[MOBY-dev] Moby objects in Taverna. Where do they come from?

Pieter Neerincx Pieter.Neerincx at wur.nl
Mon Sep 19 14:46:19 UTC 2005 

Hi Eddie,

On 19-Sep-2005, at 3:11 PM, Edward Kawas wrote:

> Hi,
>
> [mobycentral]
> dbname = mobycentral
> rdfagent = /usr/local/apache2/MOBY/rdfagent
> lsid_authority = biomoby.org
> lsid_namespace = serviceinstance
> resourceURL =
> http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances
> allResources = http://biomoby.org/RESOURCES/MOBY-S/FULL
>
> [mobyobject]
> dbname = mobyobject
> lsid_authority = biomoby.org
> lsid_namespace = objectclass
> resourceURL = http://biomoby.org/RESOURCES/MOBY-S/Objects
>
> [mobynamespace]
> dbname = mobynamespace
> lsid_authority = biomoby.org
> lsid_namespace = namespacetype
> resourceURL = http://biomoby.org/RESOURCES/MOBY-S/Namespaces
>
> [mobyservice]
> dbname = mobyservice
> lsid_authority = biomoby.org
> lsid_namespace = servicetype
> resourceURL = http://biomoby.org/RESOURCES/MOBY-S/Services
>
> [mobyrelationship]
> dbname = mobyrelationship
> lsid_authority = biomoby.org
> #lsid_namespace = relationshiptype
>
> Those are the new lines (as far as I know) that should be
> added to the config file.

Thanks, I already guessed some of the URLs, but not all of them :). I  
created a small Perl script to test MOBY::Client::Central- 
 >retrieveResourceURLs. This works now, but unfortunately still no  
fun with Taverna. When I start Taverna with my local central appended  
in the mygrid.properties file, nothing happens: no custom objects  
form my local central and also no error messages. When I add my local  
central manually using right-click->add new biomoby scavanger, I got  
the error below. Taverna complains it can't process the RDF document  
for the biomoby objects :(. So I pointed my browser to the URL for  
the biomoby objects RDF file and had a look: The RDF looks pretty  
normal, but I did notice <cr> elements and the xml parser fails on  
those. (Do you happen to develop on a windows machine?) So I stripped  
the carriage returns from RDF objects file, saved it and changed the  
URL for the objects RDF to this static file: tada.... That finally  
got the show on the road :).

