From drepchevski at dev.open-bio.org  Tue Feb 19 08:17:48 2013
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 19 Feb 2013 08:17:48 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <201302191317.r1JDHmps013873@dev.open-bio.org>


drepchevski
Tue Feb 19 08:17:47 EST 2013
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central
In directory dev.open-bio.org:/tmp/cvs-serv13838/central

Modified Files:
	MobyCentralOperations.java 
Log Message:
some fixes
moby-live/Java/src/main/org/inb/biomoby/central MobyCentralOperations.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/MobyCentralOperations.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/MobyCentralOperations.java	2009/09/09 19:47:48	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/MobyCentralOperations.java	2013/02/19 13:17:47	1.2
@@ -23,7 +23,7 @@
 
 public interface MobyCentralOperations
 {
-    public ServiceType retrieveService(ServiceType serviceType) throws Exception;
+    public Service retrieveService(Service service) throws Exception;
     public Registration registerService(Service service) throws Exception;
     public List<Service> findService(Service service, List<String> keywords, boolean isExpandServices, boolean isExpandObjects) throws Exception;
     


From drepchevski at dev.open-bio.org  Tue Feb 19 08:17:48 2013
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 19 Feb 2013 08:17:48 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <201302191317.r1JDHm5Y013945@dev.open-bio.org>


drepchevski
Tue Feb 19 08:17:48 EST 2013
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv13838/client

Modified Files:
	MobyDispatch.java 
Log Message:
some fixes
moby-live/Java/src/main/org/inb/biomoby/client MobyDispatch.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/MobyDispatch.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/MobyDispatch.java	2011/02/03 17:34:00	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/MobyDispatch.java	2013/02/19 13:17:48	1.4
@@ -16,7 +16,6 @@
 import java.util.List;
 import java.util.logging.Logger;
 import javax.xml.XMLConstants;
-import org.inb.biomoby.MobyMessageContext;
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBElement;
 import javax.xml.bind.JAXBException;
@@ -48,9 +47,10 @@
 import javax.xml.ws.soap.MTOMFeature;
 import javax.xml.ws.soap.SOAPBinding;
 import javax.xml.ws.wsaddressing.W3CEndpointReference;
-import org.inb.biomoby.shared.registry.Service.CATEGORY;
+import org.inb.biomoby.MobyMessageContext;
 import org.inb.biomoby.shared.message.MobyDataElement;
 import org.inb.biomoby.shared.message.MobyMessage;
+import org.inb.biomoby.shared.registry.Service.CATEGORY;
 import org.inb.biomoby.shared.wsrf.MobyEndpointReference;
 import org.inb.biomoby.shared.wsrf.PropertyResponseWrapper;
 import org.inb.biomoby.shared.wsrf.SubmitResponseWrapper;
@@ -199,7 +199,7 @@
         QName sName = service.getServiceName();
         
         SOAPMessage request = marshal(sName.getLocalPart(), message);
-     
+
         Dispatch<SOAPMessage> dispatch = service.createDispatch(sName, SOAPMessage.class, Service.Mode.MESSAGE);
 
         dispatch.getRequestContext().put(BindingProvider.SOAPACTION_USE_PROPERTY, Boolean.TRUE); //use SOAPAction!


From drepchevski at dev.open-bio.org  Tue Feb 19 08:17:48 2013
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 19 Feb 2013 08:17:48 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <201302191317.r1JDHmYk013975@dev.open-bio.org>


drepchevski
Tue Feb 19 08:17:48 EST 2013
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry
In directory dev.open-bio.org:/tmp/cvs-serv13838/shared/registry

Modified Files:
	Resource.java Service.java ServiceType.java 
Log Message:
some fixes
moby-live/Java/src/main/org/inb/biomoby/shared/registry Resource.java,1.1,1.2 Service.java,1.1,1.2 ServiceType.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/Resource.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/Resource.java	2009/09/09 19:47:49	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/Resource.java	2013/02/19 13:17:48	1.2
@@ -20,7 +20,7 @@
 @XmlRootElement(name="resource")
 public class Resource implements Serializable, Cloneable
 {
-    public static enum RESOURCE_NAME {Service, Object, ServiceInstance, Full};
+    public static enum RESOURCE_NAME {Service, Object, ServiceInstance, Namespace, Full};
     
     private RESOURCE_NAME name;
     private String url;

