From edward.kawas at gmail.com  Tue Sep  4 10:25:43 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 4 Sep 2007 07:25:43 -0700
Subject: [MOBY-dev] Services in registry
In-Reply-To: <620875BF-7DB2-47F8-A673-92CBFD27F93C@farmbio.uu.se>
References: <45EA4928-D121-4FCA-BB05-DB7067632F1F@farmbio.uu.se><002401c7eb1b$32d28410$6500a8c0@notebook>
	<620875BF-7DB2-47F8-A673-92CBFD27F93C@farmbio.uu.se>
Message-ID: <002f01c7eeff$7a9a9250$6500a8c0@notebook>

Hi, 
> I have not really understood this. Why do services require a 
> namespace?

When you register a service, the namespaces are specified for each
input/output. Depending on your client (or if you are using the API), the
namespace information is very easy to determine. In Taverna, this is
available as tooltips. In dashboard, you can get this information from the
'registry browser' when you click on individual services, etc.

Why do services require a namespace? Because it is the namespace and
identifier of an object that uniquely identifies data. Put another way, the
namespace helps narrow the scope of your data. Imagine that someone gave you
data identified by the string "424360". The question now becomes, what is
it? Now when you specify the namespace of "NCBI_gi", we know exactly what it
is and can use it.

Hopefully others can build upon my explanation if it doesn't make sense.

> If I am a novice user and have an aminoacid 
> sequence, how can I find available services for it then? 

Making a findService call to the registry stating that you want all services
that consume AminoAcidSequence. In fact, you probably could also search for
services that consume, FASTA, etc. Here you may or may not specify
namespace. It depends on the type of services that you will be invoking. For
instance, a service that performs blast against the DragonDB may not be what
you want to do if you have some human sequence.

> should not services respond with "namespace is required"?
They should, but they might not. Some older services might return an 'empty
moby data block', die and return stack traces, or perform the service on
your data giving you unexpected results.

Hope ths helps,

Eddie


From martin.senger at gmail.com  Tue Sep  4 13:31:03 2007
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 4 Sep 2007 18:31:03 +0100
Subject: [MOBY-dev] to jMoby developers: please fix the javadoc warnings
Message-ID: <4d93f07c0709041031v6c56d52ah35c873a5953fad18@mail.gmail.com>

docs:
  [javadoc] Generating Javadoc
  [javadoc] Javadoc execution
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/CentralFactory.java:51:
warning - @uml.property is an unknown tag.
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/CentralFactory.java:66:
warning - @uml.property is an unknown tag.
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/AbstractMobyHandler.java:60:
warning - Tag @see: can't find change(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/AbstractMobyHandler.java:88:
warning - @param argument "localList" is not a parameter name.
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/DataTypeHandler.java:19:
warning - Tag @see: can't find register(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/DataTypeHandler.java:35:
warning - Tag @see: can't find unregister(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/NamespaceHandler.java:19:
warning - Tag @see: can't find register(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/NamespaceHandler.java:34:
warning - Tag @see: can't find unregister(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/ServiceHandler.java:106:
warning - Tag @see: can't find register(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/ServiceHandler.java:82:
warning - Tag @see: can't find unregister(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/ServiceTypeHandler.java:20:
warning - Tag @see: can't find register(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/ServiceTypeHandler.java:35:
warning - Tag @see: can't find unregister(T) in
org.biomoby.registry.sync.handler.MobyHandler

Thanks,
Martin

-- 
Martin Senger
   email: martin.senger at gmail.com
   skype: martinsenger

From Pieter.Neerincx at wur.nl  Wed Sep  5 12:29:03 2007
From: Pieter.Neerincx at wur.nl (Pieter Neerincx)
Date: Wed, 5 Sep 2007 18:29:03 +0200
Subject: [MOBY-dev] BioMOBY errors in Taverna 1.6+
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0C7@scomp0040.wurnet.nl>
Message-ID: <04A5F4E0-255D-4B4F-9F77-24D4CB15E30F@wur.nl>

Hi Eddie,

I just tried Taverna 1.6.0 and 1.6.1 and the processors to decompose  
complex BioMOBY objects are failing on me :(. Below is the output of  
a service that produces a generic Object object. All I tried to do  
was decompose the Object to get the value of the id attribute... It  
works beautifully in Taverna 1.5.2. Do I have to do something  
different in 1.6+ or is this a bug?

Cheers,

Pi
ERROR 2007-09-05 17:41:16,696 Error finding class  
org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
1.1} from 24248500
java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
         at java.lang.ClassLoader.defineClass1(Native Method)
         at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
         at java.security.SecureClassLoader.defineClass 
(SecureClassLoader.java:124)
         at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
         at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
         at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
         at java.security.AccessController.doPrivileged(Native Method)
         at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
         at  
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass( 
LocalArtifactClassLoader.java:178)
         at  
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass( 
LocalArtifactClassLoader.java:154)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
         at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
319)
         at org.biomoby.shared.data.MobyContentInstance.<init> 
(MobyContentInstance.java:108)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:93)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:48)
         at  
org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType 
(ParseMobyXML.java:75)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute 
(MobyParseDatatypeTask.java:100)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:576)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:517)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:436)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWi 
thoutIteration(ProcessorTask.java:642)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke 
(ProcessorTask.java:353)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRu 
n(ProcessorTask.java:280)
         at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run 
(NewState.java:67)
Exception in thread "Thread-106" java.lang.NoClassDefFoundError: org/ 
biomoby/shared/MobyPrefixResolver
         at org.biomoby.shared.data.MobyContentInstance.<init> 
(MobyContentInstance.java:108)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:93)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:48)
         at  
org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType 
(ParseMobyXML.java:75)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute 
(MobyParseDatatypeTask.java:100)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:576)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:517)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:436)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWi 
thoutIteration(ProcessorTask.java:642)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke 
(ProcessorTask.java:353)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRu 
n(ProcessorTask.java:280)
         at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run 
(NewState.java:67)
ERROR 2007-09-05 17:41:16,708 Error finding class  
org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
1.1} from 24248500
java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
         at java.lang.ClassLoader.defineClass1(Native Method)
         at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
         at java.security.SecureClassLoader.defineClass 
(SecureClassLoader.java:124)
         at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
         at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
         at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
         at java.security.AccessController.doPrivileged(Native Method)
         at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
         at  
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass( 
LocalArtifactClassLoader.java:178)
         at  
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass( 
LocalArtifactClassLoader.java:154)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
         at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
319)
         at org.biomoby.shared.data.MobyContentInstance.<init> 
(MobyContentInstance.java:108)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:93)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:48)
         at  
org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType 
(ParseMobyXML.java:75)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute 
(MobyParseDatatypeTask.java:100)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:576)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:517)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:436)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWi 
thoutIteration(ProcessorTask.java:642)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke 
(ProcessorTask.java:353)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRu 
n(ProcessorTask.java:280)
         at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run 
(NewState.java:67)
Exception in thread "Thread-104" java.lang.NoClassDefFoundError: org/ 
biomoby/shared/MobyPrefixResolver
         at org.biomoby.shared.data.MobyContentInstance.<init> 
(MobyContentInstance.java:108)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:93)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:48)
         at  
org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType 
(ParseMobyXML.java:75)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute 
(MobyParseDatatypeTask.java:100)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:576)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:517)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:436)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWi 
thoutIteration(ProcessorTask.java:642)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke 
(ProcessorTask.java:353)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRu 
n(ProcessorTask.java:280)
         at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run 
(NewState.java:67)
ERROR 2007-09-05 17:41:19,020 Error finding class  
org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
1.1} from 24248500
java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
         at java.lang.ClassLoader.defineClass1(Native Method)
         at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
         at java.security.SecureClassLoader.defineClass 
(SecureClassLoader.java:124)
         at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
         at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
         at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
         at java.security.AccessController.doPrivileged(Native Method)
         at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
         at  
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass( 
LocalArtifactClassLoader.java:178)
         at  
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass( 
LocalArtifactClassLoader.java:154)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
         at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
319)
         at org.biomoby.shared.data.MobyContentInstance.<init> 
(MobyContentInstance.java:108)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:93)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:48)
         at  
org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType 
(ParseMobyXML.java:75)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute 
(MobyParseDatatypeTask.java:100)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:576)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:517)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:436)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWi 
thoutIteration(ProcessorTask.java:642)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke 
(ProcessorTask.java:353)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRu 
n(ProcessorTask.java:280)
         at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run 
(NewState.java:67)
Exception in thread "Thread-116" java.lang.NoClassDefFoundError: org/ 
biomoby/shared/MobyPrefixResolver
         at org.biomoby.shared.data.MobyContentInstance.<init> 
(MobyContentInstance.java:108)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:93)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:48)
         at  
org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType 
(ParseMobyXML.java:75)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute 
(MobyParseDatatypeTask.java:100)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:576)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:517)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:436)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWi 
thoutIteration(ProcessorTask.java:642)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke 
(ProcessorTask.java:353)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRu 
n(ProcessorTask.java:280)
         at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run 
(NewState.java:67)


-------------------------------------------------------------
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
mail: pieter.neerincx at wur.nl
skype: pieter.online
------------------------------------------------------------


From edward.kawas at gmail.com  Wed Sep  5 13:20:51 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 5 Sep 2007 10:20:51 -0700
Subject: [MOBY-dev] BioMOBY errors in Taverna 1.6+
In-Reply-To: <04A5F4E0-255D-4B4F-9F77-24D4CB15E30F@wur.nl>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0C7@scomp0040.wurnet.nl>
	<04A5F4E0-255D-4B4F-9F77-24D4CB15E30F@wur.nl>
Message-ID: <000001c7efe1$1c77ecd0$6500a8c0@notebook>

Hi Pieter,

I will look into it. Something must have happened to the dependencies for
the plugin during the release of the latest version of taverna. Hopefully
its minor!

