[MOBY-dev] [Taverna-users] Add BioMOBY Parser functionality in taverna (1.6.2)

Fri Nov 9 16:50:09 UTC 2007

Hi Eddie,

I'm not sure if this is related, but recently I'm having problems  
with the BioMOBY Parsers as well. For example try to decompose the  
base64_encoded_svgz object to get to the SVGZ out... doesn't work. It  
gives me an "empty list".

Simple Objects without childs (primitives) work fine, but  
decomposition of more complex objects either doesn't work or  
sometimes I can not even add the parser. If the latter happens it  
takes a long time and my local test Central is hammered with queries,  
but if I leave it overnight there is no parser the next morning. I do  
get java errors on the commandline though. See below for the details.  
For an example try to decompose the collection "GI_Clusters" produced  
by the service GeneIlluminator_Disambiguate. For an example workflow  
for this service (without decomposition so far) have a look at  
https://www.bioinformatics.nl/phenolink/home/ -> Gene Illuminator  
services -> GeneIlluminator_Disambiguate.

Could you please look into this?

Cheers,

Pi

----------------------------------------------

exception in thread "AWT-EventQueue-0" java.lang.StackOverflowError
         at java.lang.ClassLoader.findBootstrapClass(Native Method)
         at java.lang.ClassLoader.findBootstrapClass0 
(ClassLoader.java:891)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:301)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:299)
         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java: 
268)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:299)
         at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
         at  
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass( 
LocalArtifactClassLoader.java:224)
         at  
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass( 
LocalArtifactClassLoader.java:184)
         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 java.lang.Class.getDeclaredMethods0(Native Method)
         at java.lang.Class.privateGetDeclaredMethods(Class.java:2395)
         at java.lang.Class.getDeclaredMethod(Class.java:1907)
         at  
org.apache.commons.discovery.tools.ClassUtils.findPublicStaticMethod 
(ClassUtils.java:116)
         at  
org.apache.axis.configuration.EngineConfigurationFactoryFinder.newFactor 
y(EngineConfigurationFactoryFinder.java:178)
         at  
org.apache.axis.configuration.EngineConfigurationFactoryFinder.access 
$200(EngineConfigurationFactoryFinder.java:46)
         at  
org.apache.axis.configuration.EngineConfigurationFactoryFinder$1.run 
(EngineConfigurationFactoryFinder.java:128)
         at java.security.AccessController.doPrivileged(Native Method)
         at  
org.apache.axis.configuration.EngineConfigurationFactoryFinder.newFactor 
y(EngineConfigurationFactoryFinder.java:113)
         at  
org.apache.axis.configuration.EngineConfigurationFactoryFinder.newFactor 
y(EngineConfigurationFactoryFinder.java:160)
         at org.apache.axis.client.Service.getEngineConfiguration 
(Service.java:813)
         at org.apache.axis.client.Service.getAxisClient(Service.java: 
104)
         at org.apache.axis.client.Service.<init>(Service.java:113)
         at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:192)
         at org.biomoby.client.CentralImpl.getDataTypeAsXML 
(CentralImpl.java:1045)
         at org.biomoby.client.CentralImpl.getDataType 
(CentralImpl.java:1038)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeProcessor.flattenChil 
dType(MobyParseDatatypeProcessor.java:271)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeProcessor.processData 
type(MobyParseDatatypeProcessor.java:211)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeProcessor.flattenChil 
dType(MobyParseDatatypeProcessor.java:283)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeProcessor.processData 
type(MobyParseDatatypeProcessor.java:211)
         at  
org.biomoby.client.taverna.plugin.MobyParseDatatypeProcessor.flattenChil 
dType(MobyParseDatatypeProcessor.java:283)
	... last two messages repeated many times ...

----------------------------------------------

On 5-nov-2007, at 11:51, Stian Soiland wrote:

> Eddie, who's one of the BioMoby developers, will have a look at  
> this bug.
>
> On 11/2/07, Edward Kawas <edward.kawas at gmail.com> wrote:
>> Hi Arnaud,
>>
>> That must be a bug. I will try to track it down and fix it.
>>
>> Thanks for the thorough report!
>>
>> Eddie
>>
>>> -----Original Message-----
>>> From: moby-dev-bounces at lists.open-bio.org
>>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of
>>> Arnaud Kerhornou
>>> Sent: Friday, November 02, 2007 12:29 PM
>>> To: taverna-users mailing list; Core developer announcements
>>> Subject: [MOBY-dev] Add BioMOBY Parser functionality in
>>> taverna (1.6.2)
>>>
>>> Hi everyone,
>>>
>>> I can not get a BioMOBY Parser for a Moby service called
>>> fromGenericSequenceCollectionToFASTA.
>>> I have no problem getting a parser with
>>> fromGenericSequenceToFASTA, which is very similar, the only
>>> difference is that it takes a GenericSequence object, instead
>>> of a collection of GenericSequence objects.
>>>
>>> I have attached a workflow and an input document,
>>>
>>> Any idea why I can't get a parser for
>>> fromGenericSequenceCollectionToFASTA service ?
>>>
>>> Thanks
>>> Arnaud
>>>
>>>
>>>
>>>
>>>
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>
>
> -- 
> Stian Soiland, myGrid team
> School of Computer Science
> The University of Manchester
> http://www.cs.man.ac.uk/~ssoiland/
>
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-------------------------------------------------------------
Wageningen University and Research centre (WUR)
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phone:  0317-483 039
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