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/Service.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/Service.java	2009/09/09 19:47:49	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/Service.java	2013/02/19 13:17:48	1.2
@@ -38,6 +38,8 @@
     private Input input;
     private Output output;
     
+    private String wsdl;
+    
     private ArrayList<Parameter> secondaryArticles;
     
     public Service() {}
@@ -140,6 +142,16 @@
         return secondaryArticles;
     }
 
+    public String getWSDL()
+    {
+        return wsdl;
+    }
+    
+    public void setWSDL(String wsdl)
+    {
+        this.wsdl = wsdl;
+    }
+
     @Override
     public Service clone()
     {

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/ServiceType.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/ServiceType.java	2009/09/09 19:47:49	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/ServiceType.java	2013/02/19 13:17:48	1.2
@@ -24,8 +24,6 @@
 {
     private ArrayList<Relationship<ServiceType>> relationships;
 
-    private String wsdl;
-    
     public ServiceType() {}
     
     public ServiceType(String name)
@@ -52,16 +50,6 @@
         
         return relationships;
     }
-    
-    public String getWSDL()
-    {
-        return wsdl;
-    }
-    
-    public void setWSDL(String wsdl)
-    {
-        this.wsdl = wsdl;
-    }
 
     @Override
     public ServiceType clone()


From drepchevski at dev.open-bio.org  Tue Feb 19 08:17:48 2013
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 19 Feb 2013 08:17:48 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <201302191317.r1JDHmDO013895@dev.open-bio.org>


drepchevski
Tue Feb 19 08:17:48 EST 2013
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb
In directory dev.open-bio.org:/tmp/cvs-serv13838/central/factory/jaxb

Modified Files:
	JAXBMobyCentralImpl.java ModelConverter.java 
Log Message:
some fixes
moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb JAXBMobyCentralImpl.java,1.2,1.3 ModelConverter.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/JAXBMobyCentralImpl.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/JAXBMobyCentralImpl.java	2011/02/02 13:23:40	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/JAXBMobyCentralImpl.java	2013/02/19 13:17:48	1.3
@@ -10,8 +10,6 @@
 
 package org.inb.biomoby.central.factory.jaxb;
 
-import org.inb.biomoby.central.factory.*;
-import org.inb.biomoby.shared.registry.*;
 import java.util.ArrayList;
 import java.util.List;
 import org.inb.biomoby.central.MobyCentral;
@@ -47,6 +45,7 @@
 import org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceProvidersOperation;
 import org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation;
 import org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceTypes;
+import org.inb.biomoby.shared.registry.*;
 
 /**
  * @author Dmitry Repchevsky
@@ -477,26 +476,24 @@
         return registration;
     }
     
-    public ServiceType retrieveService(ServiceType serviceType) throws Exception
+    public Service retrieveService(Service service) throws Exception
     {
         RetrieveServiceOperation endpoint = new RetrieveServiceOperation(central);
         
         RetrieveService request = new RetrieveService();
         
-        ServiceTemplate service = new ServiceTemplate();
-        service.setServiceName(serviceType.getName());
-        service.setAuthURI(serviceType.getAuthURI());
-        service.setLsid(serviceType.getLsid());
+        ServiceTemplate template = new ServiceTemplate();
+        template.setServiceName(service.getName());
+        template.setAuthURI(service.getAuthURI());
+        template.setLsid(service.getLsid());
         
-        request.setService(service);
+        request.setService(template);
         
         ServiceTemplate response = endpoint.call(request);
 
-        ServiceType st = new ServiceType(response.getServiceName(), response.getAuthURI());
-        st.setLsid(response.getLsid());
-        st.setWSDL(response.getWSDL());
+        service.setWSDL(response.getWSDL());
         
-        return st;
+        return service;
     }
     
     public List<Relationship<ServiceType>> relationships(ServiceType serviceType, List<Relationship.RELATIONSHIP_TYPE> relationships, Relationship.DIRECTION_TYPE direction, boolean expandRelationship) throws Exception

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/ModelConverter.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/ModelConverter.java	2009/09/09 19:47:48	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/ModelConverter.java	2013/02/19 13:17:48	1.2
@@ -160,6 +160,8 @@
     {
         Service service = new Service(sv.getServiceName(), sv.getAuthURI());
 
+        service.setLsid(sv.getLsid());
+        
         service.setContactEmail(sv.getContactEmail());
         service.setDescription(sv.getDescription());
         


