[MOBY-dev] Registrying a moby service that takes an input collection

[Arnaud Kerhornou]

Hi everyone,

I want to register, at icapture registry, a moby service that takes a 
collection of DNASequence objects (the service is called 
'runMatScanGFFCollection')

The registration seems fine, but i get this message errors when trying 
to retrieve information from the registry (using a customised perl 
script of ours):

------------------------------->

../retrieveService.pl -x 4 -s runMatScanGFFCollection -w genome.imim.es
        * Name: runMatScanGFFCollection
        * Contact e-mail: akerhornou at imim.es
        * Provider: genome.imim.es
        * URL: http://genome.imim.es/cgi-bin/moby/MobyServices.cgi
        * Type: Analysis
        * Category: moby
        * Description: Promoter regions analysis program. Matscan is a 
program to search putative binding sites in genomic sequences. You can 
search for example the Transfac database, but also MEME or jaspar 
matrices. This service only accepts a collection of DNASequence objects 
and returns a collection of GFF objects (one GFF object for each 
DNASequence). If you want to give MatScan output to Meta-alignment 
program, you MUST use the 'log-likelihood matrix' mode.
        * Input:
                articleName: upstream_sequences collection of =>
                        articleName:  objectType: DNASequence
Use of uninitialized value in pattern match (m//) at 
/home/ug/arnau/cvs/moby-live/Perl/MOBY/Client/CollectionArticle.pm line 189.
Use of uninitialized value in pattern match (m//) at 
/home/ug/arnau/cvs/moby-live/Perl/MOBY/Client/CollectionArticle.pm line 189.
No such method: MOBY::Client::CollectionArticle::namespaces at 
../retrieveService.pl line 162

<------------------------------------

Does it mean the registration has failed ?

Anyway, the service is visible and i have also tried to execute it using 
taverna 1.3 and it fails (i have attached a workflow).

i get this error,

ERROR                                      2005-11-03 17:55:52,228 
(org.biomoby.client.taverna.plugin.BiomobyTask:233) - Error invoking 
biomoby service for biomoby
java.lang.ClassCastException
        at 
org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:95)
        at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:462)
        at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:407)        
at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:329)
        at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithoutIteration(ProcessorTask.java:521)
        at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:261)
        at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:199)
        at 
uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)

Any idea why it fails ?

thanks,
Arnaud
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