 16 19:27:29 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/terms
In directory pub.open-bio.org:/tmp/cvs-serv22493/S-MOBY/ref-impl/server/WebRoot/terms

Added Files:
	operatesOn oneLineDescription objectProperty.n3 __Seq.n3 
	__NonCollection.n3 providerAboutURI.n3 index.html Provider 
	Subject mapsTo __Collection.n3 __List.n3 Object.n3 hasMapping 
	providerAboutURI Graph.n3 subjectProperty mapsTo.n3 __List 
	name.n3 oneLineDescription.n3 __Alt __Bag.n3 __Bag Graph __Seq 
	objectProperty name operatesOn.n3 Provider.n3 hasMapping.n3 
	subjectProperty.n3 __NonCollection __Collection __Alt.n3 
	Subject.n3 Object 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/server/WebRoot/terms operatesOn,NONE,1.1 oneLineDescription,NONE,1.1 objectProperty.n3,NONE,1.1 __Seq.n3,NONE,1.1 __NonCollection.n3,NONE,1.1 providerAboutURI.n3,NONE,1.1 index.html,NONE,1.1 Provider,NONE,1.1 Subject,NONE,1.1 mapsTo,NONE,1.1 __Collection.n3,NONE,1.1 __List.n3,NONE,1.1 Object.n3,NONE,1.1 hasMapping,NONE,1.1 providerAboutURI,NONE,1.1 Graph.n3,NONE,1.1 subjectProperty,NONE,1.1 mapsTo.n3,NONE,1.1 __List,NONE,1.1 name.n3,NONE,1.1 oneLineDescription.n3,NONE,1.1 __Alt,NONE,1.1 __Bag.n3,NONE,1.1 __Bag,NONE,1.1 Graph,NONE,1.1 __Seq,NONE,1.1 objectProperty,NONE,1.1 name,NONE,1.1 operatesOn.n3,NONE,1.1 Provider.n3,NONE,1.1 hasMapping.n3,NONE,1.1 subjectProperty.n3,NONE,1.1 __NonCollection,NONE,1.1 __Collection,NONE,1.1 __Alt.n3,NONE,1.1 Subject.n3,NONE,1.1 Object,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 23:28:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:28:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162328.i5GNS0EK022541@pub.open-bio.org>


gss
Wed Jun 16 19:28:00 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv22519/S-MOBY/ref-impl/server/WebRoot

Removed Files:
	terms.n3 
Log Message:
Separated terms from provider description graphs

moby-live/S-MOBY/ref-impl/server/WebRoot terms.n3,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/RCS/terms.n3,v: No such file or directory



From gss at pub.open-bio.org  Wed Jun 16 23:29:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:29:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162329.i5GNTK4q022587@pub.open-bio.org>


gss
Wed Jun 16 19:29:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv22562/S-MOBY/ref-impl/core/src/org/smoby/parser

Modified Files:
	Parser.java 
Log Message:
Documentation

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/05/24 22:05:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/16 23:29:20	1.2
@@ -3,15 +3,17 @@
 import java.io.*;
 import java.net.*;
 import java.util.*;
-
 import org.smoby.graph.*;
 import org.smoby.graph.impl.*;
 import org.smoby.parser.*;
 import org.smoby.vocabulary.*;
-
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.vocabulary.*;
 
+/**
+ * This class is used to parse OWL models, stored as Jena2 models, into
+ * objects that implement interfaces from the org.smoby.graph package.
+ */
 public class Parser
 {
     /**
@@ -25,15 +27,17 @@
     public final static String LANGUAGE_N3 = "N3";
     
     /**
-     * The underlying Jena model on which the parsed graph is based
+     * Inference models containing inferred statements derived using
+     * rdfs:subClassOf relationships.
      */
-    private Model model;
+    private Map inferenceModels = new HashMap();
     
     /**
-     * An inference model containing inferred statements derived using
-     * rdfs:subClassOf relationships.
+     * Return the inference model associated with a given plain model
      */
-    private InfModel inferenceModel;
+    private InfModel getInferenceModel(Model model) {
+    	return (InfModel) inferenceModels.get(model);
+    }
 
     /**
      * Create and return a parser for parsing an N3 file
@@ -86,8 +90,8 @@
 	}
 
     /**
-     * Create and return a parser for parsing an input stream having
-     * the given format
+     * Create and return a parser for parsing an input stream containing
+     * the given language
      * @return a new instance of Parser
      * @throws IOException if reading the stream 
      * @throws UnparsableGraphException if the file doesn't contain a
@@ -105,6 +109,11 @@
         return new Parser(model);
     }
     
+    /**
+     * Create and return a parser for parsing a string in a given language
+     * @param graphString the string containing the graph
+     * @param language the language the model is expressed in
+     */
     public static Parser forString(String graphString, String language)
     	throws UnparsableGraphException
 	{
@@ -114,28 +123,71 @@
 	}
     
     /**
-     * Create an instance for parsing from the given model
+     * Create an instance for parsing the given model.
      */
     public Parser(Model model)
     {
-        this.model = model;
-        this.inferenceModel = ModelFactory.createRDFSModel(model);
-    }
-    
-    /**
-     * Return the underlying model
-     */
-    public Model getModel()
-    {
-        return model;
+    	
+        StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
+        while (it.hasNext())
+        {
+        	Statement stmt = it.nextStatement();
+        	Model subModel = ModelFactory.createDefaultModel();
+        	subModel.setNsPrefixes(model.getNsPrefixMap());
+        	Resource subject = stmt.getSubject();
+        	addReachableStmts(subModel, subject, subject.getURI());
+        	inferenceModels.put(subModel,
+        		ModelFactory.createRDFSModel(subModel));
+        }
     }
     
+	private void addReachableStmts(Model model, Resource subject, String uri)
+	{
+		// For each statement whose subject is the given resource
+		//
+		StmtIterator it = subject.getModel().listStatements(
+			subject, null, (RDFNode) null);
+		
+		while (it.hasNext())
+		{
+			Statement stmt = it.nextStatement();
+			
+			// The statement itself should be added
+			//
+			model.add(model.createStatement(
+				stmt.getSubject(), stmt.getPredicate(), stmt.getObject()));
+			
+			// If the object of the statement is a blank node or a
+			// resource whose URI starts with the provider URI, then
+			// recursively add the statements that are reachable
+			// from the object
+			//
+			if (stmt.getObject().canAs(Resource.class))
+			{
+				Resource object = (Resource) stmt.getObject().as(Resource.class);
+				if (object.isAnon() || object.getURI().startsWith(uri)) {
+					addReachableStmts(model, object, uri);
+				}
+			}
+		}
+	}
+
     /**
-     * Return the inference model
+     * Parse a provider from the model. If the model contains
+     * multiple providers, only one will be returned (at random). If
+     * the model is expected to contain multiple providers, then call
+     * parseProviders() instead to get all the providers in a
+     * MOBYCollection.
      */
-    public InfModel getInferenceModel()
+    public MOBYProvider parseProvider()
     {
-        return inferenceModel;
+    	MOBYUnorderedCollection providers = parseProviders();
+    	
+    	if (providers.size() == 0) {
+    		return null;
+    	} else {
+    		return (MOBYProvider) providers.iterator().next();
+    	}
     }
     
     /**
@@ -147,38 +199,28 @@
         
         // Find the statements that say something is of type Provider
         //
-        StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
+//        StmtIterator it = underlying.listStatements(null, RDF.type, MOBY.Provider);
+        
+        Iterator it = inferenceModels.keySet().iterator();
         
         // Parse each provider
         //
         while (it.hasNext())
         {
-            Statement stmt = it.nextStatement();
-            Resource provider = stmt.getSubject();
-            providers.add(parseProvider(provider));
+        	Model model = (Model) it.next();
+        	StmtIterator it2 = model.listStatements(null, RDF.type, MOBY.Provider);
+        	
+        	if (it2 != null)
+        	{
+        		Statement stmt = it2.nextStatement();
+	            Resource provider = stmt.getSubject();
+	            providers.add(parseProvider(provider));
+        	}
         }
         
         // Create and return an unordered collection of the parsed providers
         //
-        return MOBYObjectFactory.newUnorderedCollection(null, providers, model);
-    }
-
-    /**
-     * Parse a provider from the model. If the model contains
-     * multiple providers, only one will be parsed (at random). If
-     * the model is expected to contain multiple providers, then call
-     * parseProviders() instead to get all the providers in a
-     * MOBYCollection.
-     */
-    public MOBYProvider parseProvider()
-    {
-        StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
-        
-        if (it.hasNext()) {
-            return parseProvider(it.nextStatement().getSubject());
-        } else {
-            return null;
-        }
+        return MOBYObjectFactory.newUnorderedCollection(null, providers, null);
     }
     
     /**
@@ -187,6 +229,8 @@
      */
     public MOBYProvider parseProvider(Resource provider)
     {
+    	Model model = provider.getModel();
+    	
         // First parse the scalar properties name, oneLineDescription, and aboutURI
         //
         String name 	= getDataPropertyValue(provider, MOBY.name);
@@ -223,6 +267,8 @@
      */
     private MOBYGraphNode parseOperatesOn(Resource res)
     {
+    	Model model = res.getModel();
+    	
         if (isGraph(res))
         {
             // The resource is a MOBY Graph, so should have exactly one
@@ -263,6 +309,8 @@
      */
     private MOBYSubject parseHasMapping(Resource res)
     {
+    	Model model = res.getModel();
+    	
         // Collect the properties of this subject resource that are
         // subproperties of moby:Property, and create MOBY statements
         // for each.
@@ -354,6 +402,7 @@
         
         // Create and return a new MOBYObject
         //
+        Model model = res.getModel();
         return MOBYObjectFactory.newObject(res.getURI(),
             MOBYObjectFactory.newFixedCollection(null, statements, model),
             collectionFor(res, nested), model);
@@ -375,6 +424,9 @@
             Property p = stmt.getPredicate();
             RDFNode pval = stmt.getObject();
             
+            Model model = res.getModel();
+            Model inferenceModel = getInferenceModel(model);
+            
             if (model.contains(res, p, pval) &&
                 inferenceModel.contains(p, RDFS.subPropertyOf, MOBY.Property))
             {
@@ -409,13 +461,13 @@
     
     private String getDataPropertyValue(Resource subject, Property property)
     {
-        Statement s = model.getProperty(subject, property);
+        Statement s = subject.getModel().getProperty(subject, property);
         return (s == null) ? null : s.getObject().toString();
     }
     
     private Resource getResourcePropertyValue(Resource subject, Property property)
     {
-        Statement s = model.getProperty(subject, property);
+        Statement s = subject.getModel().getProperty(subject, property);
         return (s == null) ? null : (Resource) s.getObject();
     }
     
@@ -445,185 +497,100 @@
     private MOBYCollection collectionFor(Resource res, List elements)
     {
         if (isList(res)) {
-            return MOBYObjectFactory.newFixedCollection(null, elements, model);
+            return MOBYObjectFactory.newFixedCollection(null, elements, res.getModel());
         } else if (isBag(res)) {
-            return MOBYObjectFactory.newUnorderedCollection(null, elements, model);
+            return MOBYObjectFactory.newUnorderedCollection(null, elements, res.getModel());
         } else if (isSeq(res)) {
-            return MOBYObjectFactory.newOrderedCollection(null, elements, model);
+            return MOBYObjectFactory.newOrderedCollection(null, elements, res.getModel());
         } else if (isAlt(res)) {
-            return MOBYObjectFactory.newEnumeration(null, elements, model);
+            return MOBYObjectFactory.newEnumeration(null, elements, res.getModel());
         } else {
             return null;
         }
     }
     
-    private boolean isList(Resource res) { return res.canAs(RDFList.class); }
-    private boolean isBag (Resource res) { return isType(res, RDF.Bag);  }
-    private boolean isSeq (Resource res) { return isType(res, RDF.Seq);  }
-    private boolean isAlt (Resource res) { return isType(res, RDF.Alt);  }
-    
-    private boolean isDataStructure(Resource r) {
-        return isList(r) || isBag(r) || isSeq(r) || isAlt(r);
+    /**
+     * Return whether or not the given resource is an RDF List
+     */
+    private boolean isList(Resource res)
+    {
+    	return res.canAs(RDFList.class);
     }
-    
-    private boolean isGraph(Resource r) {
-        return isType(r, MOBY.Graph);
+
+    /**
+     * Return whether or not the given resource is an RDF Bag
+     */
+    private boolean isBag (Resource res)
+    {
+    	return isType(res, RDF.Bag);
     }
-    
-    private boolean isSubject(Resource res) {
-        return isType(res, MOBY.Subject);
+
+    /**
+     * Return whether or not the given resource is an RDF Seq
+     */
+    private boolean isSeq (Resource res)
+    {
+    	return isType(res, RDF.Seq);
     }
-    
-    private boolean isObject(Resource res) {
-        return isType(res, MOBY.Object);
+
+    /**
+     * Return whether or not the given resource is an RDF Alt
+     */
+    private boolean isAlt (Resource res)
+    {
+    	return isType(res, RDF.Alt);
     }
     
-    private boolean isType(Resource res, Resource type) {
-        return model.contains(res, RDF.type, type);
+    /**
+     * Return whether or not the given resource is an RDF data structure,
+     * i.e. a List, Bag, Seq, or Alt
+     */
+    private boolean isDataStructure(Resource r)
+    {
+        return isList(r) || isBag(r) || isSeq(r) || isAlt(r);
     }
     