From drepchevski at dev.open-bio.org  Tue Feb 19 08:17:48 2013
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 19 Feb 2013 08:17:48 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <201302191317.r1JDHmaq013923@dev.open-bio.org>


drepchevski
Tue Feb 19 08:17:48 EST 2013
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry
In directory dev.open-bio.org:/tmp/cvs-serv13838/central/factory/jaxb/registry

Modified Files:
	RetrieveServiceProvidersOperation.java 
	RetrieveServiceTypesOperation.java 
Log Message:
some fixes
moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry RetrieveServiceProvidersOperation.java,1.1,1.2 RetrieveServiceTypesOperation.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceProvidersOperation.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceProvidersOperation.java	2009/09/09 19:47:48	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceProvidersOperation.java	2013/02/19 13:17:48	1.2
@@ -13,6 +13,7 @@
 import java.util.ArrayList;
 import java.util.List;
 import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 import org.inb.biomoby.central.MobyCentral;
@@ -43,6 +44,7 @@
     {
         private List<ServiceProvider> serviceProviders;
 
+        @XmlElement(name="serviceProvider")
         public List<ServiceProvider> getServiceProviders()
         {
             if (serviceProviders == null)
@@ -55,7 +57,7 @@
 
 // *****************************************************************************
 
-    @XmlType(name = "")
+    @XmlType
     public static class ServiceProvider
     {
         private String name;

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceTypesOperation.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceTypesOperation.java	2009/09/09 19:47:48	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceTypesOperation.java	2013/02/19 13:17:48	1.2
@@ -44,6 +44,7 @@
     {
         private List<ServiceType> serviceType;
 
+        @XmlElement
         public List<ServiceType> getServiceType()
         {
             if (serviceType == null)


From drepchevski at dev.open-bio.org  Tue Feb 19 09:15:37 2013
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 19 Feb 2013 09:15:37 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <201302191415.r1JEFbZC017035@dev.open-bio.org>


drepchevski
Tue Feb 19 09:15:37 EST 2013
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv17000

Modified Files:
	inb_moby_central.html 
Log Message:
doc fix
moby-live/Java/docs inb_moby_central.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/inb_moby_central.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/inb_moby_central.html	2009/09/15 17:18:23	1.1
+++ /home/repository/moby/moby-live/Java/docs/inb_moby_central.html	2013/02/19 14:15:37	1.2
@@ -124,7 +124,7 @@
         <tr>
           <td rowspan="2">retrieveService</td>
           <td style="white-space: nowrap; font-size: 9pt; font-weight: bold; color: #000099;">
-            public ServiceType retrieveService(ServiceType serviceType) throws Exception
+            public Service retrieveService(Service service) throws Exception
           </td>
         </tr>
         <tr>


From mwilkinson at dev.open-bio.org  Wed Feb 20 09:01:02 2013
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Wed, 20 Feb 2013 09:01:02 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <201302201401.r1KE12sh020712@dev.open-bio.org>


mwilkinson
Wed Feb 20 09:01:01 EST 2013
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv20691

Modified Files:
	Central.pm 
Log Message:
fixed bug reported by J Rodriguez.  retrieveService was returning Services as an xml tag.  Fixed to return Service as the tagname.
moby-live/Perl/MOBY-Server/lib/MOBY Central.pm,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm	2010/05/03 18:34:40	1.13
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm	2013/02/20 14:01:01	1.14
@@ -2622,14 +2622,14 @@
 	my ( $pkg, $payload ) = @_;
 	my ( $AuthURI, $serviceName, $InputXML, $OutputXML, $SecondaryXML ) =
 	  &_retrieveServicePayload($payload);
-	unless ( $AuthURI && $serviceName ) { return "<Services/>" }
+	unless ( $AuthURI && $serviceName ) { return "<Service/>" }
 	my $SI = MOBY::service_instance->new(
 		authority_uri => $AuthURI,
 		servicename   => $serviceName
 	);
+	return "<Service/>" unless ($SI);
 	my $servlsid = $SI->lsid;
 	my $wsdls;
-	return "<Services/>" unless ($SI);
 	&listener(authority => $AuthURI, servicename => $serviceName);  # log the requst for research purposes	
 	my $wsdl = &_getServiceWSDL( $SI, $InputXML, $OutputXML, $SecondaryXML );
 	if ($wsdl) {