Eddie 

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org 
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of 
> Pieter Neerincx
> Sent: Wednesday, September 05, 2007 9:29 AM
> To: Core developer announcements
> Subject: [MOBY-dev] BioMOBY errors in Taverna 1.6+
> 
> Hi Eddie,
> 
> I just tried Taverna 1.6.0 and 1.6.1 and the processors to 
> decompose complex BioMOBY objects are failing on me :(. Below 
> is the output of a service that produces a generic Object 
> object. All I tried to do was decompose the Object to get the 
> value of the id attribute... It works beautifully in Taverna 
> 1.5.2. Do I have to do something different in 1.6+ or is this a bug?
> 
> Cheers,
> 
> Pi
> ERROR 2007-09-05 17:41:16,696 Error finding class 
> org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
> 1.1} from 24248500
> java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
>          at java.lang.ClassLoader.defineClass1(Native Method)
>          at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
>          at java.security.SecureClassLoader.defineClass
> (SecureClassLoader.java:124)
>          at 
> java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
>          at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
>          at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
>          at java.security.AccessController.doPrivileged(Native Method)
>          at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:178)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:154)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
>          at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
> 319)
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:93)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:48)
>          at
> org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType
> (ParseMobyXML.java:75)
>          at
> org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute
> (MobyParseDatatypeTask.java:100)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> Exception in thread "Thread-106" 
> java.lang.NoClassDefFoundError: org/ biomoby/shared/MobyPrefixResolver
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:93)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:48)
>          at
> org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType
> (ParseMobyXML.java:75)
>          at
> org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute
> (MobyParseDatatypeTask.java:100)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> ERROR 2007-09-05 17:41:16,708 Error finding class 
> org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
> 1.1} from 24248500
> java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
>          at java.lang.ClassLoader.defineClass1(Native Method)
>          at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
>          at java.security.SecureClassLoader.defineClass
> (SecureClassLoader.java:124)
>          at 
> java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
>          at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
>          at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
>          at java.security.AccessController.doPrivileged(Native Method)
>          at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:178)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:154)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
>          at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
> 319)
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:93)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:48)
>          at
> org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType
> (ParseMobyXML.java:75)
>          at
> org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute
> (MobyParseDatatypeTask.java:100)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> Exception in thread "Thread-104" 
> java.lang.NoClassDefFoundError: org/ biomoby/shared/MobyPrefixResolver
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:93)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:48)
>          at
> org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType
> (ParseMobyXML.java:75)
>          at
> org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute
> (MobyParseDatatypeTask.java:100)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> ERROR 2007-09-05 17:41:19,020 Error finding class 
> org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
> 1.1} from 24248500
> java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
>          at java.lang.ClassLoader.defineClass1(Native Method)
>          at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
>          at java.security.SecureClassLoader.defineClass
> (SecureClassLoader.java:124)
>          at 
> java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
>          at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
>          at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
>          at java.security.AccessController.doPrivileged(Native Method)
>          at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:178)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:154)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
>          at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
> 319)
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:93)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:48)
>          at
> org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType
> (ParseMobyXML.java:75)
>          at
> org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute
> (MobyParseDatatypeTask.java:100)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> Exception in thread "Thread-116" 
> java.lang.NoClassDefFoundError: org/ biomoby/shared/MobyPrefixResolver
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:93)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:48)
>          at
> org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType
> (ParseMobyXML.java:75)
>          at
> org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute
> (MobyParseDatatypeTask.java:100)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> 
> 
> -------------------------------------------------------------
> 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
> mail: pieter.neerincx at wur.nl
> skype: pieter.online
> ------------------------------------------------------------
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From ssoiland at cs.man.ac.uk  Thu Sep  6 09:06:18 2007
From: ssoiland at cs.man.ac.uk (Stian Soiland)
Date: Thu, 6 Sep 2007 14:06:18 +0100
Subject: [MOBY-dev] BioMOBY errors in Taverna 1.6+
In-Reply-To: <000001c7efe1$1c77ecd0$6500a8c0@notebook>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0C7@scomp0040.wurnet.nl>
	<04A5F4E0-255D-4B4F-9F77-24D4CB15E30F@wur.nl>
	<000001c7efe1$1c77ecd0$6500a8c0@notebook>
Message-ID: <43abb4040709060606n7d6619bie06958263647476d@mail.gmail.com>

On 9/5/07, Edward Kawas <edward.kawas at gmail.com> wrote:
> I will look into it. Something must have happened to the dependencies for
> the plugin during the release of the latest version of taverna. Hopefully
> its minor!
>

Hi!

This was due to that we missed out the xalan dependency of biomoby in
the 1.6.* releases of Taverna. The error you reported seems to not
occur on Mac OS X, but on Windows.

We have made a minor update that fixes this issue. If you have already
updated to Taverna 1.6.1.0 [1], click the yellow arrow in the right
corner to update to the latest version, 1.6.1.1. After a restart it
should work again.

[1] http://taverna.sourceforge.net/index.php?doc=download.html

-- 
Stian Soiland, myGrid team
School of Computer Science
The University of Manchester
http://www.cs.man.ac.uk/~ssoiland/

From Pieter.Neerincx at wur.nl  Thu Sep  6 11:31:17 2007
From: Pieter.Neerincx at wur.nl (Pieter Neerincx)
Date: Thu, 6 Sep 2007 17:31:17 +0200
Subject: [MOBY-dev] BioMOBY errors in Taverna 1.6+
In-Reply-To: <43abb4040709060606n7d6619bie06958263647476d@mail.gmail.com>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0C7@scomp0040.wurnet.nl>
	<04A5F4E0-255D-4B4F-9F77-24D4CB15E30F@wur.nl>
	<000001c7efe1$1c77ecd0$6500a8c0@notebook>
	<43abb4040709060606n7d6619bie06958263647476d@mail.gmail.com>
Message-ID: <9025C6AD-31B2-4364-AE9A-90868D6E93A7@wur.nl>

Hi Stian,

I was on Linux :) and hereby confirm decomposition of BioMOBY Objects  
works well again :)

Thanks!

Pi


On 6-sep-2007, at 15:06, Stian Soiland wrote:

> On 9/5/07, Edward Kawas <edward.kawas at gmail.com> wrote:
>> I will look into it. Something must have happened to the  
>> dependencies for
>> the plugin during the release of the latest version of taverna.  
>> Hopefully
>> its minor!
>>
>
> Hi!
>
> This was due to that we missed out the xalan dependency of biomoby in
> the 1.6.* releases of Taverna. The error you reported seems to not
> occur on Mac OS X, but on Windows.
>
> We have made a minor update that fixes this issue. If you have already
> updated to Taverna 1.6.1.0 [1], click the yellow arrow in the right
> corner to update to the latest version, 1.6.1.1. After a restart it
> should work again.
>
> [1] http://taverna.sourceforge.net/index.php?doc=download.html
>
> -- 
> Stian Soiland, myGrid team
> School of Computer Science
> The University of Manchester
> http://www.cs.man.ac.uk/~ssoiland/
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.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
mail: pieter.neerincx at wur.nl
skype: pieter.online
------------------------------------------------------------


From pieter.neerincx at wur.nl  Wed Sep 12 13:32:17 2007
From: pieter.neerincx at wur.nl (Pieter Neerincx)
Date: Wed, 12 Sep 2007 19:32:17 +0200
Subject: [MOBY-dev] Custom BioMOBY Central
Message-ID: <B09B6CF9-17F4-4018-9CC7-4A7009023EE6@wur.nl>

Hi Eddie,

I need your help once more. Recently I'm trying to update my alpha  
and beta test Centrals, so they'll have the same functionality as the  
official one. I've got the default stuff up and running on the code  
base (CVS checkout) of about a week ago. Works fine. I updated the  
servlets as well. Some of them work, but some don't. The ones  
required for Taverna are working, but I also wanted to use RDF docs  
for registration of services and updating of existing services. So  
far non of my services used a url to an RDF doc. After fiddling for  
some time with the servlets I found out I need a custom RDF Agent as  
well, but that wasn't mentioned in the docs for setting up a custom  
Central ... I'll update that once I have it all complete and running,  
but I can't get that RDF Agent fully functional :(.

The documentation for setting up an RDF Agent mentions the  
RDFagent_config.txt configuration file. I made the necessary changes  
there, but there's also RDFagent_config.xml. It's not modified  
automatically based on RDFagent_config.txt, so I was wondering what  
it's for and if I have to tweak that one as well.

Secondly, registering or deleting a service based on an RDF doc  
works, but my RDF Agent doesn't detect changes. The last thing it  
logs is:

                 Found a service (Boomerang/dev.bioinformatics.nl) in  
the registry that matches the one in the RDF ...
          Comparing them ...