-    public static String unparse(MOBYProvider provider) {
-        return Unparser.unparse(provider, 0);
+    /**
+     * Return whether or not the given resource is a MOBY Graph,
+     * i.e. the model contains a statement with the given resource
+     * as its subject, a predicate of rdf:type, and an object of
+     * moby:Graph
+     */
+    private boolean isGraph(Resource r)
+    {
+        return isType(r, MOBY.Graph);
     }
-    
-    public static String unparse(MOBYGraph graph) {
-        return Unparser.unparse(graph, 0);
+
+    /**
+     * Return whether or not the given resource is a MOBY Subject,
+     * i.e. the model contains a statement with the given resource
+     * as its subject, a predicate of rdf:type, and an object of
+     * moby:Subject
+     */
+    private boolean isSubject(Resource res)
+    {
+        return isType(res, MOBY.Subject);
     }
-    
-    public static String unparse(MOBYCollection collection) {
-        return Unparser.unparse(collection, 0);
+
+    /**
+     * Return whether or not the given resource is a MOBY Object,
+     * i.e. the model contains a statement with the given resource
+     * as its subject, a predicate of rdf:type, and an object of
+     * moby:Object
+     */
+    private boolean isObject(Resource res)
+    {
+        return isType(res, MOBY.Object);
     }
-    
-    private static class Unparser
+
+    /**
+     * Return whether or not the given resource is of the given type,
+     * i.e. the model contains a statement with the given resource
+     * as its subject, a predicate of rdf:type, and an object of the
+     * given type
+     */
+    private boolean isType(Resource res, Resource type)
     {
-        private static String unparse(MOBYProvider provider, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            
-            indent(sb, indent);
-            sb.append("Provider {");
-            newline(sb);
-            indent(sb, indent+4);
-            sb.append("name=\""); sb.append(provider.getName()); sb.append("\"");
-            newline(sb);
-            indent(sb, indent+4);
-            sb.append("oneLineDescription=\"");
-            sb.append(provider.getOneLineDescription()); sb.append("\"");
-            newline(sb);
-            indent(sb, indent+4);
-            sb.append("moreInfoURI=\"");
-            sb.append(provider.getMoreInfoURI().toString()); sb.append("\"");
-            
-            for (Iterator it = provider.getOperatesOn().iterator(); it.hasNext();)
-            {
-                MOBYGraphNode node = (MOBYGraphNode) it.next();
-                newline(sb);
-                indent(sb, indent+4);
-                sb.append("Operates on:");
-                newline(sb);
-                if (node.isSingular()) {
-                    sb.append(unparse((MOBYGraph) node, indent+8));
-                } else {
-                    sb.append(unparse((MOBYCollection) node, indent+8));
-                }
-            }
-            newline(sb);
-            indent(sb, indent);
-            sb.append("}");
-            
-            return sb.toString();
-        }
-        
-        private static String unparse(MOBYGraph graph, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            
-            indent(sb, indent);
-            sb.append("Graph {");
-            newline(sb);
-            MOBYGraphNode node = graph.gethasMapping();
-            if (node.isSingular()) {
-                sb.append(unparse((MOBYSubject) node, indent+4));
-            } else {
-                sb.append(unparse((MOBYCollection) node, indent+4));
-            }
-            indent(sb, indent);
-            sb.append("}");
-            
-            return sb.toString();
-        }
-        
-        private static String unparse(MOBYSubject subject, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            indent(sb, indent);
-            if (subject.isBlank()) {
-                sb.append("<bnode>");
-            } else {
-                sb.append("<"); sb.append(subject.getURI()); sb.append(">");
-            }
-            newline(sb);
-            
-            return sb.toString();
-        }
-        
-        private static String unparse(MOBYObject object, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            
-            return sb.toString();
-        }
-        
-        private static String unparse(MOBYCollection c, int indent)
-        {
-            StringBuffer sb = new StringBuffer();
-            indent(sb, indent);
-            sb.append(descriptionOf(c));
-            sb.append(" {");
-            for (Iterator it = c.iterator(); it.hasNext();)
-            {
-                newline(sb);
-                Object element = it.next();
-                if (element instanceof MOBYProvider) {
-                    sb.append(unparse((MOBYProvider) element, indent+4));
-                } else if (element instanceof MOBYCollection) {
-                    sb.append(unparse((MOBYCollection) element, indent+4));
-                } else if (element instanceof MOBYGraph) {
-                    sb.append(unparse((MOBYGraph) element, indent+4));
-                } else if (element instanceof MOBYSubject) {
-                    sb.append(unparse((MOBYSubject) element, indent+4));
-                } else if (element instanceof MOBYObject) {
-                    sb.append(unparse((MOBYObject) element, indent+4));
-                } else {
-                    indent(sb, indent+4);
-                    sb.append(element.toString());
-                }
-            }
-            newline(sb);
-            indent(sb, indent);
-            sb.append("}");
-            return sb.toString();
-        }
-        
-        private static void newline(StringBuffer sb) {
-            sb.append("\n");
-        }
-        
-        private static void indent(StringBuffer sb, int count) {
-            for (int i = 0; i < count; i++) {
-                sb.append(' ');
-            }
-        }
-        
-        private static String descriptionOf(MOBYCollection c) {
-            
-            String name = "Collection";
-                 if (c instanceof MOBYFixedCollection)     name = "Fixed collection";
-            else if (c instanceof MOBYEnumeration)         name = "Choice collection";
-            else if (c instanceof MOBYOrderedCollection)   name = "Ordered collection";
-            else if (c instanceof MOBYUnorderedCollection) name = "Unordered collection";
-            
-            return name + " of " + c.size() + " elements";
-        }
+        return res.getModel().contains(res, RDF.type, type);
     }
 }
\ No newline at end of file



From gss at pub.open-bio.org  Wed Jun 16 23:29:32 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:29:32 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162329.i5GNTWJc022617@pub.open-bio.org>


gss
Wed Jun 16 19:29:32 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv22592/S-MOBY/ref-impl/core/src/org/smoby/parser/test

Modified Files:
	Test.java 
Log Message:
Documentation

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test Test.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java	2004/05/24 22:05:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/Test.java	2004/06/16 23:29:32	1.2
@@ -17,7 +17,5 @@
             "C|//Documents and Settings/gss/Desktop/citationSearch.n3");
         Parser parser = Parser.forN3File(inputFile);
         MOBYCollection coll = parser.parseProviders();
-        System.out.println("Providers:");
-        System.out.println(Parser.unparse(coll));
     }
 }



From gss at pub.open-bio.org  Wed Jun 16 23:30:14 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:30:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162330.i5GNUEaO022676@pub.open-bio.org>


gss
Wed Jun 16 19:30:13 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv22651/S-MOBY/ref-impl/core/src/org/smoby/vocabulary

Modified Files:
	MOBY.java 
Log Message:
No longer need registeredBy property

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/05/24 22:05:34	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/16 23:30:13	1.2
@@ -24,7 +24,6 @@
     public static final Property operatesOn			= property(getURI(), "operatesOn");
     public static final Property hasMapping			= property(getURI(), "hasMapping");
     public static final Property mapsTo				= property(getURI(), "mapsTo");
-    public static final Property registeredBy		= property(getURI(), "registeredBy");
     public static final Property lastModifiedDate	= property(getURI(), "lastModifiedDate");
     public static final Property Property			= property(getURI(), "Property");
 }
\ No newline at end of file



From gss at pub.open-bio.org  Wed Jun 16 23:30:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:30:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162330.i5GNUir3022714@pub.open-bio.org>


gss
Wed Jun 16 19:30:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev
In directory pub.open-bio.org:/tmp/cvs-serv22689/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev

Modified Files:
	RepositoryPrintServlet.java 
Log Message:
Print individual statements as N-triples

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev RepositoryPrintServlet.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java	2004/06/14 20:59:36	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/RepositoryPrintServlet.java	2004/06/16 23:30:44	1.3
@@ -22,7 +22,10 @@
             if (model.isEmpty()) {
             	out.println("The repository is empty");
             } else {
-            	model.write(out, "RDF/XML-ABBREV");
+            	StmtIterator it = model.listStatements();
+            	while (it.hasNext()) {
+            		out.println(it.nextStatement());
+            	}
             }
             model.close();
         } catch (StorageException e) {



From gss at pub.open-bio.org  Wed Jun 16 23:31:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:31:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162331.i5GNVbrM022756@pub.open-bio.org>


gss
Wed Jun 16 19:31:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv22735/S-MOBY/ref-impl/server/src/org/smoby/ref/tools

Added Files:
	ProviderRemover.java 
Log Message:
Utility class to remove a provider's statements from a model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools ProviderRemover.java,NONE,1.1


From gss at pub.open-bio.org  Wed Jun 16 23:33:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:33:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162333.i5GNX02f022802@pub.open-bio.org>


gss
Wed Jun 16 19:33:00 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db
In directory pub.open-bio.org:/tmp/cvs-serv22777/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db

Modified Files:
	StorageManager.java 
Log Message:
No longer cache separate model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/05/19 18:26:41	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/06/16 23:33:00	1.4
@@ -1,7 +1,7 @@
 package org.smoby.ref.tools.db;
 
 import org.smoby.graph.*;
-import org.smoby.graph.impl.MOBYProviderImpl;
+import org.smoby.graph.impl.*;
 import org.smoby.ref.tools.*;
 import org.smoby.vocabulary.*;
 import com.hp.hpl.jena.db.*;
@@ -17,19 +17,6 @@
 public class StorageManager
 {
     /**
-     * Return whether or not the database contains a provider with a
-     * given URI.
-     * @param providerURI URI of the provider in question
-     * @return boolean flag indicating if the database contains the provider in question
-     * @throws StorageException if unable to access the model in the database
-     */
-    public boolean containsProvider(String providerURI)
-        throws StorageException
-    {
-        return getModelMaker().hasModel(providerURI);
-    }
-    
-    /**
      * Return the date when a given provider was registered
      * @param providerURL URI of the provider
      * @return the registration date if the provider has been registered in
@@ -41,20 +28,19 @@
     {
         Date registrationDate = null;
         
-        ModelMaker maker = getModelMaker();
+        Model dbModel = openDBModel();
         
-        Model model = maker.openModel(providerURI);
+        Resource provider = dbModel.createResource(providerURI);
         
-        Resource provider = model.createResource(providerURI);
-        
-        NodeIterator it = model.listObjectsOfProperty(provider, MOBY.lastModifiedDate);
+        NodeIterator it = dbModel.listObjectsOfProperty(
+        	provider, MOBY.lastModifiedDate);
         
         if (it.hasNext()) {
             Literal lit = (Literal) it.nextNode().as(Literal.class);
             registrationDate = new Date(lit.getLong());
         }
         
-        model.close();
+        dbModel.close();
         
         return registrationDate;
     }
@@ -73,7 +59,8 @@
 	{
 	    Model model = ((MOBYProviderImpl) provider).getUnderlying();
         Model dbModel = null;
-        Resource uri = model.createResource(provider.getURI());
+        String uriString = provider.getURI();
+        Resource uri = model.createResource(uriString);
         
         try
         {
@@ -84,50 +71,32 @@
             // Open the database model
             //
             dbModel = openDBModel(maker);
-            
-            // First check if the database already has a graph registered under
-            // the URI of the new graph. If so, then throw an exception
-            //
-            if (dbModel.contains(null, MOBY.registeredBy, uri)) {
-                throw new StorageException("Graph already exists for " + uri);
-            }
 
             // Start a transaction on the database model
             //
             dbModel.begin();
             
-            // Add to the database the statements from providerGraph whose
-            // subjects are in the same namespace as the provider
+            // Add to the database all statements whose subjects are
+            // at the URI or deeper
             //
-            String providerNameSpace = uri.getNameSpace();
+            StmtIterator it = model.listStatements();
+            while (it.hasNext()) {
+            	Statement stmt = it.nextStatement();
+            	Resource subject = stmt.getSubject();
+            	if (subject.isAnon() || subject.getURI().startsWith(uriString)) {
+            		dbModel.add(stmt);
+            	}
+            }
             
-            for (StmtIterator it = model.listStatements(); it.hasNext();)
-            {
-                Statement stmt = it.nextStatement();
-                Resource subject = stmt.getSubject();
-                String nameSpace = subject.getNameSpace();
-                
-                if (subject.isAnon() || providerNameSpace.equals(nameSpace)) {
-                    dbModel.add(stmt);
-                }
+            // Add a statement asserting when the model was added
+            //
+            if (lastModifiedDate != null) {
+            	dbModel.add(uri, MOBY.lastModifiedDate, lastModifiedDate.getTime());
             }
             
             // Commit the transaction on the database model
             //
             dbModel.commit();
-            
-            // Add to the database another model, with the provider URL as its name
-            //
-            Model providerModel = maker.createModel(uri.getURI());
-            providerModel.add(model);
-            providerModel.setNsPrefixes(model.getNsPrefixMap());
-            
-            // Add a statement asserting when the model was added to the database
-            //
-            if (lastModifiedDate != null) {
-                providerModel.add(uri, MOBY.lastModifiedDate, lastModifiedDate.getTime());
-            }
-            providerModel.close();
         }
         catch (StorageException se) {
             throw se;
@@ -160,21 +129,16 @@
             Resource provider = dbModel.createResource(providerURI);
             String providerNameSpace = provider.getNameSpace();
             
-            Model modelToRemove = maker.openModel(providerURI);
-            
+            // Start a transaction on the database
+            //
             dbModel.begin();
-            for (StmtIterator it = modelToRemove.listStatements(); it.hasNext();)
-            {
-                Statement stmt = it.nextStatement();
-                Resource subject = stmt.getSubject();
-                String nameSpace = subject.getNameSpace();
-                
-                if (subject.isAnon() || providerNameSpace.equals(nameSpace)) {
-                	dbModel.remove(stmt);
-                }
-            }
-            modelToRemove.close();
-            maker.removeModel(providerURI);
+            
+            // Remove all statements that are reachable from the provider URI
+            //
+            ProviderRemover.remove(dbModel, providerURI);
+            
+            // Commit the transaction on the database
+            //
             dbModel.commit();
         }
         catch (StorageException se) {



From gss at pub.open-bio.org  Wed Jun 16 23:33:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 16 Jun 2004 19:33:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406162333.i5GNXPOW022832@pub.open-bio.org>


gss
Wed Jun 16 19:33:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv22807/S-MOBY/ref-impl/server/src/org/smoby/ref/tools

Modified Files:
	URIInvestigator.java 
Log Message:
Use new StorageManager protocol

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/05/19 18:26:40	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/06/16 23:33:25	1.4
@@ -131,33 +131,21 @@
         StorageManager manager = new StorageManager();
     
         // Find out if the provider is already registered, and if so, when
-        // was its graph last modified. If either operation fail, log a
-        // message and return.
+        // was its graph last modified.
         //
-        boolean alreadyRegistered = false;
         Date lastModifiedDate = null;
+        boolean alreadyRegistered = false;
         
         try {
-            alreadyRegistered = manager.containsProvider(providerURI);
+        	lastModifiedDate = manager.getLastModifiedDate(providerURI);
+            alreadyRegistered = (lastModifiedDate != null);
         }
         catch (StorageException e)
         {
-        	syncLog.error("Couldn't check if provider URL " + providerURI + " exists", e);
+        	syncLog.error("Couldn't check for last modified date of provider URL " + providerURI, e);
             return;
         }
         
-        if (alreadyRegistered)
-        {
-            try {
-            	lastModifiedDate = manager.getLastModifiedDate(providerURI);
-            }
-            catch (StorageException e)
-            {
-            	syncLog.error("Couldn't check for last modified date of provider URL " + providerURI, e);
-                return;
-            }
-        }
-        
         // Helper class for making the HTTP GET call
         //
         HTTPRequest request = HTTPRequest.newGetRequest(providerURI);



From gss at pub.open-bio.org  Thu Jun 17 17:34:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:34:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171734.i5HHYHoV025365@pub.open-bio.org>


gss
Thu Jun 17 13:34:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25340/S-MOBY/ref-impl/core/src/org/smoby/vocabulary

Modified Files:
	MOBY.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/16 23:30:13	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/17 17:34:17	1.3
@@ -10,7 +10,7 @@
 
     public static String getURI()
     {
-        return "http://www.s-moby.org:8080/terms#";
+        return "http://www.s-moby.org:8080/terms/";
     }
     
     public static final Resource Provider   		= resource(getURI(), "Provider");



From gss at pub.open-bio.org  Thu Jun 17 17:35:01 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:35:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171735.i5HHZ1eA025407@pub.open-bio.org>


gss
Thu Jun 17 13:35:01 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv25380/S-MOBY/ref-impl/core/src/org/smoby/parser

Modified Files:
	Parser.java 
Log Message:
Fixed typo

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/16 23:29:20	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/17 17:35:01	1.3
@@ -127,8 +127,7 @@
      */
     public Parser(Model model)
     {
-    	
-        StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
+    	StmtIterator it = model.listStatements(null, RDF.type, MOBY.Provider);
         while (it.hasNext())
         {
         	Statement stmt = it.nextStatement();



