[MOBY-dev] [Taverna-users] Add BioMOBY Parser functionality in taverna (1.6.2)
Eddie Kawas
edward.kawas at gmail.com
Fri Nov 9 17:57:19 UTC 2007
Hi Pieter,
I will look into it and hopefully fix it shortly. Not sure why its
failing ... I bet the base case for the parser is incorrect and thats
why you get the stack overflow.
Eddie
On Nov 9, 2007 8:50 AM, Pieter Neerincx <Pieter.Neerincx at wur.nl> wrote:
> 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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> > _______________________________________________
> > Taverna-users mailing list
> > Taverna-users at lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/taverna-users
> > Documentation: http://www.mygrid.org.uk/usermanual1.6/
> > FAQ: http://www.mygrid.org.uk/wiki/Mygrid/TavernaFaq
> > Biological Services: http://www.mygrid.org.uk/wiki/Mygrid/
> > BiologicalWebServices
> >
>
> -------------------------------------------------------------
> Wageningen University and Research centre (WUR)
> Laboratory of Bioinformatics
> Transitorium (building 312) room 1034
>
> Dreijenlaan 3
> 6703 HA Wageningen
> The Netherlands
>
> phone: 0317-483 039
> fax: 0317-483 584
> mobile: 06-143 66 783
> mail: pieter.neerincx at wur.nl
> skype: pieter.online
> ------------------------------------------------------------
>
>
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