I remember the discussion about LSIDs and was wondering if my Agent  
needs an LSID server to see that the service has changed. The  
context.xml configuration file for the servlets mentions an LSID  
server and LSID port, but since I don't have an LSID server I  
disabled that part. The docs for the RDF Agent nor for setting up a  
Central nor for installing the servlets mentioned setting up an LSID  
server... So do I need one or can I use the LSID server in Canada  
with my custom BioMOBY Central or can I forget about the LSID server  
completely and should I look somewhere else for a solution?

Cheers,

Pi

-------------------------------------------------------------
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
mail: pieter.neerincx at wur.nl
skype: pieter.online
------------------------------------------------------------


From edward.kawas at gmail.com  Wed Sep 12 14:19:56 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 12 Sep 2007 11:19:56 -0700
Subject: [MOBY-dev] Custom BioMOBY Central
In-Reply-To: <B09B6CF9-17F4-4018-9CC7-4A7009023EE6@wur.nl>
References: <B09B6CF9-17F4-4018-9CC7-4A7009023EE6@wur.nl>
Message-ID: <002a01c7f569$875e8bc0$6400a8c0@notebook>

Hi Pieter,

> Hi Eddie,
> 
> I need your help once more. Recently I'm trying to update my 
> alpha and beta test Centrals, so they'll have the same 
> functionality as the official one. I've got the default stuff 
> up and running on the code base (CVS checkout) of about a 
> week ago. Works fine. I updated the servlets as well. Some of 
> them work, but some don't. The ones required for Taverna are 
> working, but I also wanted to use RDF docs for registration 
> of services and updating of existing services. So far non of 
> my services used a url to an RDF doc. After fiddling for some 
> time with the servlets I found out I need a custom RDF Agent 
> as well, but that wasn't mentioned in the docs for setting up 
> a custom Central ... I'll update that once I have it all 
> complete and running, but I can't get that RDF Agent fully 
> functional :(.

This summer, during the moby 'java' developers meeting, we decided to remove
all of the java registry servlets and replace them with Perl ones so that we
could make the registry pure Perl (leading to a cpan release in the very
near future). While I have ported most of the code, there still remains some
work to do. That is why the documentation isn't 100% complete.

Having said that, I would take a look at the following webpage and set up
the Perl versions of the servlets: 
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/RegistrySc
ripts.html

The installation is fairly straight-forward and isn't as involved as the
servlets. Let me know if you  encounter any problems or irregularities so
that I can address them. So far, our Spanish colleagues and the main/testing
registry are using some or all of the Perl scripts.

> 
> The documentation for setting up an RDF Agent mentions the 
> RDFagent_config.txt configuration file. I made the necessary 
> changes there, but there's also RDFagent_config.xml. It's not 
> modified automatically based on RDFagent_config.txt, so I was 
> wondering what it's for and if I have to tweak that one as well.

You can ignore the xml file. It doesn't do anything (yet).

> 
> Secondly, registering or deleting a service based on an RDF 
> doc works, but my RDF Agent doesn't detect changes. The last 
> thing it logs is:
> I remember the discussion about LSIDs and was wondering if my 

The registry should update the LSIDs automatically upon registration, so you
don't have to worry about having your own lsid server. In fact, the java
servlets are only used for resolution and not generating the lsids.

You said that the log stated that it found differences ... 'Comparing them
...' Is that the only thing that it says? Do you think that you could send
me the RDF so I can play around with it?

Also, you may just want to check whether service updates are enabled in the
config file. 


> Cheers,
> 
> Pi

Thanks a lot!

Eddie


From edward.kawas at gmail.com  Wed Sep 12 14:26:34 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 12 Sep 2007 11:26:34 -0700
Subject: [MOBY-dev] Custom BioMOBY Central
References: <B09B6CF9-17F4-4018-9CC7-4A7009023EE6@wur.nl> 
Message-ID: <002f01c7f56a$75efd960$6400a8c0@notebook>

 

> Having said that, I would take a look at the following 
> webpage and set up the Perl versions of the servlets: 
> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_
> API/RegistryScripts.html

Sorry, I forgot to mention that the page mentioned above contains a
reference to a page 'moby.html'. That file doesn't exist yet so please don't
try looking for it!

Eddie


From markw at illuminae.com  Fri Sep 14 10:57:13 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 14 Sep 2007 07:57:13 -0700
Subject: [MOBY-dev] Heads-up: CVS copy of Perl Moby may be broken for a few
	hours
Message-ID: <op.tynftnvinbznux@personalpc>

Hi all,

Just a heads-up that I'm working on the data access layer of Moby Central  
and am committing changes as I go so that i can test them on various  
machines.  It's probably best to avoid checking-out the code for  
production use today.  There's a new release of the Perl code on the Moby  
homepage if you need it.

Cheers!

Mark



-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
dissemination, distribution or copying of this communication by  
unauthorized individuals is strictly prohibited. If you have received this  
communication in error, please notify the sender immediately by reply  
e-mail and delete the original and all copies from your system.
 

From markw at illuminae.com  Fri Sep 14 13:43:29 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 14 Sep 2007 10:43:29 -0700
Subject: [MOBY-dev] Small extension to the MOBY Central API
Message-ID: <op.tynnirmqnbznux@personalpc>

Hi all,

I just committed a small extension to the MOBY Central API and the Perl  
Client code.  It makes it easier to reconstruct the Service ontology from  
a call to the registry API (rather than getting the raw RDF from a  
getResourceLocations call).

When you call retrieveServiceTypes on MOBY Central, the returned XML now  
has one additional element "ISA" in it:

<serviceTypes>
<serviceType name="serviceTypeName" lsid="urn:lsid...">
   <Description><![CDATA[free text description here]]></Description>
   <contactEmail>your at email.here</contactEmail>
   <authURI>authority.uri.here</authURI>
*****->>  <ISA lsid="urn:lsid...">parentTypeName</ISA>
</serviceType>
   ...
   ...
</serviceTypes>


ISA provides the immediate parent of a Service ontology term (or is blank  
if you're at the root node).  The lsid attribute provides the lsid of that  
parent term (or is blank).  the ISA element is always provided.

Hopefully that will be useful to others, and hopefully wont break anyone!  
...it shouldn't... it's just one extra tag, the rest of the message is  
unchanged.

Please alert me if this breaks anything and I'll roll-back.  All tests  
pass from the Perl side.  Eddie, can you check the Java side?

M



-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
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From Pieter.Neerincx at wur.nl  Mon Sep 17 08:25:16 2007
From: Pieter.Neerincx at wur.nl (Pieter Neerincx)
Date: Mon, 17 Sep 2007 14:25:16 +0200
Subject: [MOBY-dev] Custom BioMOBY Central
In-Reply-To: <002f01c7f56a$75efd960$6400a8c0@notebook>
References: <B09B6CF9-17F4-4018-9CC7-4A7009023EE6@wur.nl>
	<002f01c7f56a$75efd960$6400a8c0@notebook>
Message-ID: <5AD7F388-51EF-4B59-B994-5E583D3AA17C@wur.nl>

Hi Eddie,

Thanks for the info. I think it's a good thing to move all the  
BioMOBY Central stuff to a single language. The installation  
intructions for BioMOBY Centrals were getting loooooong and debugging  
dependencies between all the different components involved was not  
really trivial anymore.

If I understand correctly the 'moby.html' page, which is not yet  
there, is the thing that would allow me to test whether the  
installation was successful and which explains how to use the  
different scripts. Without this documentation I'm more or less blind : 
(. (Ok, I could read the source code and try to reverse engineer, but  
would take a lot of time.) Is the RDF generator functionality not yet  
implemented in the Perl version or do I miss something? Maybe I  
should stick to the Perl/Java combi for now. At least it works with  
Taverna. I'm looking forward to testing the complete Perl solution  
though, so let me know if moby.html is born...