From gss at pub.open-bio.org  Thu Jun 17 17:35:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:35:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171735.i5HHZqHf025445@pub.open-bio.org>


gss
Thu Jun 17 13:35:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools
In directory pub.open-bio.org:/tmp/cvs-serv25420/S-MOBY/ref-impl/server/WebRoot/tools

Modified Files:
	developer.html 
Log Message:
Minor fixes

moby-live/S-MOBY/ref-impl/server/WebRoot/tools developer.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html	2004/06/16 22:27:14	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/developer.html	2004/06/17 17:35:52	1.4
@@ -40,7 +40,9 @@
       "Convert Graph"></p>
 
       <p><textarea name="graph" rows="15" cols="80">
-                                              
+                                                          
+                                                             
+                                                     
                                                
                                        
                                  
@@ -56,8 +58,7 @@
     <form method="get" action=
     "http://www.s-moby.org:8080/list-providers">
       &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; <input type="submit"
-      value="List Providers">&nbsp;&nbsp; <input type="checkbox" name=
-      "show-contents" value="true"> Show provider description graphs
+      value="List Providers">
     </form>
 
     <h4><u>List&nbsp;all statements&nbsp;in the S-MOBY metadata
@@ -79,7 +80,9 @@
       <p><input type="submit" value="Validate"></p>
 
       <p><textarea name="graph" rows="15" cols="80">
-                                              
+                                                          
+                                                             
+                                                     
                                                
                                        
                                  
@@ -99,7 +102,9 @@
       <p><input type="submit" value="Validate"></p>
 
       <p><textarea name="graph" rows="15" cols="80">
-                                              
+                                                          
+                                                             
+                                                     
                                                
                                        
                                  



From gss at pub.open-bio.org  Thu Jun 17 17:35:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:35:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171735.i5HHZqgT025464@pub.open-bio.org>


gss
Thu Jun 17 13:35:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv25420/S-MOBY/ref-impl/server/WebRoot

Modified Files:
	domains.html 
Log Message:
Minor fixes

moby-live/S-MOBY/ref-impl/server/WebRoot domains.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html	2004/04/01 00:34:23	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/domains.html	2004/06/17 17:35:52	1.4
@@ -1,178 +1,176 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
 <html>
-<head>
-  <title>Semantic MOBY Server - Hosted Pages</title>
-</head>
-<body>
-<table style="text-align: center; width: 100%;" border="1"
- cellpadding="0" cellspacing="0">
-  <tbody>
-    <tr>
-      <td
- style="vertical-align: top; background-color: rgb(204, 204, 204);"> <b>Semantic
-MOBY Server - Hosted Pages</b> </td>
-    </tr>
-  </tbody>
-</table>
-<p>
-The Semantic MOBY reference implementation server hosts the following
-pages:<br>
-<br>
-<table style="text-align: left; width: 100%;" border="1" cellpadding="2"
- cellspacing="0">
-  <tbody>
-    <tr>
-      <td style="vertical-align: top;"><span style="font-weight: bold;">Page</span><br>
-      </td>
-      <td style="vertical-align: top;"><span style="font-weight: bold;">Description</span><br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.acmepubs.com:8080">www.acmepubs.com</a></td>
-      <td style="vertical-align: top;">Home page of an
-acmepubs.com, a hypothetical citation search provider.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.acmepubs.com:8080/citationSearch">www.acmepubs.com/citationSearch</a></td>
-      <td style="vertical-align: top;">Provider description
-graph for acmepubs.com. Note that doing an HTTP GET on this URI (e.g.
-by clicking on the link at the left), by definition returns an RDF
-graph that describes the provider. Also note that in this reference
-implementation, the URI is implemented as a Java Servlet.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.megapubs.com:8080">www.megapubs.com</a></td>
-      <td style="vertical-align: top;">Home page of an
-megapubs.com, another example citation search provider.</td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.megapubs.com:8080/citationSearch">www.megapubs.com/citationSearch</a></td>
-      <td style="vertical-align: top;">Provider description
-graph for megapubs.com. The notes regarding the
-www.acmepubs.com/citationSearch also apply to this URI.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.pubs.org:8080">www.pubs.org</a></td>
-      <td style="vertical-align: top;">Home page of a
-hypothetical vocabulary provider, pubs.org.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.pubs.org:8080/terms">www.pubs.org/terms</a></td>
-      <td style="vertical-align: top;">The vocabulary of terms
-defined by pubs.org. Note that in this reference implementation, unlike
-the two citation search providers, this vocabulary is provided in a
-resource file (terms) delivered as is by the web server - no servlets
-are involved.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a href="http://www.go.org:8080">www.go.org</a></td>
-      <td style="vertical-align: top;">Home page of a
-hypothetical vocabulary provider, go.org. This provider is meant to be
-representative of the type of vocabulary information that the real Gene
-Ontology (GO) Consortium would need to provide in order to be a
-Semantic MOBY vocabulary provider.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.go.org:8080/terms">www.go.org/terms</a></td>
-      <td style="vertical-align: top;">The vocabulary of terms
-defined by go.org. The notes regarding www.pubs.org/terms apply
-here as well.<br>
-      </td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.sgd.org:8080/">www.sgd.org</a></td>
-      <td style="vertical-align: top;">Home page of a
-hypothetical vocabulary provider, sgd.org. This provider is meant to be
-representative of the type of vocabulary
-information that the real <i>Saccharomyces Gene Database </i>would
-need to
-provide in order to be a Semantic MOBY vocabulary provider.</td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.sgd.org:8080/terms">www.sgd.org/terms</a></td>
-      <td style="vertical-align: top;">The vocabulary of terms
-defined by go.org. The notes regarding www.pubs.org/terms apply
-here as well.</td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;">www.s-moby.org</td>
-      <td style="vertical-align: top;">This page you're
-currently viewing.</td>
-    </tr>
-    <tr>
-      <td style="vertical-align: top;"><a
- href="http://www.s-moby.org:8080/terms">www.s-moby.org/terms</a></td>
-      <td style="vertical-align: top;">The Semantic MOBY
-vocabulary terms. The notes regarding www.pubs.org/terms
-apply here as well.</td>
-    </tr>
-  </tbody>
-</table>
-<span style="font-weight: bold;"></span><br>
-</p>
-<div style="margin-left: 40px;">
-<div style="margin-left: 40px;"></div>
-</div>
-Since these hosts are virtual, in order to access their pages by name,
-you will need to modify how hosts are looked up. This can most easily
-be
-done by adding
-entries to the <code>hosts</code> file, making the host names refer to
-the
-local host (<code>127.0.0.1</code>). The Tomcat web server / servlet
-container then resolves to a virtual host by name. The following
-entries
-should be added
-to the <code>hosts</code> file of the given operating system on which
-the
-test server is running:
-<p><u>Under Linux/Unix, add to <code>/etc/hosts</code></u>
-</p>
-<ul>
-  <code>
-127.0.0.1 www.acmepubs.com acmepubs.com<br>
-127.0.0.1 www.megapubs.com megapubs.com<br>
-127.0.0.1 www.pubs.org pubs.org<br>
-127.0.0.1 www.go.org go.org<br>
-127.0.0.1 www.sgd.org sgd.org<br>
-127.0.0.1 www.s-moby.org s-moby.org<br>
-127.0.0.1 www.smobydev.org smobydev.org<br>
-  </code>
-</ul>
-<p>
-<u>Under Windows NT/2000/XP, add to
-<code>&lt;WIN_DIR&gt;/system32/drivers/etc/hosts</code></u>
-</p>
-<ul>
-  <code>
-127.0.0.1 acmepubs.com<br>
-127.0.0.1 www.acmepubs.com<br>
-127.0.0.1 megapubs.com<br>
-127.0.0.1 www.megapubs.com<br>
-127.0.0.1 go.org<br>
-127.0.0.1 www.go.org<br>
-127.0.0.1 sgd.org<br>
-127.0.0.1 www.sgd.org<br>
-127.0.0.1 pubs.org<br>
-127.0.0.1 www.pubs.org<br>
-127.0.0.1 s-moby.org<br>
-127.0.0.1 www.s-moby.org<br>
-  </code>
-</ul>
-</body>
+  <head>
+    <meta name="generator" content="HTML Tidy, see www.w3.org">
+
+    <title>Semantic MOBY Server - Hosted Pages</title>
+  </head>
+
+  <body>
+    <table style="WIDTH: 100%; TEXT-ALIGN: center" border="1"
+    cellpadding="0" cellspacing="0">
+      <tbody>
+        <tr>
+          <td style=
+          "VERTICAL-ALIGN: top; BACKGROUND-COLOR: rgb(204,204,204)">
+          <b>Semantic MOBY Server - Hosted Pages</b></td>
+        </tr>
+      </tbody>
+    </table>
+
+    <p>The Semantic MOBY reference implementation server hosts the
+    following pages:<br>
+    <br>
+    </p>
+
+    <table style="WIDTH: 100%; TEXT-ALIGN: left" border="1"
+    cellpadding="2" cellspacing="0">
+      <tbody>
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><span style=
+          "FONT-WEIGHT: bold">Page</span><br>
+          </td>
+
+          <td style="VERTICAL-ALIGN: top"><span style=
+          "FONT-WEIGHT: bold">Description</span><br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.acmepubs.com:8080">www.acmepubs.com</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of an acmepubs.com,
+          a hypothetical citation search provider.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td><a href=
+          "http://www.acmepubs.com:8080/terms">http://www.acmepubs.com/terms</a></td>
+
+          <td>The vocabulary of terms defined by acmepubs.com.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.acmepubs.com:8080/citationSearch">www.acmepubs.com/citationSearch</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Provider description graph
+          for acmepubs.com. Note that doing an HTTP GET on this URI
+          (e.g. by clicking on the link at the left), by definition
+          returns an RDF graph that describes the provider. Also note
+          that in this reference implementation, the URI is implemented
+          as a Java Servlet.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.megapubs.com:8080">www.megapubs.com</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of an megapubs.com,
+          another example citation search provider.</td>
+        </tr>
+
+        <tr>
+          <td><a href=
+          "http://www.megapubs.com:8080/terms">www.megapubs.com/terms</a></td>
+
+          <td>The vocabulary of terms defined by megapubs.com.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.megapubs.com:8080/citationSearch">www.megapubs.com/citationSearch</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Provider description graph
+          for megapubs.com. The notes regarding the
+          www.acmepubs.com/citationSearch also apply to this URI.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.pubs.org:8080">www.pubs.org</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of a hypothetical
+          vocabulary provider, pubs.org.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.pubs.org:8080/terms">www.pubs.org/terms</a></td>
+
+          <td style="VERTICAL-ALIGN: top">The vocabulary of terms
+          defined by pubs.org. Note that in this reference
+          implementation, unlike the two citation search providers,
+          this vocabulary is provided in a resource file (terms)
+          delivered as is by the web server - no servlets are
+          involved.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.go.org:8080">www.go.org</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of a hypothetical
+          vocabulary provider, go.org. This provider is meant to be
+          representative of the type of vocabulary information that the
+          real Gene Ontology (GO) Consortium would need to provide in
+          order to be a Semantic MOBY vocabulary provider.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.go.org:8080/terms">www.go.org/terms</a></td>
+
+          <td style="VERTICAL-ALIGN: top">The vocabulary of terms
+          defined by go.org. The notes regarding www.pubs.org/terms
+          apply here as well.<br>
+          </td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.sgd.org:8080/">www.sgd.org</a></td>
+
+          <td style="VERTICAL-ALIGN: top">Home page of a hypothetical
+          vocabulary provider, sgd.org. This provider is meant to be
+          representative of the type of vocabulary information that the
+          real <i>Saccharomyces Gene Database</i> would need to provide
+          in order to be a Semantic MOBY vocabulary provider.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.sgd.org:8080/terms">www.sgd.org/terms</a></td>
+
+          <td style="VERTICAL-ALIGN: top">The vocabulary of terms
+          defined by go.org. The notes regarding www.pubs.org/terms
+          apply here as well.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top">www.s-moby.org</td>
+
+          <td style="VERTICAL-ALIGN: top">This page you're currently
+          viewing.</td>
+        </tr>
+
+        <tr>
+          <td style="VERTICAL-ALIGN: top"><a href=
+          "http://www.s-moby.org:8080/terms">www.s-moby.org/terms</a></td>
+
+          <td style="VERTICAL-ALIGN: top">The Semantic MOBY vocabulary
+          terms. The notes regarding www.pubs.org/terms apply here as
+          well.</td>
+        </tr>
+      </tbody>
+    </table>
+  </body>
 </html>



From gss at pub.open-bio.org  Thu Jun 17 17:37:05 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:37:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171737.i5HHb5Mf025523@pub.open-bio.org>


gss
Thu Jun 17 13:37:05 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv25498/S-MOBY/ref-impl/server/src/org/smoby/ref/tools

Modified Files:
	URIInvestigator.java 
Log Message:
Cleanup

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/06/16 23:33:25	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/06/17 17:37:05	1.5
@@ -176,10 +176,30 @@
         
         switch (status)
         {
+            case HttpServletResponse.SC_NOT_MODIFIED:
+                
+                // The resource has not been modified since it was
+                // registered, so there is nothing to do but log a message.
+                //
+            	syncLog.info("IN-SYNC : " + providerURI);
+                break;
+            
+            case HttpServletResponse.SC_NOT_FOUND:
+                
+                // The resource is no longer accessible, so de-register it
+                // from the database.
+                //
+                if (alreadyRegistered) {
+                	deregisterProvider(manager, true);
+                } else {
+                	syncLog.info("IGNORED : " + providerURI + " doesn't exist");
+                }
+                break;
+                
             case HttpServletResponse.SC_OK:
                 
-                // The call succeeded, so graphString should contain a valid graph.
-                // Try to parse it.
+                // The call succeeded, so see if graphString contains
+            	// a valid graph by trying to parse it.
                 //
                 lastModifiedDate = null;
                 
@@ -226,61 +246,30 @@
                     Parser parser = Parser.forInputStream(in, Parser.LANGUAGE_RDF_XML);
                     provider = parser.parseProvider();
                 }
-                catch (UnparsableGraphException e)
-                {
-                	syncLog.warn("Unparsable graph found at " + providerURI +
-                        (alreadyRegistered ? "; deregistering" : "; ignoring"));
-                    if (alreadyRegistered) {
-                        deregisterProvider(manager);
-                    }
-                    return;
-                }
+                catch (Throwable t) {}
                 
-                if (alreadyRegistered) {
-                    deregisterProvider(manager);
-                }
-                
-                try
-                {
-                    manager.registerProvider(provider, lastModifiedDate);
-                    
-                    // Log a message about successfully registering the graph:
-                    //
-                    syncLog.info((alreadyRegistered ? "UPDATED : " : "ADDED   : ") + providerURI);
-                }
-                catch (StorageException e) {
-                	syncLog.error("Error storing graph for " + providerURI, e);
-                }
-                
-                break;
-                
-            case HttpServletResponse.SC_NOT_MODIFIED:
-                
-                // The resource has not been modified since it was
-                // registered, so there is nothing to do but log a message.
+                // De-register the provider, printing a removal message if
+                // a provider couldn't be parsed
                 //
-            	syncLog.info("IN-SYNC : " + providerURI);
-                break;
-            
-            case HttpServletResponse.SC_NOT_FOUND:
+                deregisterProvider(manager, provider==null);
                 