From drepchevski at dev.open-bio.org  Tue Feb 19 13:17:48 2013
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 19 Feb 2013 08:17:48 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <201302191317.r1JDHmps013873@dev.open-bio.org>


drepchevski
Tue Feb 19 08:17:47 EST 2013
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central
In directory dev.open-bio.org:/tmp/cvs-serv13838/central

Modified Files:
	MobyCentralOperations.java 
Log Message:
some fixes
moby-live/Java/src/main/org/inb/biomoby/central MobyCentralOperations.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/MobyCentralOperations.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/MobyCentralOperations.java	2009/09/09 19:47:48	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/MobyCentralOperations.java	2013/02/19 13:17:47	1.2
@@ -23,7 +23,7 @@
 
 public interface MobyCentralOperations
 {
-    public ServiceType retrieveService(ServiceType serviceType) throws Exception;
+    public Service retrieveService(Service service) throws Exception;
     public Registration registerService(Service service) throws Exception;
     public List<Service> findService(Service service, List<String> keywords, boolean isExpandServices, boolean isExpandObjects) throws Exception;
     



From drepchevski at dev.open-bio.org  Tue Feb 19 13:17:48 2013
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 19 Feb 2013 08:17:48 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <201302191317.r1JDHm5Y013945@dev.open-bio.org>


drepchevski
Tue Feb 19 08:17:48 EST 2013
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv13838/client

Modified Files:
	MobyDispatch.java 
Log Message:
some fixes
moby-live/Java/src/main/org/inb/biomoby/client MobyDispatch.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/MobyDispatch.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/MobyDispatch.java	2011/02/03 17:34:00	1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/MobyDispatch.java	2013/02/19 13:17:48	1.4
@@ -16,7 +16,6 @@
 import java.util.List;
 import java.util.logging.Logger;
 import javax.xml.XMLConstants;
-import org.inb.biomoby.MobyMessageContext;
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBElement;
 import javax.xml.bind.JAXBException;
@@ -48,9 +47,10 @@
 import javax.xml.ws.soap.MTOMFeature;
 import javax.xml.ws.soap.SOAPBinding;
 import javax.xml.ws.wsaddressing.W3CEndpointReference;
-import org.inb.biomoby.shared.registry.Service.CATEGORY;
+import org.inb.biomoby.MobyMessageContext;
 import org.inb.biomoby.shared.message.MobyDataElement;
 import org.inb.biomoby.shared.message.MobyMessage;
+import org.inb.biomoby.shared.registry.Service.CATEGORY;
 import org.inb.biomoby.shared.wsrf.MobyEndpointReference;
 import org.inb.biomoby.shared.wsrf.PropertyResponseWrapper;
 import org.inb.biomoby.shared.wsrf.SubmitResponseWrapper;
@@ -199,7 +199,7 @@
         QName sName = service.getServiceName();
         
         SOAPMessage request = marshal(sName.getLocalPart(), message);
-     
+
         Dispatch<SOAPMessage> dispatch = service.createDispatch(sName, SOAPMessage.class, Service.Mode.MESSAGE);
 
         dispatch.getRequestContext().put(BindingProvider.SOAPACTION_USE_PROPERTY, Boolean.TRUE); //use SOAPAction!



From drepchevski at dev.open-bio.org  Tue Feb 19 13:17:48 2013
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 19 Feb 2013 08:17:48 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <201302191317.r1JDHmYk013975@dev.open-bio.org>


drepchevski
Tue Feb 19 08:17:48 EST 2013
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry
In directory dev.open-bio.org:/tmp/cvs-serv13838/shared/registry

Modified Files:
	Resource.java Service.java ServiceType.java 
Log Message:
some fixes
moby-live/Java/src/main/org/inb/biomoby/shared/registry Resource.java,1.1,1.2 Service.java,1.1,1.2 ServiceType.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/Resource.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/Resource.java	2009/09/09 19:47:49	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/Resource.java	2013/02/19 13:17:48	1.2
@@ -20,7 +20,7 @@
 @XmlRootElement(name="resource")
 public class Resource implements Serializable, Cloneable
 {
-    public static enum RESOURCE_NAME {Service, Object, ServiceInstance, Full};
+    public static enum RESOURCE_NAME {Service, Object, ServiceInstance, Namespace, Full};
     
     private RESOURCE_NAME name;
     private String url;