Cheers,

Pi



On 12-sep-2007, at 20:26, Edward Kawas wrote:

>
>
>> Having said that, I would take a look at the following
>> webpage and set up the Perl versions of the servlets:
>> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_
>> API/RegistryScripts.html
>
> Sorry, I forgot to mention that the page mentioned above contains a
> reference to a page 'moby.html'. That file doesn't exist yet so  
> please don't
> try looking for it!
>
> Eddie
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.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
mail: pieter.neerincx at wur.nl
skype: pieter.online
------------------------------------------------------------


From edward.kawas at gmail.com  Mon Sep 17 09:08:46 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 17 Sep 2007 06:08:46 -0700
Subject: [MOBY-dev] Custom BioMOBY Central
In-Reply-To: <5AD7F388-51EF-4B59-B994-5E583D3AA17C@wur.nl>
References: <B09B6CF9-17F4-4018-9CC7-4A7009023EE6@wur.nl><002f01c7f56a$75efd960$6400a8c0@notebook>
	<5AD7F388-51EF-4B59-B994-5E583D3AA17C@wur.nl>
Message-ID: <000e01c7f92b$e3016d60$6400a8c0@notebook>

Hi Pieter, 
 
> If I understand correctly the 'moby.html' page, which is not 
> yet there, is the thing that would allow me to test whether 
> the installation was successful and which explains how to use 
> the different scripts. Without this documentation I'm more or 
> less blind : 
> Cheers,

So moby.html is just a test page that would allow you to see whether or not
the scripts are successfully installed. The documentation for the
installation of the scripts is available at
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/RegistrySc
ripts.html

Eddie

> 
> Pi
> 
> 
> 
> On 12-sep-2007, at 20:26, Edward Kawas wrote:
> 
> >
> >
> >> Having said that, I would take a look at the following webpage and 
> >> set up the Perl versions of the servlets:
> >> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_
> >> API/RegistryScripts.html
> >
> > Sorry, I forgot to mention that the page mentioned above contains a 
> > reference to a page 'moby.html'. That file doesn't exist 
> yet so please 
> > don't try looking for it!
> >
> > Eddie
> >
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.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
> mail: pieter.neerincx at wur.nl
> skype: pieter.online
> ------------------------------------------------------------
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From joecker at mpiz-koeln.mpg.de  Fri Sep 28 05:03:11 2007
From: joecker at mpiz-koeln.mpg.de (Anika Joecker)
Date: Fri, 28 Sep 2007 11:03:11 +0200
Subject: [MOBY-dev] Problems with a new registered service
Message-ID: <200709281103.11522.joecker@mpiz-koeln.mpg.de>

Hi all,

I just registered a new service at the test registry, which outputs a 
collection of the new datatype "Annotated_GO_Term" (child of GO_Term).
Calling the service returns an empty list, although I can print out the 
results for this input in the jboss log.
We are not sure, if this is a problem of my implementation or if there is a 
problem in the BioMOBY API with the new datatype.

Here I send you an abstract of my code:

// store goterm from hash in GOTerm output objects
			Annotated_GO_Term[] gos = new Annotated_GO_Term[results.size()];

			Iterator it2 = results.iterator();
			int counter = 0;
			
			while (it2.hasNext()) {
				GOTerm go = (GOTerm) it2.next();
				Annotated_GO_Term goresult = new Annotated_GO_Term();
				goresult.set_Definition(new MobyString(go.getGo_term_name()));
				goresult.set_Term(new MobyString(go.getGo_term()));
				goresult.set_detailed_description(new MobyString(go.getDescription()));
				goresult.set_evidence_code(new MobyString(go.getConf()));
				goresult.set_process(new MobyString(go.getProcess()));
				gos[counter] = goresult;
				counter++;
			}
			conn.close();
			System.out.println("1.GO Term" + gos[0].get_Term());
			
			super.set_go_termSet(request, gos);

We tried to set the attributes of Annotated_GO_Term with Moby String or just 
as String, but neither worked.

Any idea how to solve this problem?

Thanks in advance!

Best,
Anika 


-- 
/--------------------------------------------------
  Dipl. Inf. Anika Joecker
  PHD student
  Plant Computational Biology group
  Max-Planck Institute for plant breeding research
  Carl-von-Linne Weg 10
  50829 Cologne
  Germany
  +49(0) 221 5062449
---------------------------------------------------/

From edward.kawas at gmail.com  Fri Sep 28 09:36:19 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 28 Sep 2007 06:36:19 -0700
Subject: [MOBY-dev] Problems with a new registered service
In-Reply-To: <200709281103.11522.joecker@mpiz-koeln.mpg.de>
References: <200709281103.11522.joecker@mpiz-koeln.mpg.de>
Message-ID: <000901c801d4$8f4530b0$6400a8c0@notebook>

Hi,

super.set_go_termSet(request, gos); 

should read

set_go_termSet(response, gos);

Hope that helps,

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org 
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of 
> Anika Joecker
> Sent: Friday, September 28, 2007 2:03 AM
> To: moby-dev at biomoby.org
> Subject: [MOBY-dev] Problems with a new registered service
> 
> Hi all,
> 
> I just registered a new service at the test registry, which 
> outputs a collection of the new datatype "Annotated_GO_Term" 
> (child of GO_Term).
> Calling the service returns an empty list, although I can 
> print out the results for this input in the jboss log.
> We are not sure, if this is a problem of my implementation or 
> if there is a problem in the BioMOBY API with the new datatype.
> 
> Here I send you an abstract of my code:
> 
> // store goterm from hash in GOTerm output objects
> 			Annotated_GO_Term[] gos = new 
> Annotated_GO_Term[results.size()];
> 
> 			Iterator it2 = results.iterator();
> 			int counter = 0;
> 			
> 			while (it2.hasNext()) {
> 				GOTerm go = (GOTerm) it2.next();
> 				Annotated_GO_Term goresult = 
> new Annotated_GO_Term();
> 				goresult.set_Definition(new 
> MobyString(go.getGo_term_name()));
> 				goresult.set_Term(new 
> MobyString(go.getGo_term()));
> 				
> goresult.set_detailed_description(new 
> MobyString(go.getDescription()));
> 				goresult.set_evidence_code(new 
> MobyString(go.getConf()));
> 				goresult.set_process(new 
> MobyString(go.getProcess()));
> 				gos[counter] = goresult;
> 				counter++;
> 			}
> 			conn.close();
> 			System.out.println("1.GO Term" + 
> gos[0].get_Term());
> 			
> 			super.set_go_termSet(request, gos);
> 
> We tried to set the attributes of Annotated_GO_Term with Moby 
> String or just as String, but neither worked.
> 
> Any idea how to solve this problem?
> 
> Thanks in advance!
> 
> Best,
> Anika 
> 
> 
> --
> /--------------------------------------------------
>   Dipl. Inf. Anika Joecker
>   PHD student
>   Plant Computational Biology group
>   Max-Planck Institute for plant breeding research
>   Carl-von-Linne Weg 10
>   50829 Cologne
>   Germany
>   +49(0) 221 5062449
> ---------------------------------------------------/
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From edward.kawas at gmail.com  Fri Sep 28 09:36:19 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 28 Sep 2007 06:36:19 -0700
Subject: [MOBY-dev] Problems with a new registered service
In-Reply-To: <200709281103.11522.joecker@mpiz-koeln.mpg.de>
References: <200709281103.11522.joecker@mpiz-koeln.mpg.de>
Message-ID: <000901c801d4$8f4530b0$6400a8c0@notebook>

Hi,

super.set_go_termSet(request, gos); 

should read

set_go_termSet(response, gos);

Hope that helps,

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org 
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of 
> Anika Joecker
> Sent: Friday, September 28, 2007 2:03 AM
> To: moby-dev at biomoby.org
> Subject: [MOBY-dev] Problems with a new registered service
> 
> Hi all,
> 
> I just registered a new service at the test registry, which 
> outputs a collection of the new datatype "Annotated_GO_Term" 
> (child of GO_Term).
> Calling the service returns an empty list, although I can 
> print out the results for this input in the jboss log.
> We are not sure, if this is a problem of my implementation or 
> if there is a problem in the BioMOBY API with the new datatype.
> 
> Here I send you an abstract of my code:
> 
> // store goterm from hash in GOTerm output objects
> 			Annotated_GO_Term[] gos = new 
> Annotated_GO_Term[results.size()];
> 
> 			Iterator it2 = results.iterator();
> 			int counter = 0;
> 			
> 			while (it2.hasNext()) {
> 				GOTerm go = (GOTerm) it2.next();
> 				Annotated_GO_Term goresult = 
> new Annotated_GO_Term();
> 				goresult.set_Definition(new 
> MobyString(go.getGo_term_name()));
> 				goresult.set_Term(new 
> MobyString(go.getGo_term()));
> 				
> goresult.set_detailed_description(new 
> MobyString(go.getDescription()));
> 				goresult.set_evidence_code(new 
> MobyString(go.getConf()));
> 				goresult.set_process(new 
> MobyString(go.getProcess()));
> 				gos[counter] = goresult;
> 				counter++;
> 			}
> 			conn.close();
> 			System.out.println("1.GO Term" + 
> gos[0].get_Term());
> 			
> 			super.set_go_termSet(request, gos);
> 
> We tried to set the attributes of Annotated_GO_Term with Moby 
> String or just as String, but neither worked.
> 
> Any idea how to solve this problem?
> 
> Thanks in advance!
> 
> Best,
> Anika 
> 
> 
> --
> /--------------------------------------------------
>   Dipl. Inf. Anika Joecker
>   PHD student
>   Plant Computational Biology group
>   Max-Planck Institute for plant breeding research
>   Carl-von-Linne Weg 10
>   50829 Cologne
>   Germany
>   +49(0) 221 5062449
> ---------------------------------------------------/
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From edward.kawas at gmail.com  Tue Sep  4 14:25:43 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 4 Sep 2007 07:25:43 -0700
Subject: [MOBY-dev] Services in registry
In-Reply-To: <620875BF-7DB2-47F8-A673-92CBFD27F93C@farmbio.uu.se>
References: <45EA4928-D121-4FCA-BB05-DB7067632F1F@farmbio.uu.se><002401c7eb1b$32d28410$6500a8c0@notebook>
	<620875BF-7DB2-47F8-A673-92CBFD27F93C@farmbio.uu.se>
Message-ID: <002f01c7eeff$7a9a9250$6500a8c0@notebook>

Hi, 
> I have not really understood this. Why do services require a 
> namespace?

When you register a service, the namespaces are specified for each
input/output. Depending on your client (or if you are using the API), the
namespace information is very easy to determine. In Taverna, this is
available as tooltips. In dashboard, you can get this information from the
'registry browser' when you click on individual services, etc.