-                // The resource is no longer accessible, so de-register it
-                // from the database.
+                // If a provider was parsed, then register it
                 //
-                if (alreadyRegistered)
-                {    
-                    try
-                    {
-                    	manager.deregisterProvider(providerURI);
-                    	syncLog.info("REMOVED : " + providerURI);
-                    }
-                    catch (StorageException e) {
-                    	syncLog.error("Unable to de-register provider " + providerURI, e);
-                    }
-                }
-                else {
-                	syncLog.info("IGNORED : " + providerURI + " doesn't exist");
+                if (provider != null)
+                {
+	                try
+	                {
+	                    manager.registerProvider(provider, lastModifiedDate);
+	                    
+	                    // Log a message about successfully registering the graph:
+	                    //
+	                    syncLog.info((alreadyRegistered ? "UPDATED : " : "ADDED   : ") + providerURI);
+	                }
+	                catch (StorageException e) {
+	                	syncLog.error("Error storing graph for " + providerURI, e);
+	                }
                 }
+                
                 break;
             
             default:
@@ -293,10 +282,13 @@
         }
     }
     
-    private void deregisterProvider(StorageManager manager)
+    private void deregisterProvider(StorageManager manager, boolean removing)
     {
         try {
         	manager.deregisterProvider(providerURI);
+        	if (removing) {
+            	syncLog.info("REMOVED : " + providerURI);
+        	}
         }
         catch (StorageException e) {
         	syncLog.error("Unable to de-register provider " + providerURI, e);



From gss at pub.open-bio.org  Thu Jun 17 17:37:58 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:37:58 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171737.i5HHbwhw025564@pub.open-bio.org>


gss
Thu Jun 17 13:37:58 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev
In directory pub.open-bio.org:/tmp/cvs-serv25539/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev

Modified Files:
	ProviderListServlet.java 
Log Message:
Since only global model saved, iterate over its rdf:type moby:Provider statements

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev ProviderListServlet.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/06/14 20:59:36	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/06/17 17:37:57	1.4
@@ -1,12 +1,10 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.servlet.*;
-import org.smoby.tools.*;
-import org.smoby.ref.servlets.BaseServlet;
+import org.smoby.vocabulary.*;
+import org.smoby.ref.servlets.*;
 import org.smoby.ref.tools.db.*;
-import org.smoby.ref.tools.*;
-
 import com.hp.hpl.jena.rdf.model.*;
+import com.hp.hpl.jena.vocabulary.*;
 import java.io.*;
 import java.util.*;
 import javax.servlet.*;
@@ -22,23 +20,19 @@
         
         try
         {
-            boolean showContents = (request.getParameter("show-contents") != null);
-            String globalModelName = MOBYProperties.getProperty("DB_REPOSITORY_NAME", true);
-            ModelMaker maker = manager.getModelMaker();
+        	Model dbModel = manager.openDBModel();
             int count = 0;
-            for (Iterator it = maker.listModels(); it.hasNext();) {
-            	String modelName = it.next().toString();
-                if (! modelName.equals(globalModelName)) {
-                    count++;
-                    if (showContents) {
-                        Model model = maker.openModel(modelName);
-                        model.write(out, "RDF/XML-ABBREV");
-                        model.close();
-                    } else {
-                    	out.println(modelName);
-                    }
-                }
+            StmtIterator it = dbModel.listStatements(
+            	null, RDF.type, MOBY.Provider);
+            
+            while (it.hasNext()) {
+            	Statement stmt = it.nextStatement();
+            	out.println(stmt.getSubject().getURI());
+            	count++;
             }
+            
+            dbModel.close();
+            
             if (count < 1) {
             	out.println("No providers are defined");
             }
@@ -46,8 +40,5 @@
         catch (StorageException e) {
             throw new ServletException(e);
         }
-        catch (MissingPropertyException e) {
-            throw new ServletException(e);
-        }
     }
 }
\ No newline at end of file



From gss at pub.open-bio.org  Thu Jun 17 17:38:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:38:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171738.i5HHcx4E025602@pub.open-bio.org>


gss
Thu Jun 17 13:38:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary

Modified Files:
	MegaPubs.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary MegaPubs.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java	2004/05/19 18:26:48	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java	2004/06/17 17:38:59	1.4
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.megapubs.com:8080/";
+        return "http://www.megapubs.com:8080/terms/";
     }
     
     public static final Property geneSymbol  = property(getURI(), "geneSymbol");



From gss at pub.open-bio.org  Thu Jun 17 17:38:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:38:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171738.i5HHcxiZ025621@pub.open-bio.org>


gss
Thu Jun 17 13:38:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary

Modified Files:
	Go.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary Go.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java	2004/05/19 18:26:55	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java	2004/06/17 17:38:59	1.3
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.go.org:8080/";
+        return "http://www.go.org:8080/terms/";
     }
     
     public static final Resource GeneSymbol = resource(getURI(), "GeneSymbol");



From gss at pub.open-bio.org  Thu Jun 17 17:39:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:39:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171739.i5HHd0wp025641@pub.open-bio.org>


gss
Thu Jun 17 13:38:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary

Modified Files:
	SGD.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary SGD.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java	2004/05/19 18:26:22	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java	2004/06/17 17:38:59	1.3
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.sgd.org:8080/";
+        return "http://www.sgd.org:8080/terms/";
     }
     
     public static final Resource LiteratureGuide = resource(getURI(), "LiteratureGuide");



From gss at pub.open-bio.org  Thu Jun 17 17:39:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:39:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171739.i5HHd0Ft025663@pub.open-bio.org>


gss
Thu Jun 17 13:38:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary

Modified Files:
	AcmePubs.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary AcmePubs.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java	2004/05/19 18:26:52	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java	2004/06/17 17:38:59	1.5
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.acmepubs.com:8080/";
+        return "http://www.acmepubs.com:8080/terms/";
     }
     
     public static final Property geneSymbol  = property(getURI(), "geneSymbol");



From gss at pub.open-bio.org  Thu Jun 17 17:39:00 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 17 Jun 2004 13:39:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406171739.i5HHd0Fp025684@pub.open-bio.org>


gss
Thu Jun 17 13:39:00 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv25577/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary

Modified Files:
	Pubs.java 
Log Message:
New base URI for terms

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Pubs.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java	2004/05/19 18:26:25	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java	2004/06/17 17:39:00	1.4
@@ -8,7 +8,7 @@
 {
     public static String getURI()
     {
-        return "http://www.pubs.org:8080/";
+        return "http://www.pubs.org:8080/terms/";
     }
     
     public static final Resource PubAbstract = resource(getURI(), "PubAbstract");



From gss at pub.open-bio.org  Fri Jun 18 21:37:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:37:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182137.i5ILbqHC029781@pub.open-bio.org>


gss
Fri Jun 18 17:37:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv29756/src/org/smoby/graph/impl

Modified Files:
	MOBYObjectFactory.java 
Added Files:
	MOBYProviderSetImpl.java 
Log Message:
New class to represent a set of providers

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl MOBYProviderSetImpl.java,NONE,1.1 MOBYObjectFactory.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java	2004/05/24 22:05:35	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/MOBYObjectFactory.java	2004/06/18 21:37:52	1.2
@@ -40,6 +40,11 @@
                 					underlying);
     }
     
+    public static MOBYProviderSet newProviderSet()
+    {
+    	return new MOBYProviderSetImpl();
+    }
+    
     public static MOBYGraph newGraph(String uri, MOBYGraphNode hasMapping, Model underlying)
     {
         return new MOBYGraphImpl(uri, hasMapping, underlying);



From gss at pub.open-bio.org  Fri Jun 18 21:37:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:37:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182137.i5ILbqEZ029796@pub.open-bio.org>


gss
Fri Jun 18 17:37:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv29756/src/org/smoby/graph

Added Files:
	MOBYProviderSet.java 
Log Message:
New class to represent a set of providers

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYProviderSet.java,NONE,1.1


From gss at pub.open-bio.org  Fri Jun 18 21:38:27 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:38:27 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182138.i5ILcRMk029838@pub.open-bio.org>


gss
Fri Jun 18 17:38:27 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv29813/src/org/smoby/parser

Modified Files:
	Parser.java 
Log Message:
Minor small fixes

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/17 17:35:01	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java	2004/06/18 21:38:27	1.4
@@ -6,6 +6,7 @@
 import org.smoby.graph.*;
 import org.smoby.graph.impl.*;
 import org.smoby.parser.*;
+import org.smoby.tools.Util;
 import org.smoby.vocabulary.*;
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.vocabulary.*;
@@ -100,7 +101,7 @@
     public static Parser forInputStream(InputStream is, String language)
 		throws UnparsableGraphException
     {
-        Model model = ModelFactory.createDefaultModel();
+        Model model = Util.newJenaModel();
         try {
             model.read(is, "", language);
         } catch (Throwable t) {
@@ -131,45 +132,14 @@
         while (it.hasNext())
         {
         	Statement stmt = it.nextStatement();
-        	Model subModel = ModelFactory.createDefaultModel();
+        	Model subModel = Util.newJenaModel();
         	subModel.setNsPrefixes(model.getNsPrefixMap());
         	Resource subject = stmt.getSubject();
-        	addReachableStmts(subModel, subject, subject.getURI());
+        	Util.addReachableStmts(model, subModel, subject, subject.getURI());
         	inferenceModels.put(subModel,
         		ModelFactory.createRDFSModel(subModel));
         }
     }
-    
-	private void addReachableStmts(Model model, Resource subject, String uri)
-	{
-		// For each statement whose subject is the given resource
-		//
-		StmtIterator it = subject.getModel().listStatements(
-			subject, null, (RDFNode) null);
-		
-		while (it.hasNext())
-		{
-			Statement stmt = it.nextStatement();
-			
-			// The statement itself should be added
-			//
-			model.add(model.createStatement(
-				stmt.getSubject(), stmt.getPredicate(), stmt.getObject()));
-			
-			// If the object of the statement is a blank node or a
-			// resource whose URI starts with the provider URI, then
-			// recursively add the statements that are reachable
-			// from the object
-			//
-			if (stmt.getObject().canAs(Resource.class))
-			{
-				Resource object = (Resource) stmt.getObject().as(Resource.class);
-				if (object.isAnon() || object.getURI().startsWith(uri)) {
-					addReachableStmts(model, object, uri);
-				}
-			}
-		}
-	}
 
     /**
      * Parse a provider from the model. If the model contains
@@ -196,14 +166,9 @@
     {
         ArrayList providers = new ArrayList();
         
-        // Find the statements that say something is of type Provider
-        //
-//        StmtIterator it = underlying.listStatements(null, RDF.type, MOBY.Provider);
-        
-        Iterator it = inferenceModels.keySet().iterator();
-        
         // Parse each provider
         //
+        Iterator it = inferenceModels.keySet().iterator();
         while (it.hasNext())
         {
         	Model model = (Model) it.next();



From gss at pub.open-bio.org  Fri Jun 18 21:38:46 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:38:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182138.i5ILckEJ029877@pub.open-bio.org>


gss
Fri Jun 18 17:38:46 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv29852/src/org/smoby/tools

Modified Files:
	Util.java 
Log Message:
New utility methods

moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools Util.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/Util.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/Util.java	2004/05/24 22:05:36	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/Util.java	2004/06/18 21:38:46	1.2
@@ -4,6 +4,15 @@
 import java.util.*;
 
 import org.apache.commons.httpclient.util.DateParser;
+import org.smoby.vocabulary.MOBY;
+
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.NsIterator;
+import com.hp.hpl.jena.rdf.model.RDFNode;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.rdf.model.StmtIterator;
 
 /**
  * This abstract class contains a miscellaneous set of useful static methods
@@ -26,4 +35,119 @@
     {
     	return HTTP_DATE_FORMAT.format(date);
     }
+    
+    public static Model newJenaModel()
+    {
+    	Model model = ModelFactory.createDefaultModel();
+    	MOBY.addNsPrefix(model);
+    	return model;
+    }
+    
+	public static void addReachableStmts(
+		Model source, Model dest, Resource subject, String uri)
+	{
+		// For each statement whose subject is the given resource
+		//
+		StmtIterator it = source.listStatements(
+			subject, null, (RDFNode) null);
+		
+		while (it.hasNext())
+		{
+			Statement stmt = it.nextStatement();
+			
+			// The statement itself should be added
+			//
+			dest.add(dest.createStatement(
+				stmt.getSubject(), stmt.getPredicate(), stmt.getObject()));
+			
+			// If the object of the statement is a blank node or a
+			// resource whose URI starts with the provider URI, then
+			// recursively add the statements that are reachable
+			// from the object
+			//
+			if (stmt.getObject().canAs(Resource.class))
+			{
+				Resource object = (Resource) stmt.getObject().as(Resource.class);
+				if (object.isAnon() || (uri != null && object.getURI().startsWith(uri))) {
+					addReachableStmts(source, dest, object, uri);
+				}
+			}
+		}
+	}
+	
+	/**
+	 * Add the namespace prefix mappings from a source model to a destination
+	 * model. A prefix mapping associates a qualified name (e.g. 'moby') with
+	 * a full URL (e.g. 'http://www.s-moby.org:8080/terms/'). In case a prefix
+	 * is already in the destination model, then use the next available prefix
+	 * formed by adding a number to the end of the prefix (e.g. if 'foo' is
+	 * taken, then add 'foo_1' if it is available, or 'foo_2' if not...).
+	 */
+	public static void addNsPrefixes(Model source, Model dest)
+	{
+		Map prefixes = source.getNsPrefixMap();
+		Iterator it = prefixes.keySet().iterator();
+		
+		while (it.hasNext())
+		{
+			// Prefix and associated URI to be added
+			//
+			String prefix = it.next().toString();
+			String uri = prefixes.get(prefix).toString();
+			
+			// Check to see if the prefix is already in the destination model
+			//
+			String prevURI = dest.getNsPrefixURI(prefix);
+			
+			if (prevURI == null)
+			{
+				// Not used, so just add it
+				//
+				dest.setNsPrefix(prefix, uri);
+			}
+			else if (! prevURI.equals(uri))
+			{
+				// Used and doesn't match previous, so add the next
+				// available prefix
+				//
+				boolean added = false;
+				for (int i = 1; (! added); i++)
+				{
+					String newPrefix = prefix + "_" + i;
+					if (dest.getNsPrefixURI(newPrefix) == null)
+					{
+						dest.setNsPrefix(newPrefix, uri);
+						added = true;
+					}
+				}
+			}
+		}
+	}
+	
+	/**
+	 * Remove unused namespace prefixes from the given model.
+	 */
+	public static void removeUnusedNsPrefixes(Model model)
+	{
+		Map newMap = new HashMap();
+		
+		for (NsIterator it = model.listNameSpaces(); it.hasNext();)
+		{
+			String uri = it.nextNs();
+			String prefix = model.getNsURIPrefix(uri);
+			newMap.put(prefix, uri);
+		}
+		
+		List toRemove = new ArrayList();
+		Iterator it = model.getNsPrefixMap().keySet().iterator();
+		while (it.hasNext()) {
+			toRemove.add(it.next());
+		}
+		it = toRemove.iterator();
+		while (it.hasNext()) {
+			model.removeNsPrefix(it.next().toString());
+		}
+		
+		model.setNsPrefixes(newMap);
+	}
 }