Cheers,

Pieter

Taverna command line error messages:
---------------------------------------
Creating biomoby scavenger : 'https://bioinfw05/phenolink/biomoby/ 
central/cgi-bin/MOBY-Central.pl'
ERROR                                      2005-09-19 16:01:16,854  
(com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler:44) - http:// 
www.w3.org/TR/html4/loose.dtd[31:3]: {E301} The declaration for the  
entity "HTML.Version" must end with '>'.
Failed: rethrew: com.hp.hpl.jena.rdf.arp.ParseException: {E301} The  
declaration for the entity "HTML.Version" must end with '>'.
[Ljava.lang.StackTraceElement;@c9f71b
org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException:  
Could not retrieve and or process RDF document for BioMoby Objects
         at org.biomoby.client.taverna.plugin.BiomobyScavenger.<init> 
(BiomobyScavenger.java:95)
         at org.biomoby.client.taverna.plugin.BiomobyScavengerHelper 
$2.actionPerformed(BiomobyScavengerHelper.java:83)
         at javax.swing.AbstractButton.fireActionPerformed 
(AbstractButton.java:1786)
         at javax.swing.AbstractButton 
$ForwardActionEvents.actionPerformed(AbstractButton.java:1839)
         at javax.swing.DefaultButtonModel.fireActionPerformed 
(DefaultButtonModel.java:420)
         at javax.swing.DefaultButtonModel.setPressed 
(DefaultButtonModel.java:258)
         at javax.swing.plaf.basic.BasicButtonListener.mouseReleased 
(BasicButtonListener.java:245)
         at java.awt.Component.processMouseEvent(Component.java:5100)
         at java.awt.Component.processEvent(Component.java:4897)
         at java.awt.Container.processEvent(Container.java:1569)
         at java.awt.Component.dispatchEventImpl(Component.java:3615)
         at java.awt.Container.dispatchEventImpl(Container.java:1627)
         at java.awt.Component.dispatchEvent(Component.java:3477)
         at java.awt.LightweightDispatcher.retargetMouseEvent 
(Container.java:3483)
         at java.awt.LightweightDispatcher.processMouseEvent 
(Container.java:3198)
         at java.awt.LightweightDispatcher.dispatchEvent 
(Container.java:3128)
         at java.awt.Container.dispatchEventImpl(Container.java:1613)
         at java.awt.Window.dispatchEventImpl(Window.java:1606)
         at java.awt.Component.dispatchEvent(Component.java:3477)
         at java.awt.EventQueue.dispatchEvent(EventQueue.java:456)
         at java.awt.EventDispatchThread.pumpOneEventForHierarchy 
(EventDispatchThread.java:201)
         at java.awt.EventDispatchThread.pumpEventsForHierarchy 
(EventDispatchThread.java:151)
         at java.awt.EventDispatchThread.pumpEventsForHierarchy 
(EventDispatchThread.java:141)
         at java.awt.Dialog$1.run(Dialog.java:540)
         at java.awt.Dialog.show(Dialog.java:561)
         at java.awt.Component.show(Component.java:1133)
         at java.awt.Component.setVisible(Component.java:1088)
         at org.biomoby.client.taverna.plugin.BiomobyScavengerHelper 
$1.actionPerformed(BiomobyScavengerHelper.java:119)
         at javax.swing.AbstractButton.fireActionPerformed 
(AbstractButton.java:1786)
         at javax.swing.AbstractButton 
$ForwardActionEvents.actionPerformed(AbstractButton.java:1839)
         at javax.swing.DefaultButtonModel.fireActionPerformed 
(DefaultButtonModel.java:420)
         at javax.swing.DefaultButtonModel.setPressed 
(DefaultButtonModel.java:258)
         at javax.swing.AbstractButton.doClick(AbstractButton.java:289)
         at javax.swing.plaf.basic.BasicMenuItemUI.doClick 
(BasicMenuItemUI.java:1113)
         at javax.swing.plaf.basic.BasicMenuItemUI 
$MouseInputHandler.mouseReleased(BasicMenuItemUI.java:943)
         at java.awt.Component.processMouseEvent(Component.java:5100)
         at java.awt.Component.processEvent(Component.java:4897)
         at java.awt.Container.processEvent(Container.java:1569)
         at java.awt.Component.dispatchEventImpl(Component.java:3615)
         at java.awt.Container.dispatchEventImpl(Container.java:1627)
         at java.awt.Component.dispatchEvent(Component.java:3477)
         at java.awt.LightweightDispatcher.retargetMouseEvent 
(Container.java:3483)
         at java.awt.LightweightDispatcher.processMouseEvent 
(Container.java:3198)
         at java.awt.LightweightDispatcher.dispatchEvent 
(Container.java:3128)
         at java.awt.Container.dispatchEventImpl(Container.java:1613)
         at java.awt.Window.dispatchEventImpl(Window.java:1606)
         at java.awt.Component.dispatchEvent(Component.java:3477)
         at java.awt.EventQueue.dispatchEvent(EventQueue.java:456)
         at java.awt.EventDispatchThread.pumpOneEventForHierarchy 
(EventDispatchThread.java:201)
         at java.awt.EventDispatchThread.pumpEventsForHierarchy 
(EventDispatchThread.java:151)
         at java.awt.EventDispatchThread.pumpEvents 
(EventDispatchThread.java:145)
         at java.awt.EventDispatchThread.pumpEvents 
(EventDispatchThread.java:137)
         at java.awt.EventDispatchThread.run(EventDispatchThread.java: 
100)
Caused by: java.lang.NullPointerException
         at org.biomoby.client.taverna.plugin.BiomobyScavenger.<init> 
(BiomobyScavenger.java:92)
         ... 52 more
---------------------------------------



>
> Eddie
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at biomoby.org
> http://www.biomoby.org/mailman/listinfo/moby-dev
>


Wageningen University and Research centre (WUR)
Laboratory of Bioinformatics
Transitorium (building 312) room 1034
Dreijenlaan 3
6703 HA Wageningen
The Netherlands
phone: 0317-483 060
fax: 0317-483 584
mobile: 06-143 66 783
pieter.neerincx at wur.nl

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