Why do services require a namespace? Because it is the namespace and
identifier of an object that uniquely identifies data. Put another way, the
namespace helps narrow the scope of your data. Imagine that someone gave you
data identified by the string "424360". The question now becomes, what is
it? Now when you specify the namespace of "NCBI_gi", we know exactly what it
is and can use it.

Hopefully others can build upon my explanation if it doesn't make sense.

> If I am a novice user and have an aminoacid 
> sequence, how can I find available services for it then? 

Making a findService call to the registry stating that you want all services
that consume AminoAcidSequence. In fact, you probably could also search for
services that consume, FASTA, etc. Here you may or may not specify
namespace. It depends on the type of services that you will be invoking. For
instance, a service that performs blast against the DragonDB may not be what
you want to do if you have some human sequence.

> should not services respond with "namespace is required"?
They should, but they might not. Some older services might return an 'empty
moby data block', die and return stack traces, or perform the service on
your data giving you unexpected results.

Hope ths helps,

Eddie



From martin.senger at gmail.com  Tue Sep  4 17:31:03 2007
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 4 Sep 2007 18:31:03 +0100
Subject: [MOBY-dev] to jMoby developers: please fix the javadoc warnings
Message-ID: <4d93f07c0709041031v6c56d52ah35c873a5953fad18@mail.gmail.com>

docs:
  [javadoc] Generating Javadoc
  [javadoc] Javadoc execution
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/CentralFactory.java:51:
warning - @uml.property is an unknown tag.
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/CentralFactory.java:66:
warning - @uml.property is an unknown tag.
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/AbstractMobyHandler.java:60:
warning - Tag @see: can't find change(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/AbstractMobyHandler.java:88:
warning - @param argument "localList" is not a parameter name.
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/DataTypeHandler.java:19:
warning - Tag @see: can't find register(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/DataTypeHandler.java:35:
warning - Tag @see: can't find unregister(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/NamespaceHandler.java:19:
warning - Tag @see: can't find register(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/NamespaceHandler.java:34:
warning - Tag @see: can't find unregister(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/ServiceHandler.java:106:
warning - Tag @see: can't find register(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/ServiceHandler.java:82:
warning - Tag @see: can't find unregister(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/ServiceTypeHandler.java:20:
warning - Tag @see: can't find register(T) in
org.biomoby.registry.sync.handler.MobyHandler
  [javadoc]
/home/websites/biomoby.org/html/CVS_CONTENT/moby-live/Java/src/main/org/biomoby/registry/sync/handler/ServiceTypeHandler.java:35:
warning - Tag @see: can't find unregister(T) in
org.biomoby.registry.sync.handler.MobyHandler

Thanks,
Martin

-- 
Martin Senger
   email: martin.senger at gmail.com
   skype: martinsenger


From Pieter.Neerincx at wur.nl  Wed Sep  5 16:29:03 2007
From: Pieter.Neerincx at wur.nl (Pieter Neerincx)
Date: Wed, 5 Sep 2007 18:29:03 +0200
Subject: [MOBY-dev] BioMOBY errors in Taverna 1.6+
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0C7@scomp0040.wurnet.nl>
Message-ID: <04A5F4E0-255D-4B4F-9F77-24D4CB15E30F@wur.nl>

Hi Eddie,

I just tried Taverna 1.6.0 and 1.6.1 and the processors to decompose  
complex BioMOBY objects are failing on me :(. Below is the output of  
a service that produces a generic Object object. All I tried to do  
was decompose the Object to get the value of the id attribute... It  
works beautifully in Taverna 1.5.2. Do I have to do something  
different in 1.6+ or is this a bug?

Cheers,

Pi
ERROR 2007-09-05 17:41:16,696 Error finding class  
org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
1.1} from 24248500
java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
         at java.lang.ClassLoader.defineClass1(Native Method)
         at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
         at java.security.SecureClassLoader.defineClass 
(SecureClassLoader.java:124)
         at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
         at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
         at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
         at java.security.AccessController.doPrivileged(Native Method)
         at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
         at  
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass( 
LocalArtifactClassLoader.java:178)
         at  
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass( 
LocalArtifactClassLoader.java:154)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
         at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
319)
         at org.biomoby.shared.data.MobyContentInstance.<init> 
(MobyContentInstance.java:108)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:93)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:48)
         at  
org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType 
(ParseMobyXML.java:75)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute 
(MobyParseDatatypeTask.java:100)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:576)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:517)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:436)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWi 
thoutIteration(ProcessorTask.java:642)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke 
(ProcessorTask.java:353)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRu 
n(ProcessorTask.java:280)
         at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run 
(NewState.java:67)
Exception in thread "Thread-106" java.lang.NoClassDefFoundError: org/ 
biomoby/shared/MobyPrefixResolver
         at org.biomoby.shared.data.MobyContentInstance.<init> 
(MobyContentInstance.java:108)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:93)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:48)
         at  
org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType 
(ParseMobyXML.java:75)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute 
(MobyParseDatatypeTask.java:100)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:576)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:517)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:436)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWi 
thoutIteration(ProcessorTask.java:642)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke 
(ProcessorTask.java:353)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRu 
n(ProcessorTask.java:280)
         at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run 
(NewState.java:67)
ERROR 2007-09-05 17:41:16,708 Error finding class  
org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
1.1} from 24248500
java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
         at java.lang.ClassLoader.defineClass1(Native Method)
         at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
         at java.security.SecureClassLoader.defineClass 
(SecureClassLoader.java:124)
         at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
         at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
         at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
         at java.security.AccessController.doPrivileged(Native Method)
         at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
         at  
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass( 
LocalArtifactClassLoader.java:178)
         at  
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass( 
LocalArtifactClassLoader.java:154)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
         at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
319)
         at org.biomoby.shared.data.MobyContentInstance.<init> 
(MobyContentInstance.java:108)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:93)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:48)
         at  
org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType 
(ParseMobyXML.java:75)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute 
(MobyParseDatatypeTask.java:100)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:576)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:517)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:436)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWi 
thoutIteration(ProcessorTask.java:642)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke 
(ProcessorTask.java:353)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRu 
n(ProcessorTask.java:280)
         at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run 
(NewState.java:67)
Exception in thread "Thread-104" java.lang.NoClassDefFoundError: org/ 
biomoby/shared/MobyPrefixResolver
         at org.biomoby.shared.data.MobyContentInstance.<init> 
(MobyContentInstance.java:108)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:93)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:48)
         at  
org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType 
(ParseMobyXML.java:75)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute 
(MobyParseDatatypeTask.java:100)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:576)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:517)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:436)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWi 
thoutIteration(ProcessorTask.java:642)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke 
(ProcessorTask.java:353)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRu 
n(ProcessorTask.java:280)
         at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run 
(NewState.java:67)
ERROR 2007-09-05 17:41:19,020 Error finding class  
org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
1.1} from 24248500
java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
         at java.lang.ClassLoader.defineClass1(Native Method)
         at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
         at java.security.SecureClassLoader.defineClass 
(SecureClassLoader.java:124)
         at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
         at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
         at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
         at java.security.AccessController.doPrivileged(Native Method)
         at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
         at  
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass( 
LocalArtifactClassLoader.java:178)
         at  
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass( 
LocalArtifactClassLoader.java:154)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
         at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
319)
         at org.biomoby.shared.data.MobyContentInstance.<init> 
(MobyContentInstance.java:108)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:93)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:48)
         at  
org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType 
(ParseMobyXML.java:75)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute 
(MobyParseDatatypeTask.java:100)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:576)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:517)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:436)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWi 
thoutIteration(ProcessorTask.java:642)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke 
(ProcessorTask.java:353)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRu 
n(ProcessorTask.java:280)
         at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run 
(NewState.java:67)
Exception in thread "Thread-116" java.lang.NoClassDefFoundError: org/ 
biomoby/shared/MobyPrefixResolver
         at org.biomoby.shared.data.MobyContentInstance.<init> 
(MobyContentInstance.java:108)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:93)
         at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument 
(MobyDataUtils.java:48)
         at  
org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType 
(ParseMobyXML.java:75)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute 
(MobyParseDatatypeTask.java:100)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe 
nerateTemplates(ProcessorTask.java:576)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca 
tionWithRetryLogic(ProcessorTask.java:517)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn 
ce(ProcessorTask.java:436)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWi 
thoutIteration(ProcessorTask.java:642)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke 
(ProcessorTask.java:353)
         at  
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRu 
n(ProcessorTask.java:280)
         at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run 
(NewState.java:67)


-------------------------------------------------------------
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
mail: pieter.neerincx at wur.nl
skype: pieter.online
------------------------------------------------------------



From edward.kawas at gmail.com  Wed Sep  5 17:20:51 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 5 Sep 2007 10:20:51 -0700
Subject: [MOBY-dev] BioMOBY errors in Taverna 1.6+
In-Reply-To: <04A5F4E0-255D-4B4F-9F77-24D4CB15E30F@wur.nl>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0C7@scomp0040.wurnet.nl>
	<04A5F4E0-255D-4B4F-9F77-24D4CB15E30F@wur.nl>
Message-ID: <000001c7efe1$1c77ecd0$6500a8c0@notebook>

Hi Pieter,

I will look into it. Something must have happened to the dependencies for
the plugin during the release of the latest version of taverna. Hopefully
its minor!