From gss at pub.open-bio.org  Fri Jun 18 21:39:42 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:39:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182139.i5ILdgl7029933@pub.open-bio.org>


gss
Fri Jun 18 17:39:42 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv29908/src/org/smoby/vocabulary

Modified Files:
	MOBY.java 
Log Message:
Added nsPrefix methods

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/17 17:34:17	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java	2004/06/18 21:39:42	1.4
@@ -13,6 +13,16 @@
         return "http://www.s-moby.org:8080/terms/";
     }
     
+    public static String getNsPrefix()
+    {
+    	return "moby";
+    }
+    
+    public static void addNsPrefix(Model model)
+    {
+    	model.setNsPrefix(getNsPrefix(), getURI()); 
+    }
+    
     public static final Resource Provider   		= resource(getURI(), "Provider");
     public static final Resource Graph      		= resource(getURI(), "Graph");
     public static final Resource Subject    		= resource(getURI(), "Subject");



From gss at pub.open-bio.org  Fri Jun 18 21:41:58 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:41:58 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182141.i5ILfwfr030037@pub.open-bio.org>


gss
Fri Jun 18 17:41:58 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools
In directory pub.open-bio.org:/tmp/cvs-serv30012/WebRoot/tools

Modified Files:
	client.html 
Log Message:
Minor small fixes

moby-live/S-MOBY/ref-impl/server/WebRoot/tools client.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html	2004/06/14 22:04:20	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/tools/client.html	2004/06/18 21:41:58	1.3
@@ -1,42 +1,53 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
 <html>
-<head>
-  <title>Semantic MOBY Client Tools</title>
-</head>
-<body>
-	<table style="text-align: center; width: 100%;" border="1"
+  <head>
+    <meta name="generator" content="HTML Tidy, see www.w3.org">
+
+    <title>Semantic MOBY Client Tools</title>
+  </head>
+
+  <body>
+    <table style="WIDTH: 100%; TEXT-ALIGN: center" border="1"
     cellspacing="0" cellpadding="0">
-    <tbody>
-      <tr>
-        <td style="vertical-align: top; background-color: rgb(204, 204, 204);">
-      	  <b>Semantic MOBY Client Tools</b>
-        </td>
-      </tr>
-    </tbody>
-  </table>
-
-<h4><u>Suggest a provider URL for S-MOBY to explore</u></h4>
-<form action="http://www.s-moby.org:8080/investigate" method="post">
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Provider URL:
-  <input size="60" name="provider-url">&nbsp;&nbsp;
-  <input value="Suggest" type="submit">
-</form>
-
-<h4><u>Discover matching graphs in the S-MOBY metadata repository</u></h4>
-<form action="http://www.s-moby.org:8080/find-providers" method="post">
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Paste a graph in RDF/XML format, select
-  statements to return, and press "Discover" to find matching graphs. &nbsp;&nbsp;
-  <p>
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-  Statements to return:&nbsp;&nbsp;
-  <input type="radio" name="statements" value="minimal">Minimal&nbsp;&nbsp;
-  <input type="radio" name="statements" value="query" CHECKED>Query only&nbsp;&nbsp;
-  <input type="radio" name="statements" value="cached">Cached&nbsp;&nbsp;
-  <input value="Discover" type="submit">
-  <p>
-  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-  <textarea cols="80" rows="15" name="query-graph"></textarea>
-</form>
+      <tbody>
+        <tr>
+          <td style=
+          "VERTICAL-ALIGN: top; BACKGROUND-COLOR: rgb(204,204,204)">
+          <b>Semantic MOBY Client Tools</b></td>
+        </tr>
+      </tbody>
+    </table>
+
+    <h4><u>Suggest a provider URL for S-MOBY to explore</u></h4>
+
+    <form action="http://www.s-moby.org:8080/investigate" method=
+    "post">
+      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Provider URL: <input size=
+      "60" name="provider-url">&nbsp;&nbsp; <input value="Suggest"
+      type="submit">
+    </form>
+
+    <h4><u>Discover matching graphs in the S-MOBY metadata
+    repository</u></h4>
+
+    <form action="http://www.s-moby.org:8080/find-providers" method=
+    "post">
+      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Paste a graph in RDF/XML
+      format, select statements to return, and press "Discover" to find
+      matching graphs. &nbsp;&nbsp; 
+
+      <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Statements to
+      return:&nbsp;&nbsp; <input type="radio" name="statements" value=
+      "minimal">Minimal&nbsp;&nbsp; <input type="radio" name=
+      "statements" value="query">Query only&nbsp;&nbsp; <input type=
+      "radio" name="statements" value="reachable" checked=
+      "">Reachable&nbsp; <input value="Discover" type="submit"></p>
 
-</body>
+      <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <textarea name=
+      "query-graph" rows="15" cols="80">
+          
+      </textarea></p>
+    </form>
+  </body>
 </html>



From gss at pub.open-bio.org  Fri Jun 18 21:42:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:42:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182142.i5ILgYdP030067@pub.open-bio.org>


gss
Fri Jun 18 17:42:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv30042/src/org/smoby/ref/tools

Modified Files:
	DiscoveryQuery.java 
Log Message:
Changes to utilize single model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools DiscoveryQuery.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/06/10 23:24:16	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/06/18 21:42:34	1.6
@@ -6,6 +6,7 @@
 
 import org.smoby.parser.*;
 import org.smoby.ref.tools.db.*;
+import org.smoby.tools.Util;
 import org.smoby.graph.*;
 import org.smoby.graph.impl.*;
 import org.smoby.vocabulary.*;
@@ -16,6 +17,7 @@
 import com.hp.hpl.jena.rdql.*;
 import com.hp.hpl.jena.shared.*;
 import com.hp.hpl.jena.util.iterator.*;
+import com.hp.hpl.jena.vocabulary.RDF;
 
 /**
  * This class finds graphs that match a query graph.
@@ -23,22 +25,24 @@
 public class DiscoveryQuery
 {
     /**
-     * Constant indicating that only the URI should be returned
-     * in each matching graph.
+     * Constant indicating that only the minimal statements should
+     * be returned in each matching graph.
      */
-    public final static int URI_ONLY = 0;
+    private final static int MINIMAL_STMTS = 0;
     
     /**
      * Constant indicating that only statements in the query should
      * be returned in each matching graph.
      */
-    public final static int QUERY_STMTS_ONLY = 1;
+    private final static int QUERY_STMTS = 1;
     
     /**
-     * Constants indicating that all statements (i.e. the ones found when
-     * the graph was registered) should be returned in each matching graph.
+     * Constant indicating that all reachable statements (i.e. the
+     * ones that can be traversed, starting with the provider node,
+     * without leaving the scope of the provider's URI) should be
+     * returned in each matching graph.
      */
-    public final static int ALL_STMTS = 2;
+    private final static int REACHABLE_STMTS = 2;
     
     /**
      * The graph that serves as a template for providers that match.
@@ -62,6 +66,21 @@
      */
     private int lastBnodeNumber;
     
+    public static DiscoveryQuery newMinimalStmtsQuery(MOBYProvider provider)
+    {
+    	return new DiscoveryQuery(provider, MINIMAL_STMTS);
+    }
+    
+    public static DiscoveryQuery newQueryStmtsQuery(MOBYProvider provider)
+    {
+    	return new DiscoveryQuery(provider, QUERY_STMTS);
+    }
+    
+    public static DiscoveryQuery newReachableStmtsQuery(MOBYProvider provider)
+    {
+    	return new DiscoveryQuery(provider, REACHABLE_STMTS);
+    }
+    
     /**
      * Create an instance for the given query graph and return statements
      * style.
@@ -69,7 +88,7 @@
      * @param statementsToReturn which statements should be returned: URI_ONLY,
      * QUERY_STMTS_ONLY, or ALL_STMTS (use the static constants on this class).
      */
-    public DiscoveryQuery(MOBYProvider queryProvider, int statementsToReturn)
+    private DiscoveryQuery(MOBYProvider queryProvider, int statementsToReturn)
     {
     	this.queryProvider = queryProvider;
         this.statementsToReturn = statementsToReturn;
@@ -85,21 +104,22 @@
         lastBnodeNumber = 0;
     }
     
-    public MOBYCollection findMatchingGraphs()
+    public MOBYProviderSet findMatchingGraphs()
 	{
         init();
         
+        Model dbModel = null;
 		try
 		{
 		    Model queryModel = ((MOBYProviderImpl) queryProvider).getUnderlying();
             String queryString = buildQueryString(queryModel);
             StorageManager manager = new StorageManager();
-            Model model = manager.openDBModel();
-            ((ModelRDB) model).setDoFastpath(false);
+            dbModel = manager.openDBModel();
+            ((ModelRDB) dbModel).setDoFastpath(false);
             
 			// Execute the query
 			//
-			QueryResults results = Query.exec(queryString, model);
+			QueryResults results = Query.exec(queryString, dbModel);
 			ArrayList matching = new ArrayList();
             
 			while (results.hasNext())
@@ -109,23 +129,27 @@
 			}
 			results.close();
 			
-			List returnList = new ArrayList();
+			MOBYProviderSet returnSet = MOBYObjectFactory.newProviderSet();
 			
 			for (Iterator it = matching.iterator(); it.hasNext();)
 			{
-				MOBYProvider mp = buildGraphModel(queryModel, (ResultBinding) it.next());
-				String uri = mp.getURI();
-				// YUCK!
-				Model providerModel = manager.openModel(uri);
-				Parser parser = new Parser(providerModel);
-				returnList.add(parser.parseProvider());
+				Object next = it.next();
+				MOBYProvider mp = buildGraphModel(dbModel,
+					queryModel, (ResultBinding) next);
+				returnSet.addProvider(mp);
 			}
 			
-			return MOBYObjectFactory.newUnorderedCollection(null, returnList, null);
+			return returnSet;
 			
 		} catch (Throwable t) {
 			return null;
 		}
+		finally
+		{
+			if (dbModel != null) {
+				dbModel.close();
+			}
+		}
 	}
 	
 	/**
@@ -221,11 +245,12 @@
 	 * @param binding bindings for variables
 	 * @return
 	 */
-	private MOBYProvider buildGraphModel(Model queryModel, ResultBinding binding)
+	private MOBYProvider buildGraphModel(
+		Model dbModel, Model queryModel, ResultBinding binding)
 	{
 		// Create a default model to return
 		//
-		Model model = ModelFactory.createDefaultModel();
+		Model model = Util.newJenaModel();
 		model.setNsPrefixes(queryModel.getNsPrefixMap());
 		
 		// For each statement in the query, create a new statement
@@ -244,10 +269,117 @@
 			Statement copy = model.createStatement(subject, property, object);
 			model.add(copy);
 		}
-		Parser parser = new Parser(model);
+		
+		// Add/remove statements based on the desired set, i.e.
+		// based on the value of statementsToReturn, and remove
+		// unused namespace prefixes from the model.
+		//
+		Model adjusted = adjustedModel(model, dbModel);
+		Util.removeUnusedNsPrefixes(adjusted);
+		
+		// Parse and return a MOBY provider using the adjusted model
+		//
+		Parser parser = new Parser(adjusted);
 		return parser.parseProvider();
 	}
 	
+	/**
+	 * Given a model built from the query template model, return a
+	 * model adjusted to include the statements to match the
+	 * statementsToReturn instance variable. The models that result
+	 * from performing a query consists of exactly the statements
+	 * that were in the query, with some blank nodes filled in. In
+	 * the case of QUERY_STMTS, that is the set that should be
+	 * returned. In the case of MINIMAL_STMTS, only the provider
+	 * type, name, one line description, and about URI statements
+	 * should be returned. In the case of REACHABLE_STMTS, all the
+	 * statements that are reachable from the provider URI, without
+	 * going outside the provider URI's scope, should be returned.
+	 */
+	private Model adjustedModel(Model original, Model dbModel)
+	{
+		switch (statementsToReturn)
+		{
+			case QUERY_STMTS	: return original;
+			case MINIMAL_STMTS	: return minimalModel(original, dbModel);
+			default				: return reachableModel(original, dbModel);
+		}
+	}
+	
+	/**
+	 * Return a model consisting of just the (rdf:type moby:Provider),
+	 * (moby:name <name>), (moby:oneLineDescription <description>), and
+	 * (moby:aboutURI <uri>) property statements for the provider.
+	 */
+	private Model minimalModel(Model original, Model dbModel)
+	{
+		Model minimal = Util.newJenaModel();
+		minimal.setNsPrefixes(dbModel.getNsPrefixMap());
+		
+		// Add the rdf:type MOBY:Provider statement
+		//
+		try {
+			Statement providerTypeStmt = original.listStatements(
+				null, RDF.type, MOBY.Provider).nextStatement();
+			minimal.add(providerTypeStmt);
+			
+			Resource subject = providerTypeStmt.getSubject();
+			
+			// Add a statement, if it exists in the repository, that
+			// says (<subject> moby:name <name>)
+			//
+			try {
+				minimal.add(dbModel.listStatements(subject,
+					MOBY.name, (RDFNode) null).nextStatement());
+			} catch (Throwable t) {} // There was no moby:name property
+
+			// Add a statement, if it exists in the repository, that
+			// says (<subject> moby:aboutURI <uri>)
+			//
+			try {
+				minimal.add(dbModel.listStatements(subject,
+					MOBY.aboutURI, (RDFNode) null).nextStatement());
+			} catch (Throwable t) {} // There was no moby:aboutURI property
+
+			// Add a statement, if it exists in the repository, that
+			// says <subject> moby:oneLineDescription <value>
+			//
+			try {
+				minimal.add(dbModel.listStatements(subject,
+					MOBY.oneLineDescription, (RDFNode) null).nextStatement());
+			} catch (Throwable t) {} // There was no moby:oneLineDescription
+		}
+		catch (Throwable t) {} // There was no (rdf:type moby:Provider)
+		
+		return minimal;
+	}
+	
+	/**
+	 * Return a model consisting of the statements in the original (query)
+	 * model, plus any statements not already in the model that are
+	 * reachable from the subject of the rdf:type moby:Provider statement.
+	 */
+	private Model reachableModel(Model original, Model dbModel)
+	{
+		// Start with a model consisting of the original statements
+		//
+		Model reachable = ModelFactory.createDefaultModel();
+		reachable.setNsPrefixes(dbModel.getNsPrefixMap());
+		reachable.add(original);
+		
+		// Find the subject of the (rdf:type MOBY:Provider) statement
+		//
+		try {
+			Statement providerTypeStmt = original.listStatements(
+				null, RDF.type, MOBY.Provider).nextStatement();
+			Resource subject = providerTypeStmt.getSubject();
+			Util.addReachableStmts(dbModel, reachable, subject, subject.getURI());
+		}
+		catch (Throwable t) {} // There was no (rdf:type moby:Provider)
+		
+		return reachable;
+	}
+	
 	private RDFNode getBinding(RDFNode node, ResultBinding binding)
 	{
 		// If the resource is not a blank node, then just return the
@@ -256,23 +388,16 @@
 		if (! node.asNode().isBlank()) {
 			return node;
 		}
-		//ResultBinding
 		ResultBindingIterator results = binding.iterator();
 		
 		while (results.hasNext())
 		{
-			Object object = results.next();
-			Value value = (Value) object;
+			results.next();
 			String varName = results.varName();
-//			Value value = results.value();
+			RDFNode value = (RDFNode) binding.get(varName);
 			Object cachedName = varNames.get(node.toString());
-			if (varName.equals(cachedName))
-			{
-//				if (value.isRDFLiteral()) {
-//					return value.getRDFLiteral();
-//				} else if (value.isRDFResource()) {
-//					return value.getRDFResource();
-//				}
+			if (varName.equals(cachedName)) {
+				return value;
 			}
 		}
 		return node;