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/Service.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/Service.java	2009/09/09 19:47:49	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/Service.java	2013/02/19 13:17:48	1.2
@@ -38,6 +38,8 @@
     private Input input;
     private Output output;
     
+    private String wsdl;
+    
     private ArrayList<Parameter> secondaryArticles;
     
     public Service() {}
@@ -140,6 +142,16 @@
         return secondaryArticles;
     }
 
+    public String getWSDL()
+    {
+        return wsdl;
+    }
+    
+    public void setWSDL(String wsdl)
+    {
+        this.wsdl = wsdl;
+    }
+
     @Override
     public Service clone()
     {

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/ServiceType.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/ServiceType.java	2009/09/09 19:47:49	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/ServiceType.java	2013/02/19 13:17:48	1.2
@@ -24,8 +24,6 @@
 {
     private ArrayList<Relationship<ServiceType>> relationships;
 
-    private String wsdl;
-    
     public ServiceType() {}
     
     public ServiceType(String name)
@@ -52,16 +50,6 @@
         
         return relationships;
     }
-    
-    public String getWSDL()
-    {
-        return wsdl;
-    }
-    
-    public void setWSDL(String wsdl)
-    {
-        this.wsdl = wsdl;
-    }
 
     @Override
     public ServiceType clone()



From drepchevski at dev.open-bio.org  Tue Feb 19 13:17:48 2013
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 19 Feb 2013 08:17:48 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <201302191317.r1JDHmDO013895@dev.open-bio.org>


drepchevski
Tue Feb 19 08:17:48 EST 2013
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb
In directory dev.open-bio.org:/tmp/cvs-serv13838/central/factory/jaxb

Modified Files:
	JAXBMobyCentralImpl.java ModelConverter.java 
Log Message:
some fixes
moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb JAXBMobyCentralImpl.java,1.2,1.3 ModelConverter.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/JAXBMobyCentralImpl.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/JAXBMobyCentralImpl.java	2011/02/02 13:23:40	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/JAXBMobyCentralImpl.java	2013/02/19 13:17:48	1.3
@@ -10,8 +10,6 @@
 
 package org.inb.biomoby.central.factory.jaxb;
 
-import org.inb.biomoby.central.factory.*;
-import org.inb.biomoby.shared.registry.*;
 import java.util.ArrayList;
 import java.util.List;
 import org.inb.biomoby.central.MobyCentral;
@@ -47,6 +45,7 @@
 import org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceProvidersOperation;
 import org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation;
 import org.inb.biomoby.central.factory.jaxb.registry.RetrieveServiceTypesOperation.ServiceTypes;
+import org.inb.biomoby.shared.registry.*;
 
 /**
  * @author Dmitry Repchevsky
@@ -477,26 +476,24 @@
         return registration;
     }
     
-    public ServiceType retrieveService(ServiceType serviceType) throws Exception
+    public Service retrieveService(Service service) throws Exception
     {
         RetrieveServiceOperation endpoint = new RetrieveServiceOperation(central);
         
         RetrieveService request = new RetrieveService();
         
-        ServiceTemplate service = new ServiceTemplate();
-        service.setServiceName(serviceType.getName());
-        service.setAuthURI(serviceType.getAuthURI());
-        service.setLsid(serviceType.getLsid());
+        ServiceTemplate template = new ServiceTemplate();
+        template.setServiceName(service.getName());
+        template.setAuthURI(service.getAuthURI());
+        template.setLsid(service.getLsid());
         
-        request.setService(service);
+        request.setService(template);
         
         ServiceTemplate response = endpoint.call(request);
 
-        ServiceType st = new ServiceType(response.getServiceName(), response.getAuthURI());
-        st.setLsid(response.getLsid());
-        st.setWSDL(response.getWSDL());
+        service.setWSDL(response.getWSDL());
         
-        return st;
+        return service;
     }
     
     public List<Relationship<ServiceType>> relationships(ServiceType serviceType, List<Relationship.RELATIONSHIP_TYPE> relationships, Relationship.DIRECTION_TYPE direction, boolean expandRelationship) throws Exception

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/ModelConverter.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/ModelConverter.java	2009/09/09 19:47:48	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/ModelConverter.java	2013/02/19 13:17:48	1.2
@@ -160,6 +160,8 @@
     {
         Service service = new Service(sv.getServiceName(), sv.getAuthURI());
 
+        service.setLsid(sv.getLsid());
+        
         service.setContactEmail(sv.getContactEmail());
         service.setDescription(sv.getDescription());
         