Eddie 

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org 
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of 
> Pieter Neerincx
> Sent: Wednesday, September 05, 2007 9:29 AM
> To: Core developer announcements
> Subject: [MOBY-dev] BioMOBY errors in Taverna 1.6+
> 
> Hi Eddie,
> 
> I just tried Taverna 1.6.0 and 1.6.1 and the processors to 
> decompose complex BioMOBY objects are failing on me :(. Below 
> is the output of a service that produces a generic Object 
> object. All I tried to do was decompose the Object to get the 
> value of the id attribute... It works beautifully in Taverna 
> 1.5.2. Do I have to do something different in 1.6+ or is this a bug?
> 
> Cheers,
> 
> Pi
> ERROR 2007-09-05 17:41:16,696 Error finding class 
> org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
> 1.1} from 24248500
> java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
>          at java.lang.ClassLoader.defineClass1(Native Method)
>          at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
>          at java.security.SecureClassLoader.defineClass
> (SecureClassLoader.java:124)
>          at 
> java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
>          at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
>          at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
>          at java.security.AccessController.doPrivileged(Native Method)
>          at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:178)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:154)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
>          at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
> 319)
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:93)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:48)
>          at
> org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType
> (ParseMobyXML.java:75)
>          at
> org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute
> (MobyParseDatatypeTask.java:100)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> Exception in thread "Thread-106" 
> java.lang.NoClassDefFoundError: org/ biomoby/shared/MobyPrefixResolver
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:93)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:48)
>          at
> org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType
> (ParseMobyXML.java:75)
>          at
> org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute
> (MobyParseDatatypeTask.java:100)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> ERROR 2007-09-05 17:41:16,708 Error finding class 
> org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
> 1.1} from 24248500
> java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
>          at java.lang.ClassLoader.defineClass1(Native Method)
>          at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
>          at java.security.SecureClassLoader.defineClass
> (SecureClassLoader.java:124)
>          at 
> java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
>          at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
>          at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
>          at java.security.AccessController.doPrivileged(Native Method)
>          at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:178)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:154)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
>          at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
> 319)
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:93)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:48)
>          at
> org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType
> (ParseMobyXML.java:75)
>          at
> org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute
> (MobyParseDatatypeTask.java:100)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> Exception in thread "Thread-104" 
> java.lang.NoClassDefFoundError: org/ biomoby/shared/MobyPrefixResolver
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:93)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:48)
>          at
> org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType
> (ParseMobyXML.java:75)
>          at
> org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute
> (MobyParseDatatypeTask.java:100)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> ERROR 2007-09-05 17:41:19,020 Error finding class 
> org.biomoby.shared.MobyPrefixResolver ACL=loader{biomoby.org:jmoby: 
> 1.1} from 24248500
> java.lang.NoClassDefFoundError: org/apache/xml/utils/PrefixResolver
>          at java.lang.ClassLoader.defineClass1(Native Method)
>          at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
>          at java.security.SecureClassLoader.defineClass
> (SecureClassLoader.java:124)
>          at 
> java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
>          at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
>          at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
>          at java.security.AccessController.doPrivileged(Native Method)
>          at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:178)
>          at
> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.
> findClass(
> LocalArtifactClassLoader.java:154)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
>          at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: 
> 319)
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:93)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:48)
>          at
> org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType
> (ParseMobyXML.java:75)
>          at
> org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute
> (MobyParseDatatypeTask.java:100)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> Exception in thread "Thread-116" 
> java.lang.NoClassDefFoundError: org/ biomoby/shared/MobyPrefixResolver
>          at org.biomoby.shared.data.MobyContentInstance.<init>
> (MobyContentInstance.java:108)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:93)
>          at org.biomoby.shared.data.MobyDataUtils.fromXMLDocument
> (MobyDataUtils.java:48)
>          at
> org.biomoby.client.taverna.plugin.ParseMobyXML.getContentForDataType
> (ParseMobyXML.java:75)
>          at
> org.biomoby.client.taverna.plugin.MobyParseDatatypeTask.execute
> (MobyParseDatatypeTask.java:100)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.runAndGe
> nerateTemplates(ProcessorTask.java:576)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.doInvoca
> tionWithRetryLogic(ProcessorTask.java:517)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeOn
> ce(ProcessorTask.java:436)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.invokeWi
> thoutIteration(ProcessorTask.java:642)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke
> (ProcessorTask.java:353)
>          at
> uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTas
> k.handleRu
> n(ProcessorTask.java:280)
>          at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run
> (NewState.java:67)
> 
> 
> -------------------------------------------------------------
> 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
> mail: pieter.neerincx at wur.nl
> skype: pieter.online
> ------------------------------------------------------------
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From ssoiland at cs.man.ac.uk  Thu Sep  6 13:06:18 2007
From: ssoiland at cs.man.ac.uk (Stian Soiland)
Date: Thu, 6 Sep 2007 14:06:18 +0100
Subject: [MOBY-dev] BioMOBY errors in Taverna 1.6+
In-Reply-To: <000001c7efe1$1c77ecd0$6500a8c0@notebook>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0C7@scomp0040.wurnet.nl>
	<04A5F4E0-255D-4B4F-9F77-24D4CB15E30F@wur.nl>
	<000001c7efe1$1c77ecd0$6500a8c0@notebook>
Message-ID: <43abb4040709060606n7d6619bie06958263647476d@mail.gmail.com>

On 9/5/07, Edward Kawas <edward.kawas at gmail.com> wrote:
> I will look into it. Something must have happened to the dependencies for
> the plugin during the release of the latest version of taverna. Hopefully
> its minor!
>

Hi!

This was due to that we missed out the xalan dependency of biomoby in
the 1.6.* releases of Taverna. The error you reported seems to not
occur on Mac OS X, but on Windows.

We have made a minor update that fixes this issue. If you have already
updated to Taverna 1.6.1.0 [1], click the yellow arrow in the right
corner to update to the latest version, 1.6.1.1. After a restart it
should work again.

[1] http://taverna.sourceforge.net/index.php?doc=download.html

-- 
Stian Soiland, myGrid team
School of Computer Science
The University of Manchester
http://www.cs.man.ac.uk/~ssoiland/


From Pieter.Neerincx at wur.nl  Thu Sep  6 15:31:17 2007
From: Pieter.Neerincx at wur.nl (Pieter Neerincx)
Date: Thu, 6 Sep 2007 17:31:17 +0200
Subject: [MOBY-dev] BioMOBY errors in Taverna 1.6+
In-Reply-To: <43abb4040709060606n7d6619bie06958263647476d@mail.gmail.com>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0C7@scomp0040.wurnet.nl>
	<04A5F4E0-255D-4B4F-9F77-24D4CB15E30F@wur.nl>
	<000001c7efe1$1c77ecd0$6500a8c0@notebook>
	<43abb4040709060606n7d6619bie06958263647476d@mail.gmail.com>
Message-ID: <9025C6AD-31B2-4364-AE9A-90868D6E93A7@wur.nl>

Hi Stian,

I was on Linux :) and hereby confirm decomposition of BioMOBY Objects  
works well again :)

Thanks!

Pi


On 6-sep-2007, at 15:06, Stian Soiland wrote:

> On 9/5/07, Edward Kawas <edward.kawas at gmail.com> wrote:
>> I will look into it. Something must have happened to the  
>> dependencies for
>> the plugin during the release of the latest version of taverna.  
>> Hopefully
>> its minor!
>>
>
> Hi!
>
> This was due to that we missed out the xalan dependency of biomoby in
> the 1.6.* releases of Taverna. The error you reported seems to not
> occur on Mac OS X, but on Windows.
>
> We have made a minor update that fixes this issue. If you have already
> updated to Taverna 1.6.1.0 [1], click the yellow arrow in the right
> corner to update to the latest version, 1.6.1.1. After a restart it
> should work again.
>
> [1] http://taverna.sourceforge.net/index.php?doc=download.html
>
> -- 
> Stian Soiland, myGrid team
> School of Computer Science
> The University of Manchester
> http://www.cs.man.ac.uk/~ssoiland/
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.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
mail: pieter.neerincx at wur.nl
skype: pieter.online
------------------------------------------------------------



From pieter.neerincx at wur.nl  Wed Sep 12 17:32:17 2007
From: pieter.neerincx at wur.nl (Pieter Neerincx)
Date: Wed, 12 Sep 2007 19:32:17 +0200
Subject: [MOBY-dev] Custom BioMOBY Central
Message-ID: <B09B6CF9-17F4-4018-9CC7-4A7009023EE6@wur.nl>

Hi Eddie,

I need your help once more. Recently I'm trying to update my alpha  
and beta test Centrals, so they'll have the same functionality as the  
official one. I've got the default stuff up and running on the code  
base (CVS checkout) of about a week ago. Works fine. I updated the  
servlets as well. Some of them work, but some don't. The ones  
required for Taverna are working, but I also wanted to use RDF docs  
for registration of services and updating of existing services. So  
far non of my services used a url to an RDF doc. After fiddling for  
some time with the servlets I found out I need a custom RDF Agent as  
well, but that wasn't mentioned in the docs for setting up a custom  
Central ... I'll update that once I have it all complete and running,  
but I can't get that RDF Agent fully functional :(.