From gss at pub.open-bio.org  Fri Jun 18 21:42:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:42:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182142.i5ILgYea030086@pub.open-bio.org>


gss
Fri Jun 18 17:42:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db
In directory pub.open-bio.org:/tmp/cvs-serv30042/src/org/smoby/ref/tools/db

Modified Files:
	StorageManager.java 
Log Message:
Changes to utilize single model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/06/16 23:33:00	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/06/18 21:42:34	1.5
@@ -3,6 +3,7 @@
 import org.smoby.graph.*;
 import org.smoby.graph.impl.*;
 import org.smoby.ref.tools.*;
+import org.smoby.tools.Util;
 import org.smoby.vocabulary.*;
 import com.hp.hpl.jena.db.*;
 import com.hp.hpl.jena.rdf.model.*;
@@ -83,11 +84,16 @@
             while (it.hasNext()) {
             	Statement stmt = it.nextStatement();
             	Resource subject = stmt.getSubject();
-            	if (subject.isAnon() || subject.getURI().startsWith(uriString)) {
+            	String subjectURI = subject.getURI();
+            	if (subject.isAnon() ||
+            		((subjectURI != null) &&
+            		  subjectURI.startsWith(uriString))) {
             		dbModel.add(stmt);
             	}
             }
             
+            Util.addNsPrefixes(model, dbModel);
+            
             // Add a statement asserting when the model was added
             //
             if (lastModifiedDate != null) {



From gss at pub.open-bio.org  Fri Jun 18 21:42:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:42:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182142.i5ILgYid030106@pub.open-bio.org>


gss
Fri Jun 18 17:42:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets
In directory pub.open-bio.org:/tmp/cvs-serv30042/src/org/smoby/ref/servlets

Modified Files:
	DiscoveryServlet.java 
Log Message:
Changes to utilize single model

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets DiscoveryServlet.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/06/14 20:59:36	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/06/18 21:42:34	1.4
@@ -2,8 +2,7 @@
 
 import org.smoby.servlet.*;
 import org.smoby.graph.*;
-import org.smoby.parser.NonCanonicalException;
-import org.smoby.parser.Parser;
+import org.smoby.parser.*;
 import org.smoby.ref.tools.*;
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.rdql.*;
@@ -17,11 +16,15 @@
  * search the metadata repository for graphs that unify with a query graph
  * in the Prolog sense. The query graph should be sent via HTTP POST in a
  * parameter named "query-graph"; a set of matching graphs is returned in
- * the response body in either human-readable text format (the default),
- * or in an efficient, machine-readable binary format. To receive the
- * response in this binary format, the client should send a parameter
- * named "binary-return" in the request, with any value. The client can
- * obtain a Java object suitable for parsing either binary or text format
+ * the response body. The statements to be included in each matching graph
+ * is controlled by sending a parameter named "statements".  If the value
+ * of the parameter is "minimal", then only a small set of statements is
+ * returned, namely the statements that encode the name, one line
+ * description, and URI of the provider. If the value of the parameter is
+ * "reachable", then all statements reachable from the provider node are
+ * returned for each matching provider.
+ * 
+ * The client can obtain a Java object suitable for parsing the graph
  * into an array of ProviderDescriptionGraph objects, by calling the
  * GraphListTransceiverFactory.newReceiver() factory method.
  */
@@ -42,14 +45,30 @@
             //
 			Parser parser = Parser.forString(graphString, Parser.LANGUAGE_RDF_XML);
 			MOBYProvider provider = parser.parseProvider();
+			
+			// Find which statements the user wishes to have returned
+			//
+			String statements = ParamReader.getParameter(
+				"statements", request, false, new String[] {
+					"minimal", "query", "reachable"
+				});
             
             // Retrieve an array of provider description graphs that unify with
             // the query graph.
             //
-            DiscoveryQuery q = new DiscoveryQuery(provider, DiscoveryQuery.ALL_STMTS);
-			MOBYCollection matching = q.findMatchingGraphs();
+            DiscoveryQuery q = null;
+            
+            if (statements.equalsIgnoreCase("minimal")) {
+            	q = DiscoveryQuery.newMinimalStmtsQuery(provider);
+            } else if (statements.equalsIgnoreCase("query")) {
+            	q = DiscoveryQuery.newQueryStmtsQuery(provider);
+            } else {
+            	q = DiscoveryQuery.newReachableStmtsQuery(provider);
+            }
+            
+			MOBYProviderSet matching = q.findMatchingGraphs();
 			
-            if ((matching.size() == 0))
+            if ((matching == null) || (matching.size() == 0))
             {
                 // The client doesn't want the graphs sent in a binary
                 // format, so show a text message indicating that there
@@ -59,20 +78,10 @@
             }
             else
             {
-                for (Iterator it = matching.iterator(); it.hasNext();) {
-                    MOBYProvider p = (MOBYProvider) it.next();
-                    p.serialize(out);
-                }
+            	matching.serialize(out);
 			}
             
 		}
-//		catch (NonCanonicalException e)
-//		{
-//            // The query graph did not have the required canonical form
-//            //
-//			response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE,
-//				"Query graph is not canonical:\n" + e);
-//		}
 		catch (ParameterException e)
         {
             // The graph parameter was missing



From gss at pub.open-bio.org  Fri Jun 18 21:45:07 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 18 Jun 2004 17:45:07 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406182145.i5ILj7TR030161@pub.open-bio.org>


gss
Fri Jun 18 17:45:07 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery
In directory pub.open-bio.org:/tmp/cvs-serv30132/S-MOBY/ref-impl/queries/discovery

Modified Files:
	query.rdf query.n3 
Log Message:
Changed prefix mappings for go, sgd, and moby

moby-live/S-MOBY/ref-impl/queries/discovery query.rdf,1.2,1.3 query.n3,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf	2004/06/10 23:28:06	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.rdf	2004/06/18 21:45:07	1.3
@@ -1,27 +1,27 @@
 <rdf:RDF
-    xmlns:go="http://www.go.org:8080/terms#"
+    xmlns:sgd="http://www.sgd.org:8080/terms/"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:moby="http://www.s-moby.org:8080/terms#"
-    xmlns:sgd="http://www.sgd.org:8080/terms#" >
+    xmlns:go="http://www.go.org:8080/terms/"
+    xmlns:moby="http://www.s-moby.org:8080/terms/" >
   <rdf:Description rdf:nodeID="A0">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <moby:hasMapping rdf:nodeID="A1"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-    <rdf:_1 rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Object"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms/LiteratureGuide"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A1">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <moby:mapsTo rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Provider"/>
+    <moby:operatesOn rdf:nodeID="A2"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A3">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Graph"/>
+    <moby:hasMapping rdf:nodeID="A4"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A2">
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A3"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A4">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <moby:operatesOn rdf:nodeID="A2"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms/GeneSymbol"/>
+    <moby:mapsTo rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms/Subject"/>
   </rdf:Description>
 </rdf:RDF>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3	2004/06/10 23:27:58	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/queries/discovery/query.n3	2004/06/18 21:45:07	1.3
@@ -1,6 +1,6 @@
- at prefix go:       <http://www.go.org:8080/terms#> .
- at prefix sgd:      <http://www.sgd.org:8080/terms#> .
- at prefix moby:     <http://www.s-moby.org:8080/terms#> .
+ at prefix go:       <http://www.go.org:8080/terms/> .
+ at prefix sgd:      <http://www.sgd.org:8080/terms/> .
+ at prefix moby:     <http://www.s-moby.org:8080/terms/> .
 @prefix rdf:      <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 
 _:provider



From mwilkinson at pub.open-bio.org  Thu Jun 24 22:30:38 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 24 Jun 2004 18:30:38 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242230.i5OMUcqB032091@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:30:38 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor
In directory pub.open-bio.org:/tmp/cvs-serv32073/MOBY/Adaptor

Log Message:
Directory /home/repository/moby/moby-live/Perl/MOBY/Adaptor added to the repository

moby-live/Perl/MOBY/Adaptor - New directory
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/RCS/directory,v: No such file or directory



From mwilkinson at pub.open-bio.org  Thu Jun 24 22:30:52 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 24 Jun 2004 18:30:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242230.i5OMUqtw032135@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:30:52 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby
In directory pub.open-bio.org:/tmp/cvs-serv32117/MOBY/Adaptor/moby

Log Message:
Directory /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby added to the repository

moby-live/Perl/MOBY/Adaptor/moby - New directory
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/RCS/directory,v: No such file or directory



From mwilkinson at pub.open-bio.org  Thu Jun 24 22:31:00 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 24 Jun 2004 18:31:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242231.i5OMV0VT032179@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:31:00 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory pub.open-bio.org:/tmp/cvs-serv32161/MOBY/Adaptor/moby/queryapi

Log Message:
Directory /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi added to the repository

moby-live/Perl/MOBY/Adaptor/moby/queryapi - New directory
rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/RCS/directory,v: No such file or directory



From mwilkinson at pub.open-bio.org  Thu Jun 24 22:32:38 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 24 Jun 2004 18:32:38 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242232.i5OMWcgc032293@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:32:38 EDT 2004
Update of /home/repository/moby/moby-live/Perl
In directory pub.open-bio.org:/tmp/cvs-serv32274

Modified Files:
	MANIFEST 
Log Message:
stratifying the SQL away from the MOBY Central module so that we can have a variety of underlying databases or SW-based data stores with teh MOBY Central API on top of them

moby-live/Perl MANIFEST,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MANIFEST,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MANIFEST	2004/06/15 00:37:55	1.10
+++ /home/repository/moby/moby-live/Perl/MANIFEST	2004/06/24 22:32:38	1.11
@@ -4,9 +4,9 @@
 Makefile.PL
 MOBY/authority.pm
 MOBY/central_db_connection.pm
-MOBY/mysql.pm
 MOBY/OntologyServer.pm
 MOBY/Config.pm
+MOBY/dbConfig.pm
 MOBY/CommonSubs.pm
 MOBY/CrossReference.pm
 MOBY/service_instance.pm
@@ -22,6 +22,8 @@
 MOBY/Client/ServiceInstance.pm
 MOBY/Client/SimpleArticle.pm
 MOBY/Client/Service.pm
+MOBY/Adaptor/moby/queryapi.pm
+MOBY/Adaptor/moby/queryapi/mysql.pm
 t/Client-Central.t
 scripts/debugYourService
 scripts/MOBY-Central.pl



From mwilkinson at pub.open-bio.org  Thu Jun 24 22:32:39 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 24 Jun 2004 18:32:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242232.i5OMWd8f032347@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:32:38 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv32274/MOBY

Modified Files:
	Central.pm Config.pm OntologyServer.pm 
	central_db_connection.pm collection_input.pm 
	collection_output.pm service_instance.pm simple_input.pm 
	simple_output.pm 
Added Files:
	dbConfig.pm 
Log Message:
stratifying the SQL away from the MOBY Central module so that we can have a variety of underlying databases or SW-based data stores with teh MOBY Central API on top of them

moby-live/Perl/MOBY dbConfig.pm,NONE,1.1 Central.pm,1.130,1.131 Config.pm,1.2,1.3 OntologyServer.pm,1.44,1.45 central_db_connection.pm,1.4,1.5 collection_input.pm,1.1,1.2 collection_output.pm,1.1,1.2 service_instance.pm,1.4,1.5 simple_input.pm,1.3,1.4 simple_output.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.130
retrieving revision 1.131
diff -u -r1.130 -r1.131
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/16 01:15:30	1.130
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/06/24 22:32:38	1.131
@@ -10,8 +10,6 @@
 use strict;
 use Carp;
 use vars qw($AUTOLOAD $WSDL_TEMPLATE);
-use DBI;
-use DBD::mysql;
 use XML::DOM;
 use MOBY::OntologyServer;
 use MOBY::service_type;
@@ -183,28 +181,6 @@
 	return 0;
 }
 
-sub _dbAccess {
-
-    my $conf = MOBY::Config->new;
-
-    my $username = $conf->{mobycentral}->{username};
-    my $password = $conf->{mobycentral}->{password};
-    my $port = $conf->{mobycentral}->{port};
-    my $dbname = $conf->{mobycentral}->{dbname};
-    my $url = $conf->{mobycentral}->{url};
-    
-	#my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
-	#my $dbname = $ENV{MOBY_CENTRAL_DBNAME}; chomp $dbname;
-	#my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
-	#my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
-	#my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
-	
-	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
-	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
-	
-	return ($dbh);
-}
-
 
 =head2 registerObjectClass
 
@@ -1264,7 +1240,7 @@
                     object_type_uri	=> $typeURI,
                     namespace_type_uris	=> $namespace_string,
                     article_name 	=> $article,
-                    collection_input_id 	=> 	$collid,
+                    collection_output_id 	=> 	$collid,
                     );
             unless ($soutput){
        			$SVC->DELETE_THYSELF; return (-1,"registration failed during registration of output object $typeURI.  Unknown reasons.");

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Config.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/Config.pm	2004/06/15 01:15:16	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/Config.pm	2004/06/24 22:32:38	1.3
@@ -6,8 +6,13 @@
 
 use strict;
 use Carp;
+use MOBY::dbConfig;
 use vars qw($AUTOLOAD);
 use Text::Shellwords;
+use vars '$VERSION','@ISA','@EXPORT','$CONFIG';
+
+ at ISA = qw(Exporter);
+ at EXPORT = ('$CONFIG');
 
 {
 	#Encapsulated class data
@@ -16,6 +21,11 @@
 	#ATTRIBUTES
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
+				   mobycentral	=> 	[undef,			'read/write'],
+				   mobyobject	=> 	[undef,			'read/write'],
+				   mobynamespace=> 	[undef,			'read/write'],
+				   mobyservice	=> 	[undef,			'read/write'],
+				   mobyrelationship	=> 	[undef,			'read/write'],
                     );
 
    #_____________________________________________________________
@@ -41,15 +51,14 @@
 
 }
 
-sub id {
-	my ($self, $val) =@_;
-	$self->registration_id($val) if defined $val;
-	return $self->registration_id;
-}
+# the expected sectionons (listed above) will have their dbCOnfig objects available
+# as methods.  The unexpected sections will have their dbConfig objects available
+# by $dbConfig = $CONFIG->{section_title}
 
 sub new {
 	my ($caller, %args) = @_;
 	