From drepchevski at dev.open-bio.org  Tue Feb 19 13:17:48 2013
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 19 Feb 2013 08:17:48 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <201302191317.r1JDHmaq013923@dev.open-bio.org>


drepchevski
Tue Feb 19 08:17:48 EST 2013
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry
In directory dev.open-bio.org:/tmp/cvs-serv13838/central/factory/jaxb/registry

Modified Files:
	RetrieveServiceProvidersOperation.java 
	RetrieveServiceTypesOperation.java 
Log Message:
some fixes
moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry RetrieveServiceProvidersOperation.java,1.1,1.2 RetrieveServiceTypesOperation.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceProvidersOperation.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceProvidersOperation.java	2009/09/09 19:47:48	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceProvidersOperation.java	2013/02/19 13:17:48	1.2
@@ -13,6 +13,7 @@
 import java.util.ArrayList;
 import java.util.List;
 import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 import org.inb.biomoby.central.MobyCentral;
@@ -43,6 +44,7 @@
     {
         private List<ServiceProvider> serviceProviders;
 
+        @XmlElement(name="serviceProvider")
         public List<ServiceProvider> getServiceProviders()
         {
             if (serviceProviders == null)
@@ -55,7 +57,7 @@
 
 // *****************************************************************************
 
-    @XmlType(name = "")
+    @XmlType
     public static class ServiceProvider
     {
         private String name;

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceTypesOperation.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceTypesOperation.java	2009/09/09 19:47:48	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceTypesOperation.java	2013/02/19 13:17:48	1.2
@@ -44,6 +44,7 @@
     {
         private List<ServiceType> serviceType;
 
+        @XmlElement
         public List<ServiceType> getServiceType()
         {
             if (serviceType == null)



From drepchevski at dev.open-bio.org  Tue Feb 19 14:15:37 2013
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 19 Feb 2013 09:15:37 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <201302191415.r1JEFbZC017035@dev.open-bio.org>


drepchevski
Tue Feb 19 09:15:37 EST 2013
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv17000

Modified Files:
	inb_moby_central.html 
Log Message:
doc fix
moby-live/Java/docs inb_moby_central.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/inb_moby_central.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/inb_moby_central.html	2009/09/15 17:18:23	1.1
+++ /home/repository/moby/moby-live/Java/docs/inb_moby_central.html	2013/02/19 14:15:37	1.2
@@ -124,7 +124,7 @@
         <tr>
           <td rowspan="2">retrieveService</td>
           <td style="white-space: nowrap; font-size: 9pt; font-weight: bold; color: #000099;">
-            public ServiceType retrieveService(ServiceType serviceType) throws Exception
+            public Service retrieveService(Service service) throws Exception
           </td>
         </tr>
         <tr>



From mwilkinson at dev.open-bio.org  Wed Feb 20 14:01:02 2013
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Wed, 20 Feb 2013 09:01:02 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <201302201401.r1KE12sh020712@dev.open-bio.org>


mwilkinson
Wed Feb 20 09:01:01 EST 2013
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv20691

Modified Files:
	Central.pm 
Log Message:
fixed bug reported by J Rodriguez.  retrieveService was returning Services as an xml tag.  Fixed to return Service as the tagname.
moby-live/Perl/MOBY-Server/lib/MOBY Central.pm,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm	2010/05/03 18:34:40	1.13
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm	2013/02/20 14:01:01	1.14
@@ -2622,14 +2622,14 @@
 	my ( $pkg, $payload ) = @_;
 	my ( $AuthURI, $serviceName, $InputXML, $OutputXML, $SecondaryXML ) =
 	  &_retrieveServicePayload($payload);
-	unless ( $AuthURI && $serviceName ) { return "<Services/>" }
+	unless ( $AuthURI && $serviceName ) { return "<Service/>" }
 	my $SI = MOBY::service_instance->new(
 		authority_uri => $AuthURI,
 		servicename   => $serviceName
 	);
+	return "<Service/>" unless ($SI);
 	my $servlsid = $SI->lsid;
 	my $wsdls;
-	return "<Services/>" unless ($SI);
 	&listener(authority => $AuthURI, servicename => $serviceName);  # log the requst for research purposes	
 	my $wsdl = &_getServiceWSDL( $SI, $InputXML, $OutputXML, $SecondaryXML );
 	if ($wsdl) {