The documentation for setting up an RDF Agent mentions the  
RDFagent_config.txt configuration file. I made the necessary changes  
there, but there's also RDFagent_config.xml. It's not modified  
automatically based on RDFagent_config.txt, so I was wondering what  
it's for and if I have to tweak that one as well.

Secondly, registering or deleting a service based on an RDF doc  
works, but my RDF Agent doesn't detect changes. The last thing it  
logs is:

                 Found a service (Boomerang/dev.bioinformatics.nl) in  
the registry that matches the one in the RDF ...
          Comparing them ...

I remember the discussion about LSIDs and was wondering if my Agent  
needs an LSID server to see that the service has changed. The  
context.xml configuration file for the servlets mentions an LSID  
server and LSID port, but since I don't have an LSID server I  
disabled that part. The docs for the RDF Agent nor for setting up a  
Central nor for installing the servlets mentioned setting up an LSID  
server... So do I need one or can I use the LSID server in Canada  
with my custom BioMOBY Central or can I forget about the LSID server  
completely and should I look somewhere else for a solution?

Cheers,

Pi

-------------------------------------------------------------
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
mail: pieter.neerincx at wur.nl
skype: pieter.online
------------------------------------------------------------



From edward.kawas at gmail.com  Wed Sep 12 18:19:56 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 12 Sep 2007 11:19:56 -0700
Subject: [MOBY-dev] Custom BioMOBY Central
In-Reply-To: <B09B6CF9-17F4-4018-9CC7-4A7009023EE6@wur.nl>
References: <B09B6CF9-17F4-4018-9CC7-4A7009023EE6@wur.nl>
Message-ID: <002a01c7f569$875e8bc0$6400a8c0@notebook>

Hi Pieter,

> Hi Eddie,
> 
> I need your help once more. Recently I'm trying to update my 
> alpha and beta test Centrals, so they'll have the same 
> functionality as the official one. I've got the default stuff 
> up and running on the code base (CVS checkout) of about a 
> week ago. Works fine. I updated the servlets as well. Some of 
> them work, but some don't. The ones required for Taverna are 
> working, but I also wanted to use RDF docs for registration 
> of services and updating of existing services. So far non of 
> my services used a url to an RDF doc. After fiddling for some 
> time with the servlets I found out I need a custom RDF Agent 
> as well, but that wasn't mentioned in the docs for setting up 
> a custom Central ... I'll update that once I have it all 
> complete and running, but I can't get that RDF Agent fully 
> functional :(.

This summer, during the moby 'java' developers meeting, we decided to remove
all of the java registry servlets and replace them with Perl ones so that we
could make the registry pure Perl (leading to a cpan release in the very
near future). While I have ported most of the code, there still remains some
work to do. That is why the documentation isn't 100% complete.

Having said that, I would take a look at the following webpage and set up
the Perl versions of the servlets: 
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/RegistrySc
ripts.html

The installation is fairly straight-forward and isn't as involved as the
servlets. Let me know if you  encounter any problems or irregularities so
that I can address them. So far, our Spanish colleagues and the main/testing
registry are using some or all of the Perl scripts.

> 
> The documentation for setting up an RDF Agent mentions the 
> RDFagent_config.txt configuration file. I made the necessary 
> changes there, but there's also RDFagent_config.xml. It's not 
> modified automatically based on RDFagent_config.txt, so I was 
> wondering what it's for and if I have to tweak that one as well.

You can ignore the xml file. It doesn't do anything (yet).

> 
> Secondly, registering or deleting a service based on an RDF 
> doc works, but my RDF Agent doesn't detect changes. The last 
> thing it logs is:
> I remember the discussion about LSIDs and was wondering if my 

The registry should update the LSIDs automatically upon registration, so you
don't have to worry about having your own lsid server. In fact, the java
servlets are only used for resolution and not generating the lsids.

You said that the log stated that it found differences ... 'Comparing them
...' Is that the only thing that it says? Do you think that you could send
me the RDF so I can play around with it?

Also, you may just want to check whether service updates are enabled in the
config file. 


> Cheers,
> 
> Pi

Thanks a lot!

Eddie



From edward.kawas at gmail.com  Wed Sep 12 18:26:34 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 12 Sep 2007 11:26:34 -0700
Subject: [MOBY-dev] Custom BioMOBY Central
References: <B09B6CF9-17F4-4018-9CC7-4A7009023EE6@wur.nl> 
Message-ID: <002f01c7f56a$75efd960$6400a8c0@notebook>

 

> Having said that, I would take a look at the following 
> webpage and set up the Perl versions of the servlets: 
> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_
> API/RegistryScripts.html

Sorry, I forgot to mention that the page mentioned above contains a
reference to a page 'moby.html'. That file doesn't exist yet so please don't
try looking for it!

Eddie



From markw at illuminae.com  Fri Sep 14 14:57:13 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 14 Sep 2007 07:57:13 -0700
Subject: [MOBY-dev] Heads-up: CVS copy of Perl Moby may be broken for a few
	hours
Message-ID: <op.tynftnvinbznux@personalpc>

Hi all,

Just a heads-up that I'm working on the data access layer of Moby Central  
and am committing changes as I go so that i can test them on various  
machines.  It's probably best to avoid checking-out the code for  
production use today.  There's a new release of the Perl code on the Moby  
homepage if you need it.

Cheers!

Mark



-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
dissemination, distribution or copying of this communication by  
unauthorized individuals is strictly prohibited. If you have received this  
communication in error, please notify the sender immediately by reply  
e-mail and delete the original and all copies from your system.
 


From markw at illuminae.com  Fri Sep 14 17:43:29 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 14 Sep 2007 10:43:29 -0700
Subject: [MOBY-dev] Small extension to the MOBY Central API
Message-ID: <op.tynnirmqnbznux@personalpc>

Hi all,

I just committed a small extension to the MOBY Central API and the Perl  
Client code.  It makes it easier to reconstruct the Service ontology from  
a call to the registry API (rather than getting the raw RDF from a  
getResourceLocations call).

When you call retrieveServiceTypes on MOBY Central, the returned XML now  
has one additional element "ISA" in it:

<serviceTypes>
<serviceType name="serviceTypeName" lsid="urn:lsid...">
   <Description><![CDATA[free text description here]]></Description>
   <contactEmail>your at email.here</contactEmail>
   <authURI>authority.uri.here</authURI>
*****->>  <ISA lsid="urn:lsid...">parentTypeName</ISA>
</serviceType>
   ...
   ...
</serviceTypes>


ISA provides the immediate parent of a Service ontology term (or is blank  
if you're at the root node).  The lsid attribute provides the lsid of that  
parent term (or is blank).  the ISA element is always provided.

Hopefully that will be useful to others, and hopefully wont break anyone!  
...it shouldn't... it's just one extra tag, the rest of the message is  
unchanged.

Please alert me if this breaks anything and I'll roll-back.  All tests  
pass from the Perl side.  Eddie, can you check the Java side?

M



-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
dissemination, distribution or copying of this communication by  
unauthorized individuals is strictly prohibited. If you have received this  
communication in error, please notify the sender immediately by reply  
e-mail and delete the original and all copies from your system.
 



From Pieter.Neerincx at wur.nl  Mon Sep 17 12:25:16 2007
From: Pieter.Neerincx at wur.nl (Pieter Neerincx)
Date: Mon, 17 Sep 2007 14:25:16 +0200
Subject: [MOBY-dev] Custom BioMOBY Central
In-Reply-To: <002f01c7f56a$75efd960$6400a8c0@notebook>
References: <B09B6CF9-17F4-4018-9CC7-4A7009023EE6@wur.nl>
	<002f01c7f56a$75efd960$6400a8c0@notebook>
Message-ID: <5AD7F388-51EF-4B59-B994-5E583D3AA17C@wur.nl>

Hi Eddie,

Thanks for the info. I think it's a good thing to move all the  
BioMOBY Central stuff to a single language. The installation  
intructions for BioMOBY Centrals were getting loooooong and debugging  
dependencies between all the different components involved was not  
really trivial anymore.

If I understand correctly the 'moby.html' page, which is not yet  
there, is the thing that would allow me to test whether the  
installation was successful and which explains how to use the  
different scripts. Without this documentation I'm more or less blind : 
(. (Ok, I could read the source code and try to reverse engineer, but  
would take a lot of time.) Is the RDF generator functionality not yet  
implemented in the Perl version or do I miss something? Maybe I  
should stick to the Perl/Java combi for now. At least it works with  
Taverna. I'm looking forward to testing the complete Perl solution  
though, so let me know if moby.html is born...