+#print STDERR "creating MOBY::Config\n";
 	my $caller_is_obj = ref($caller);
     my $class = $caller_is_obj || $caller;
 
@@ -65,32 +74,69 @@
     }
 
     my $file = $ENV{MOBY_CENTRAL_CONFIG};
-    chomp $file;
+	$file || die "can't open MOBY Configuration file $!\n";
+    
+	chomp $file;
     if ((-e $file) && (!(-d $file))){
         open IN, $file || die "can't open MOBY Configuration file $!\n";
     }
-    
-    while (my $l = <IN>){
-        chomp $l;
-        next if $l=~/\s*\#/;  # ignore comments
-        
-        if ($l=~/\[(\w+)\]/){
-            my $key = $1;
-            while (my $l2 = <IN>){
-                chomp $l2;
-                last unless ($l2 =~ /\S/);
-                my @terms = shellwords($l2);
-                last unless (scalar @terms > 2);
-                
-                $self->{$key}->{$terms[0]} = $terms[2];
-            }
-        }
-    }
+    my @sections = split /(\[\s*\S+\s*\][^\[]*)/s, join "", <IN>;
+#print STDERR "split into @sections\n";
+	foreach my $section (@sections){
+#print STDERR "calling MOBY::dbConfig\n";
+		my $dbConfig = MOBY::dbConfig->new(section => $section);  # this is an object full of strings, no actual connections.  It represents the information in the config file
+		next unless $dbConfig;
+		my $dbname = $dbConfig->section_title;
+		next unless $dbname;
+#print STDERR "setting the COnfig dbConfig for the title $dbname with object $dbConfig\n\n";
+		$self->{$dbname} = $dbConfig;
+	}
 
+	$CONFIG = $self;
     return $self;
 
 }
 
+sub getDataAdaptor {
+	my ($self, %args) = @_;
+	
+	my $source = $args{datasource};
+	$source ||= $args{source};
+	$source ||="mobycentral";
+	
+	if ($self->{"${source}Adaptor"}){return $self->{"${source}Adaptor"}};  # read from cache
+
+    my $username = $self->$source->{username};  # $self->source returns a MOBY::dbConfig object
+    my $password = $self->$source->{password};
+    my $port = $self->$source->{port};
+    my $dbname = $self->$source->{dbname};
+    my $url = $self->$source->{url};
+	my $adaptor = $self->$source->{adaptor};
+	my $sourcetype = $self->$source->{sourcetype};
+	
+	eval "require $adaptor";
+	return undef if $@;
+	eval "require $sourcetype";
+	return undef if $@;
+	
+	my $ADAPTOR = $adaptor->new(  # by default, this is queryapi
+								source => $source,
+								username => $username,
+								password => $password,
+								port => $port,
+								dbname => $dbname,
+								url => $url,
+								sourcetype => $sourcetype,
+							   );
+	if ($ADAPTOR){
+		$self->{"${source}Adaptor"} = $ADAPTOR;  # cache it
+		return $ADAPTOR;
+	} else {
+		return undef
+	}
+	
+}
+
 sub DESTROY {}
 
 sub AUTOLOAD {

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.44
retrieving revision 1.45
diff -u -r1.44 -r1.45
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/15 14:55:17	1.44
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/06/24 22:32:38	1.45
@@ -140,20 +140,23 @@
     $self->ontology eq 'service' && $self->database('mobyservice');
     $self->ontology eq 'relationship' && $self->database('mobyrelationship');
 
-	
-	my $conf = MOBY::Config->new;
-	$self->username($conf->{$self->database}->{username}) unless $self->username;
-    $self->password($conf->{$self->database}->{password}) unless $self->password;
-    $self->port($conf->{$self->database}->{port}) unless $self->port;
-    $self->host($conf->{$self->database}->{url}) unless $self->host;
+#print STDERR "\n\nCONFIG object is $CONFIG\n\n";
+	$CONFIG ||=MOBY::Config->new;
+#print STDERR "got username ",($CONFIG->{mobycentral}->{username})," for mobycentral\n";
+	$self->username($CONFIG->{$self->database}->{username}) unless $self->username;
+    $self->password($CONFIG->{$self->database}->{password}) unless $self->password;
+    $self->port($CONFIG->{$self->database}->{port}) unless $self->port;
+    $self->host($CONFIG->{$self->database}->{url}) unless $self->host;
  
 	my $host = $self->host?$self->host:$ENV{MOBY_CENTRAL_URL}; chomp $host;
 	my $username = $self->username?$self->username:$ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
 	my $password = $self->password?$self->password:$ENV{MOBY_CENTRAL_DBPASS}; chomp $password if $password; $password =~ s/\s//g if $password;
     my $port = $self->port?$self->port:$ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
     
-    my ($dsn) = "DBI:mysql:".($conf->{$self->database}->{dbname}).":".($host).":".($port);
+    my ($dsn) = "DBI:mysql:".($CONFIG->{$self->database}->{dbname}).":".($host).":".($port);
 
+#print STDERR "\n\nDSN was $dsn\n\n";
+	
     my $dbh;
 #	$debug && &_LOG("connecting to db with params ",$self->database, $self->username, $self->password,"\n");
     if (defined $password){

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/15 01:00:26	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/central_db_connection.pm	2004/06/24 22:32:38	1.5
@@ -47,6 +47,7 @@
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
         db_connect_object => ["MOBY::mysql",        'read/write'],
+		datasource			=> ['mobycentral', 		'read/write'],
         #username => ["mobycentral",         'read/write'],
         #password => ["mobycentral",         'read/write'],        
         #dbname => ["mobycentral",       'read/write'],
@@ -108,25 +109,11 @@
     else {
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
-    #my $dbobj = $self->db_connect_object;
-    #my $dbh = &{$dbobj."::new"}(
-    #    $self->dbname,
-    #    $self->username,
-    #    $self->password,
-    #    $self->host,
-    #    $self->port);
-
-
-    my $conf = MOBY::Config->new;
-
-    my $username = $conf->{mobycentral}->{username};
-    my $password = $conf->{mobycentral}->{password};
-    my $port = $conf->{mobycentral}->{port};
-    my $dbname = $conf->{mobycentral}->{dbname};
-    my $url = $conf->{mobycentral}->{url};
-    	
-	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
-	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
+
+    $CONFIG ||= MOBY::Config->new;
+	
+	# getting the dbh is bad bad bad!!!
+	my $dbh = $CONFIG->getDataAdaptor(datasource => 'mobycentral')->dbh;
 	
     $self->dbh($dbh);
 	return $self;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/collection_input.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/collection_input.pm	2004/06/16 01:15:30	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/collection_input.pm	2004/06/24 22:32:38	1.2
@@ -1,9 +1,9 @@
-#!/usr/bin/perl -w
-
 package MOBY::collection_input;
 use strict;
 use Carp;
 use XML::DOM;
+use MOBY::Config;
+
 use vars qw($AUTOLOAD @ISA);
 
 
@@ -76,17 +76,6 @@
 
 }
 
-
-
-sub _dbh {
-    my ($self) = @_;
-    
-    my $central_connect = MOBY::central_db_connection->new();
-	$self->dbh($central_connect->dbh);
-	return $central_connect->dbh;
-	
-}
-
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -106,6 +95,7 @@
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
 
+
 	my $id = $self->WRITE;
 	$self->collection_input_id($id) if defined $id;
     return $self;
@@ -114,10 +104,13 @@
 
 sub WRITE {
 	my ($self) = @_;
-	my $dbh = $self->_dbh;
+	$CONFIG ||=MOBY::Config->new;  # exported by Config.pm
+	my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral');
+	my $id = $adaptor->insert_collection_input(
+									  service_instance => $self->service_instance_id,
+									  article_name	=> $self->article_name,
+									 );
 	
-	$dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($self->service_instance_id, $self->article_name));
-	my $id=$dbh->{mysql_insertid};
 	return $id;		
 }
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/collection_output.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/collection_output.pm	2004/06/16 01:15:30	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/collection_output.pm	2004/06/24 22:32:38	1.2
@@ -4,6 +4,8 @@
 use strict;
 use Carp;
 use XML::DOM;
+use MOBY::Config;
+
 use vars qw($AUTOLOAD @ISA);
 
 
@@ -76,17 +78,6 @@
 }
 
 
-
-sub _dbh {
-    my ($self) = @_;
-    
-    my $central_connect = MOBY::central_db_connection->new();
-	$self->dbh($central_connect->dbh);
-	return $central_connect->dbh;
-	
-}
-
-
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -115,10 +106,13 @@
 
 sub WRITE {
 	my ($self) = @_;
-	my $dbh = $self->_dbh;
+	$CONFIG ||=MOBY::Config->new;  # exported by Config.pm
+	my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral');
+	my $id = $adaptor->insert_collection_output(
+									  service_instance => $self->service_instance_id,
+									  article_name	=> $self->article_name,
+									 );
 	
-	$dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($self->service_instance_id, $self->article_name));
-	my $id=$dbh->{mysql_insertid};
 	return $id;		
 }
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm	2004/06/16 01:15:30	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm	2004/06/24 22:32:38	1.5
@@ -349,7 +349,7 @@
 				namespace_type_uris	=> $a{'namespace_type_uris'},
 				article_name 	=> $a{'article_name'},
 				service_instance_id	=> 	$self->service_instance_id,
-				collection_input_id 	=> 	$a{'collection_output_id'}
+				collection_output_id 	=> 	$a{'collection_output_id'}
 					   );
 
 	push @{$self->{outputs}}, $simple;

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm	2004/06/16 01:15:30	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm	2004/06/24 22:32:38	1.4
@@ -4,6 +4,7 @@
 use strict;
 use Carp;
 use XML::DOM;
+use MOBY::Config;
 use vars qw($AUTOLOAD @ISA);
 
 
@@ -80,17 +81,6 @@
 
 }
 
-
-sub _dbh {
-    my ($self) = @_;
-    
-    my $central_connect = MOBY::central_db_connection->new();
-	$self->dbh($central_connect->dbh);
-	return $central_connect->dbh;
-	
-}
-
-
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -116,25 +106,20 @@
 
 }
 
+
 sub WRITE {
-	my ($self) = @_;	
-	my $dbh = $self->_dbh;
+	my ($self) = @_;
+	$CONFIG ||=MOBY::Config->new;  # exported by Config.pm
+	my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral');
+	my $id = $adaptor->insert_simple_input(
+		object_type_uri => $self->object_type_uri,
+		namespace_type_uris => $self->namespace_type_uris,
+		article_name => $self->article_name,
+		service_instance_id => $self->service_instance_id,
+		collection_input_id => $self->collection_input_id,
+									 );
 	
-	$dbh->do("insert into simple_input
-				 (object_type_uri,
-				  namespace_type_uris,
-				  article_name,
-				  service_instance_id,
-				  collection_input_id)
-				 values (?,?,?,?,?)",
-		undef,
-		($self->object_type_uri,
-		$self->namespace_type_uris,
-		$self->article_name,
-		$self->service_instance_id,
-		$self->collection_input_id));
-	my $id=$dbh->{mysql_insertid};
-	return $id;
+	return $id;		
 }
 
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm	2004/06/16 01:15:30	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm	2004/06/24 22:32:38	1.3
@@ -3,6 +3,7 @@
 package MOBY::simple_output;
 use strict;
 use Carp;
+use MOBY::Config;
 use XML::DOM;
 use vars qw($AUTOLOAD @ISA);
 
@@ -80,17 +81,6 @@
 }
 
 
-
-sub _dbh {
-    my ($self) = @_;
-    
-    my $central_connect = MOBY::central_db_connection->new();
-	$self->dbh($central_connect->dbh);
-	return $central_connect->dbh;
-	
-}
-
-
 sub new {
 	my ($caller, %args) = @_;
 	
@@ -118,25 +108,20 @@
 
 sub WRITE {
 	my ($self) = @_;
-	my $dbh = $self->_dbh;	
-	$dbh->do("insert into simple_output
-				 (object_type_uri,
-				  namespace_type_uris,
-				  article_name,
-				  service_instance_id,
-				  collection_output_id)
-				 values (?,?,?,?,?)",
-		undef,
-		($self->object_type_uri,
-		$self->namespace_type_uris,
-		$self->article_name,
-		$self->service_instance_id,
-		$self->collection_output_id));
-	my $id=$dbh->{mysql_insertid};
+	$CONFIG ||=MOBY::Config->new;  # exported by Config.pm
+	my $adaptor = $CONFIG->getDataAdaptor(datasource => 'mobycentral');
+	my $id = $adaptor->insert_simple_output(
+		object_type_uri => $self->object_type_uri,
+		namespace_type_uris => $self->namespace_type_uris,
+		article_name => $self->article_name,
+		service_instance_id => $self->service_instance_id,
+		collection_output_id => $self->collection_output_id,
+									 );
+	
 	return $id;		
-
 }
 
+
 sub AUTOLOAD {
     no strict "refs";
     my ($self, $newval) = @_;



From mwilkinson at pub.open-bio.org  Thu Jun 24 22:32:39 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 24 Jun 2004 18:32:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242232.i5OMWd2M032362@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:32:39 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby
In directory pub.open-bio.org:/tmp/cvs-serv32274/MOBY/Adaptor/moby

Added Files:
	queryapi.pm 
Log Message:
stratifying the SQL away from the MOBY Central module so that we can have a variety of underlying databases or SW-based data stores with teh MOBY Central API on top of them

moby-live/Perl/MOBY/Adaptor/moby queryapi.pm,NONE,1.1


From mwilkinson at pub.open-bio.org  Thu Jun 24 22:32:39 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 24 Jun 2004 18:32:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406242232.i5OMWdAc032377@pub.open-bio.org>


mwilkinson
Thu Jun 24 18:32:39 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory pub.open-bio.org:/tmp/cvs-serv32274/MOBY/Adaptor/moby/queryapi

Added Files:
	mysql.pm 
Log Message:
stratifying the SQL away from the MOBY Central module so that we can have a variety of underlying databases or SW-based data stores with teh MOBY Central API on top of them

moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,NONE,1.1


From mwilkinson at pub.open-bio.org  Tue Jun 29 16:24:00 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 29 Jun 2004 12:24:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406291624.i5TGO06q025875@pub.open-bio.org>


mwilkinson
Tue Jun 29 12:23:59 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv25852/MOBY

Modified Files:
	CommonSubs.pm dbConfig.pm 
Log Message:
CommonSubs now accepts HTML markup in the service provision block.  LocalServices (the example services that I run) now correctly credit the SeqHound project.

moby-live/Perl/MOBY CommonSubs.pm,1.52,1.53 dbConfig.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.52
retrieving revision 1.53
diff -u -r1.52 -r1.53
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/06/15 00:37:55	1.52
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/06/29 16:23:59	1.53
@@ -1425,7 +1425,8 @@
     foreach my $n(0..($responses->getLength - 1)){
         my $resp = $responses->item($n);
         foreach my $response_component($resp->getChildNodes){
-            $content .= $response_component->toString;
+#            $content .= $response_component->toString;
+            $content .= $response_component->getNodeValue if ($response_component->getNodeType == TEXT_NODE);
         }
     }
     return ($content);