Cheers,

Pi



On 12-sep-2007, at 20:26, Edward Kawas wrote:

>
>
>> Having said that, I would take a look at the following
>> webpage and set up the Perl versions of the servlets:
>> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_
>> API/RegistryScripts.html
>
> Sorry, I forgot to mention that the page mentioned above contains a
> reference to a page 'moby.html'. That file doesn't exist yet so  
> please don't
> try looking for it!
>
> Eddie
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.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
mail: pieter.neerincx at wur.nl
skype: pieter.online
------------------------------------------------------------



From edward.kawas at gmail.com  Mon Sep 17 13:08:46 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 17 Sep 2007 06:08:46 -0700
Subject: [MOBY-dev] Custom BioMOBY Central
In-Reply-To: <5AD7F388-51EF-4B59-B994-5E583D3AA17C@wur.nl>
References: <B09B6CF9-17F4-4018-9CC7-4A7009023EE6@wur.nl><002f01c7f56a$75efd960$6400a8c0@notebook>
	<5AD7F388-51EF-4B59-B994-5E583D3AA17C@wur.nl>
Message-ID: <000e01c7f92b$e3016d60$6400a8c0@notebook>

Hi Pieter, 
 
> If I understand correctly the 'moby.html' page, which is not 
> yet there, is the thing that would allow me to test whether 
> the installation was successful and which explains how to use 
> the different scripts. Without this documentation I'm more or 
> less blind : 
> Cheers,

So moby.html is just a test page that would allow you to see whether or not
the scripts are successfully installed. The documentation for the
installation of the scripts is available at
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/RegistrySc
ripts.html

Eddie

> 
> Pi
> 
> 
> 
> On 12-sep-2007, at 20:26, Edward Kawas wrote:
> 
> >
> >
> >> Having said that, I would take a look at the following webpage and 
> >> set up the Perl versions of the servlets:
> >> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_
> >> API/RegistryScripts.html
> >
> > Sorry, I forgot to mention that the page mentioned above contains a 
> > reference to a page 'moby.html'. That file doesn't exist 
> yet so please 
> > don't try looking for it!
> >
> > Eddie
> >
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.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
> mail: pieter.neerincx at wur.nl
> skype: pieter.online
> ------------------------------------------------------------
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From joecker at mpiz-koeln.mpg.de  Fri Sep 28 09:03:11 2007
From: joecker at mpiz-koeln.mpg.de (Anika Joecker)
Date: Fri, 28 Sep 2007 11:03:11 +0200
Subject: [MOBY-dev] Problems with a new registered service
Message-ID: <200709281103.11522.joecker@mpiz-koeln.mpg.de>

Hi all,

I just registered a new service at the test registry, which outputs a 
collection of the new datatype "Annotated_GO_Term" (child of GO_Term).
Calling the service returns an empty list, although I can print out the 
results for this input in the jboss log.
We are not sure, if this is a problem of my implementation or if there is a 
problem in the BioMOBY API with the new datatype.

Here I send you an abstract of my code:

// store goterm from hash in GOTerm output objects
			Annotated_GO_Term[] gos = new Annotated_GO_Term[results.size()];

			Iterator it2 = results.iterator();
			int counter = 0;
			
			while (it2.hasNext()) {
				GOTerm go = (GOTerm) it2.next();
				Annotated_GO_Term goresult = new Annotated_GO_Term();
				goresult.set_Definition(new MobyString(go.getGo_term_name()));
				goresult.set_Term(new MobyString(go.getGo_term()));
				goresult.set_detailed_description(new MobyString(go.getDescription()));
				goresult.set_evidence_code(new MobyString(go.getConf()));
				goresult.set_process(new MobyString(go.getProcess()));
				gos[counter] = goresult;
				counter++;
			}
			conn.close();
			System.out.println("1.GO Term" + gos[0].get_Term());
			
			super.set_go_termSet(request, gos);

We tried to set the attributes of Annotated_GO_Term with Moby String or just 
as String, but neither worked.

Any idea how to solve this problem?

Thanks in advance!

Best,
Anika 


-- 
/--------------------------------------------------
  Dipl. Inf. Anika Joecker
  PHD student
  Plant Computational Biology group
  Max-Planck Institute for plant breeding research
  Carl-von-Linne Weg 10
  50829 Cologne
  Germany
  +49(0) 221 5062449
---------------------------------------------------/


From edward.kawas at gmail.com  Fri Sep 28 13:36:19 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 28 Sep 2007 06:36:19 -0700
Subject: [MOBY-dev] Problems with a new registered service
In-Reply-To: <200709281103.11522.joecker@mpiz-koeln.mpg.de>
References: <200709281103.11522.joecker@mpiz-koeln.mpg.de>
Message-ID: <000901c801d4$8f4530b0$6400a8c0@notebook>

Hi,

super.set_go_termSet(request, gos); 

should read

set_go_termSet(response, gos);

Hope that helps,

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org 
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of 
> Anika Joecker
> Sent: Friday, September 28, 2007 2:03 AM
> To: moby-dev at biomoby.org
> Subject: [MOBY-dev] Problems with a new registered service
> 
> Hi all,
> 
> I just registered a new service at the test registry, which 
> outputs a collection of the new datatype "Annotated_GO_Term" 
> (child of GO_Term).
> Calling the service returns an empty list, although I can 
> print out the results for this input in the jboss log.
> We are not sure, if this is a problem of my implementation or 
> if there is a problem in the BioMOBY API with the new datatype.
> 
> Here I send you an abstract of my code:
> 
> // store goterm from hash in GOTerm output objects
> 			Annotated_GO_Term[] gos = new 
> Annotated_GO_Term[results.size()];
> 
> 			Iterator it2 = results.iterator();
> 			int counter = 0;
> 			
> 			while (it2.hasNext()) {
> 				GOTerm go = (GOTerm) it2.next();
> 				Annotated_GO_Term goresult = 
> new Annotated_GO_Term();
> 				goresult.set_Definition(new 
> MobyString(go.getGo_term_name()));
> 				goresult.set_Term(new 
> MobyString(go.getGo_term()));
> 				
> goresult.set_detailed_description(new 
> MobyString(go.getDescription()));
> 				goresult.set_evidence_code(new 
> MobyString(go.getConf()));
> 				goresult.set_process(new 
> MobyString(go.getProcess()));
> 				gos[counter] = goresult;
> 				counter++;
> 			}
> 			conn.close();
> 			System.out.println("1.GO Term" + 
> gos[0].get_Term());
> 			
> 			super.set_go_termSet(request, gos);
> 
> We tried to set the attributes of Annotated_GO_Term with Moby 
> String or just as String, but neither worked.
> 
> Any idea how to solve this problem?
> 
> Thanks in advance!
> 
> Best,
> Anika 
> 
> 
> --
> /--------------------------------------------------
>   Dipl. Inf. Anika Joecker
>   PHD student
>   Plant Computational Biology group
>   Max-Planck Institute for plant breeding research
>   Carl-von-Linne Weg 10
>   50829 Cologne
>   Germany
>   +49(0) 221 5062449
> ---------------------------------------------------/
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From edward.kawas at gmail.com  Fri Sep 28 13:36:19 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 28 Sep 2007 06:36:19 -0700
Subject: [MOBY-dev] Problems with a new registered service
In-Reply-To: <200709281103.11522.joecker@mpiz-koeln.mpg.de>
References: <200709281103.11522.joecker@mpiz-koeln.mpg.de>
Message-ID: <000901c801d4$8f4530b0$6400a8c0@notebook>

Hi,

super.set_go_termSet(request, gos); 

should read

set_go_termSet(response, gos);

Hope that helps,

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org 
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of 
> Anika Joecker
> Sent: Friday, September 28, 2007 2:03 AM
> To: moby-dev at biomoby.org
> Subject: [MOBY-dev] Problems with a new registered service
> 
> Hi all,
> 
> I just registered a new service at the test registry, which 
> outputs a collection of the new datatype "Annotated_GO_Term" 
> (child of GO_Term).
> Calling the service returns an empty list, although I can 
> print out the results for this input in the jboss log.
> We are not sure, if this is a problem of my implementation or 
> if there is a problem in the BioMOBY API with the new datatype.
> 
> Here I send you an abstract of my code:
> 
> // store goterm from hash in GOTerm output objects
> 			Annotated_GO_Term[] gos = new 
> Annotated_GO_Term[results.size()];
> 
> 			Iterator it2 = results.iterator();
> 			int counter = 0;
> 			
> 			while (it2.hasNext()) {
> 				GOTerm go = (GOTerm) it2.next();
> 				Annotated_GO_Term goresult = 
> new Annotated_GO_Term();
> 				goresult.set_Definition(new 
> MobyString(go.getGo_term_name()));
> 				goresult.set_Term(new 
> MobyString(go.getGo_term()));
> 				
> goresult.set_detailed_description(new 
> MobyString(go.getDescription()));
> 				goresult.set_evidence_code(new 
> MobyString(go.getConf()));
> 				goresult.set_process(new 
> MobyString(go.getProcess()));
> 				gos[counter] = goresult;
> 				counter++;
> 			}
> 			conn.close();
> 			System.out.println("1.GO Term" + 
> gos[0].get_Term());
> 			
> 			super.set_go_termSet(request, gos);
> 
> We tried to set the attributes of Annotated_GO_Term with Moby 
> String or just as String, but neither worked.
> 
> Any idea how to solve this problem?
> 
> Thanks in advance!
> 
> Best,
> Anika 
> 
> 
> --
> /--------------------------------------------------
>   Dipl. Inf. Anika Joecker
>   PHD student
>   Plant Computational Biology group
>   Max-Planck Institute for plant breeding research
>   Carl-von-Linne Weg 10
>   50829 Cologne
>   Germany
>   +49(0) 221 5062449
> ---------------------------------------------------/
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