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm	2004/06/24 22:32:38	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/dbConfig.pm	2004/06/29 16:23:59	1.2
@@ -78,6 +78,7 @@
     $key = $self->_readSections($self->section);
 	#if ($@){die "MOBY Configuration file is misconfigured: dbConfig line 71\n";}
 #print STDERR "I received the key $key\n";
+    return undef unless $key;
     return undef unless $key =~ /\S/;
 #print STDERR "returning the dbConfig object for database title $key\n";
     $self->section_title($key);



From mwilkinson at pub.open-bio.org  Tue Jun 29 16:24:00 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 29 Jun 2004 12:24:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406291624.i5TGO0OP025895@pub.open-bio.org>


mwilkinson
Tue Jun 29 12:24:00 EDT 2004
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv25852/scripts/Services

Modified Files:
	LocalServices.pm 
Log Message:
CommonSubs now accepts HTML markup in the service provision block.  LocalServices (the example services that I run) now correctly credit the SeqHound project.

moby-live/Perl/scripts/Services LocalServices.pm,1.62,1.63
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.62
retrieving revision 1.63
diff -u -r1.62 -r1.63
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2004/02/23 21:31:53	1.62
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2004/06/29 16:24:00	1.63
@@ -46,6 +46,8 @@
 
 my $debug = 1;
 
+my $SeqHoundCredit = "This data is provided by <a HREF='http://seqhound.blueprint.org'>SeqHound</a>; <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12401134&dopt=Abstract'>Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW.  SeqHound: biological sequence and structure database as a platform forbioinformatics research. BMC Bioinformatics. 2002 Oct 25;3(1):32</a>";
+
 use vars qw(@ISA);
 
 ##################################################
@@ -118,7 +120,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 
@@ -152,7 +154,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getSHoundProteinsFromOrganism {  # WORKS
@@ -185,7 +187,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 
@@ -219,7 +221,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 
@@ -253,7 +255,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getSHoundGODBGetParentOf {  # WORKS
@@ -290,7 +292,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getSHoundGODBGetChildrenOf {  # WORKS
@@ -327,7 +329,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getSHoundDNAFromOrganism {  # WORKS
@@ -360,7 +362,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getTaxChildNodes {  # WORKS
@@ -393,7 +395,7 @@
 			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getTaxParent { # now it works.
@@ -419,7 +421,7 @@
 			$parent && ($MOBY_RESPONSE .= simpleResponse("<Object namespace='taxon' id='$parent'/>", "", $qID));
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 
@@ -449,7 +451,7 @@
 													   "</CrossReference>$name</String>", "", $qID));
         }
     }
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub getGoTerm {
@@ -679,7 +681,7 @@
     }
 	$aa = SHoundFini();
 	#print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub _makeSeqObj {
@@ -778,7 +780,7 @@
     }
 	$aa = SHoundFini();
 #	print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub MOBYSHoundGetGenBankWhateverSequence {
@@ -865,7 +867,7 @@
     }
 	$aa = SHoundFini();
 #	print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 sub MOBYSHoundGetGenBankFasta {
@@ -927,7 +929,7 @@
     }
 	$aa = SHoundFini();
 	#print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
-    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+    return SOAP::Data->type('base64' => (responseHeader(-authority => "illuminae.com", -note => $SeqHoundCredit) . $MOBY_RESPONSE . responseFooter));    
 }
 
 



From gss at pub.open-bio.org  Wed Jun 30 18:21:28 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 30 Jun 2004 14:21:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406301821.i5UILSfv031022@pub.open-bio.org>


gss
Wed Jun 30 14:21:28 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv30997/S-MOBY/ref-impl

Modified Files:
	INSTALL.html 
Log Message:
Fixed installation instructions to reflect problems that Ardavan K found.

moby-live/S-MOBY/ref-impl INSTALL.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/INSTALL.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/INSTALL.html	2004/06/10 23:10:44	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/INSTALL.html	2004/06/30 18:21:28	1.2
@@ -1,13 +1,14 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <html>
 <head>
+  <meta name="generator" content="HTML Tidy, see www.w3.org">
   <title>Building and Installing Semantic MOBY</title>
 </head>
 <body>
 <h2 style="text-align: center;">Building and Installing the Semantic
 MOBY<br>
 Reference Implementation</h2>
-<div style="text-align: justify;">This page contains step-by-step
+<div style="text-align: justify;"> This page contains step-by-step
 instructions on building and installing the complete reference
 implementation of Semantic MOBY. The complete installation includes a
 reference implementation of a discovery/registration server
@@ -23,7 +24,7 @@
 </div>
 <br>
 <h3>Prerequisites</h3>
-<div style="text-align: justify;">Before beginning to build the
+<div style="text-align: justify;"> Before beginning to build the
 reference implementation, certain software must be installed on the
 machine that is to host the installation. In the following list, the
 recommended software versions are the only ones that the author has
@@ -39,19 +40,15 @@
     <br>
   </li>
   <li>
-    <div style="text-align: justify;"><a href="http://ant.apache.org">Apache
+    <div style="text-align: justify;"> <a href="http://ant.apache.org">Apache
 Ant</a> (tested with version 1.6.1) should be installed and on the
-executable path. To check, type <code>'ant -version</code><code>' </code>(without
-the quotes) on a command line.<br>
-    </div>
-    <br>
-  </li>
-  <li style="text-align: justify;">One of the open source databases,
-either <a href="http://www.postgresql.org">PostgreSQL</a> (tested with
-version 7.4.1) or <a href="http://www.mysql.com">MySQL</a> (tested
-with version 4.0.18) should be installed and running, and a database
-named <code>smoby-dev</code> has been created.<br>
+executable path. To check, type <code>'ant -version</code><code>'</code>
+(without the quotes) on a command line.One of the open source
+databases, either <a href="http://www.postgresql.org">PostgreSQL</a>
+(tested with version 7.4.1) or <a href="http://www.mysql.com">MySQL</a>
+(tested with version 4.0.18) should be installed and running.<br>
     <br>
+    </div>
   </li>
   <li style="text-align: justify;">The Semantic MOBY distribution has
 been retrieved from CVS and saved locally. As of this writing, there
@@ -69,83 +66,108 @@
 <h3>Installation steps</h3>
 <ol type="1">
   <li>
-    <div style="text-align: justify;">Modify the <code>hosts</code>
+    <div style="text-align: justify;"> Modify the <code>hosts</code>
 file of the computer that is to host the reference implementation, as
-described in the <code>for-hosts-file </code>file located in the <code>ref-impl/config-files/</code>
+described in the <code>for-hosts-file</code> file located in the <code>ref-impl/config-files/</code>
 subdirectory of the reference implementation directory. Since one
 computer is to host several example domains (s-moby.org, acmepubs.com,
 etc.), this is the easiest way to make these virtual domain, hosted by
 Apache Tomcat (see the next step) resolve to the local host.<br>
-    </div>
     <br>
+    </div>
   </li>
   <li>
-    <div style="text-align: justify;">Install <a
+    <div style="text-align: justify;"> Install <a
  href="http://jakarta.apache.org/tomcat">Apache Tomcat 5.0</a> (tested
 with version 5.0.25) and start it. If all went well, you should be able
 to open <a href="http://localhost:8080">http://localhost:8080</a> in a
 browser. After making sure it is properly installed, shutdown Tomcat.<br>
+    <br>
     </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"> Modify Tomcat's main
+configuration file (<code>server.xml</code>), located in the <code>conf/</code>
+subdirectory of the Tomcat installation directory as instructed in the <code>for-tomcat-conf-server.xml</code>
+file, located in the <code>config-files/</code> subdirectory of the
+reference implementation directory. This modification sets up virtual
+hosts, accessible by name, that are all served by Tomcat 5.<br>
     <br>
+    </div>
   </li>
   <li>
-    <div style="text-align: justify;">Modify <tomcat-top-dir>Tomcat's
-main configuration file (<code>server.xml</code>), located in the <code>conf/</code>
-subdirectory of the Tomcat installation directory as instructed in the </tomcat-top-dir><code>for-tomcat-conf-server.xml
-    </code>file, located in the <code>config-files/</code>
-subdirectory of the reference implementation directory. This
-modification sets up virtual hosts, accessible by name, that are all
-served by Tomcat 5.<br>
-    </div>
-    <tomcat-top-dir><br>
-    </tomcat-top-dir></li>
-  <li>
-    <div style="text-align: justify;">Save a copy of the <ref-impl-top-dir><code>common.example.properties</code>
-file, located in the reference implementation<span
- style="font-family: monospace;"></span><code></code> directory, as <code>common.properties</code>
+    <div style="text-align: justify;"> Save a copy of the <code>common.example.properties</code>
+file, located in the reference implementation directory, as <code>common.properties</code>
 (in the same directory). This file is used by the Ant build scripts,
 and should be modified to reflect the system on which the reference
-implementation is being installed.</ref-impl-top-dir><br>
-    <ref-impl-top-dir></ref-impl-top-dir></div>
-    <ref-impl-top-dir><br>
-    </ref-impl-top-dir></li>
-  <li>
-    <div style="text-align: justify;">From the command line, change
-directory to the reference implementation directory and <ref-impl-top-dir>run
-    <code>'ant third-party' </code>(without the quotes). This
-retrieves third party components from CVS and builds them. Retrieving
-the components from CVS is admittedly less predictable than storing a
-version of the components with the Semantic MOBY distribution, but as
-the components (especially <a href="http://jena.sourceforge.net">Jena2</a>)
-are constantly being improved, it is considered more important to have
-the latest versions than to have stable versions. Currently, this step
-takes about three minutes on a 2GHz P4 machine with a broadband
-connection.</ref-impl-top-dir><br>
-    <ref-impl-top-dir></ref-impl-top-dir></div>
-    <br>
-    <ref-impl-top-dir></ref-impl-top-dir></li>
-  <li>
-    <div style="text-align: justify;">From the command line, while
-still in the reference implementation directory,&nbsp;<ref-impl-top-dir>
-run '<code>ant deploy-to-tomcat</code>' (without the quotes). This
-compiles the Semantic MOBY reference implementation and deploys the
-various parts to run as Java Servlets under Tomcat 5.</ref-impl-top-dir><br>
-    <ref-impl-top-dir></ref-impl-top-dir></div>
-    <ref-impl-top-dir><br>
-    </ref-impl-top-dir></li>
-  <li>
-    <div style="text-align: justify;">Copy the appropriate JDBC driver
-jar file into the <tomcat-top-dir><code>shared/lib</code>
-subdirectory of the Tomcat 5 installation. As of this writing, the
-latest PostgreSQL JDBC jar file
+implementation is being installed.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"> From the command line, change
+directory to the reference implementation directory and run <code>'ant
+third-party'</code> (without the quotes). This retrieves third party
+components from CVS and builds them. Retrieving the components from CVS
+is admittedly less predictable than storing a version of the components
+with the Semantic MOBY distribution, but as the components (especially <a
+ href="http://jena.sourceforge.net">Jena2</a>) are constantly being
+improved, it is considered more important to have the latest versions
+than to have stable versions. Currently, this step takes about three
+minutes on a 2GHz P4 machine with a broadband connection.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"> From the command line, while
+still in the reference implementation directory,&nbsp; run '<code>ant
+deploy-to-tomcat</code>' (without the quotes). This compiles the
+Semantic MOBY reference implementation and deploys the various parts to
+run as Java Servlets under Tomcat 5.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"> Copy the appropriate JDBC driver
+jar file into the <code>shared/lib</code> subdirectory of the Tomcat 5
+installation. As of this writing, the latest PostgreSQL JDBC jar file
 was named <span style="font-style: italic;">postgresql.jar</span> and
-the latest MySQL driver was named <span style="font-style: italic;">mysql-connector-java-3.0.11-stable-bin.jar</span>.</tomcat-top-dir><br>
-    <tomcat-top-dir></tomcat-top-dir></div>
-    <tomcat-top-dir><br>
-    </tomcat-top-dir></li>
+the latest MySQL driver was named <span style="font-style: italic;">mysql-connector-java-3.0.11-stable-bin.jar</span>.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"><!--StartFragment --> Using
+whatever tools are appropriate for your DBMS, create a database user
+(e.g. <code>joe</code>) with a password (e.g. <code>foobar</code>).
+For MySQL, the free MySQL Control Center works well, and for
+PostgreSQL, PGAdmin III works well.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"><!--StartFragment --> Create a
+database, and give it a name (e.g. <code>my-smoby-repository</code>).
+Make the owner of the database the user (e.g. <code>joe</code>)
+created in step&nbsp;8.<br>
+    <br>
+    </div>
+  </li>
+  <li>
+    <div style="text-align: justify;"><!--StartFragment --> Modify <code>smoby.properties</code>,
+located in the <code>webapps/s-moby.org</code> subdirectory of the
+Tomcat installation directory, setting <code>DB_USER_ID</code> to the
+user (e.g. <code>joe</code>) created in step 8, <code>DB_PASSWORD</code>
+to the password (e.g. <code>foobar</code>) of the user created in step
+8, and <code>DB_REPOSITORY_NAME</code> to the database name (e.g. <code>my-smoby-repository</code>)
+used in step 8.Also modify <code>DB_URL</code> to include the name of
+the database used in&nbsp;step 9&nbsp;(e.g. <code>jdbc:postgresql://localhost/my-smoby-repository</code>).<br>
+    <br>
+    </div>
+  </li>
   <li>Start Tomcat. If all went well, you should be able to open <a
- href="http://www.s-moby.org:8080">http://www.s-moby.org:8080</a>
-in a browser. </li>
+ href="http://www.s-moby.org:8080">http://www.s-moby.org:8080</a> in a
+browser.</li>
 </ol>
 </body>
 </html>



From gss at pub.open-bio.org  Wed Jun 30 18:21:28 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 30 Jun 2004 14:21:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200406301821.i5UILSsL031041@pub.open-bio.org>


gss
Wed Jun 30 14:21:28 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv30997/S-MOBY/ref-impl/server/WebRoot

Modified Files:
	smoby.properties 
Log Message:
Fixed installation instructions to reflect problems that Ardavan K found.

moby-live/S-MOBY/ref-impl/server/WebRoot smoby.properties,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/smoby.properties,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/smoby.properties	2004/06/10 23:25:49	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/smoby.properties	2004/06/30 18:21:28	1.2
@@ -3,9 +3,9 @@
 
 # Common values for MySQL and PostgreSQL
 #
-DB_USER_ID            = smobydev
-DB_PASSWORD           = 
-DB_REPOSITORY_NAME    = smoby-dev
+DB_USER_ID            = <change-me>
+DB_PASSWORD           = <change-me>
+DB_REPOSITORY_NAME    = <change-me>
 
 # Uncomment if using MySQL
 #
@@ -17,4 +17,4 @@
 #
 DB_DRIVER_CLASS_NAME  = org.postgresql.Driver
 DB_TYPE               = PostgreSQL
-DB_URL                = jdbc:postgresql://localhost/smoby-dev
\ No newline at end of file
+DB_URL                = jdbc:postgresql://localhost/<change-me>
\ No newline at end of file