[MOBY-dev] Taverna plugin bug?: elements missing in BioMOBYobjects

[Edward Kawas]

Sorry Pieter,

I am still looking into it. Since the last time you tested,
I fixed numerous logic errors. I think that ultimately you
will notice that the article name issue will be fixed. I
will let you know when a new test version is out. I thought
I just had one, but a workflow that executes every branch of
a service found an error.

Thanks for your patience!

Ed

> -----Original Message-----
> From: moby-dev-bounces at portal.open-bio.org [mailto:moby-
> dev-bounces at portal.open-bio.org] On Behalf Of Pieter
> Neerincx
> Sent: Thursday, October 13, 2005 8:47 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Taverna plugin bug?: elements
> missing in BioMOBYobjects
> 
> Hi Eddie,
> 
> On 11-Oct-2005, at 6:58 AM, Edward Kawas wrote:
> 
> > Hi Pieter,
> >
> > I uploaded 2 new files. I am not sure if your bug is
> fixed,
> > but I thought that I would let you know. I have made new
> > additions and I modified some of the xml parsing, so
> while I
> > haven't worked on your bug, it may be fixed (or made
> worse
> > ;-).
> 
> Well just tested the new versions and to be honest it kind
> of made it
> really bad :( I can not get any output anymore from any
> BioMOBY
> service. So I switched back to the previous versions of
> the *.jar
> files you had uploaded and apart from the missing
> articleName
> attribute things work again :).
> 
> >
> > By the way, do you think that you could send me a
> workflow
> > whenever you notice something fishy?
> 
> Sure. You mean the workflow saved as a scufl xml file I
> assume. Will
> do that in the future, but, in this case just try any
> BioMOBY
> service. Maybe some other files got updated as well in
> your
> development version apart from the 2 uploaded files...
> 
> Cheers,
> 
> Pieter
> 
> >
> > Thanks,
> >
> > Eddie
> >
> > http://bioinfo.icapture.ubc.ca/ekawas/jars/taverna-
> 1.3.jar
> > http://bioinfo.icapture.ubc.ca/ekawas/jars/jmoby.jar
> >
> >
> >> -----Original Message-----
> >> From: moby-dev-bounces at portal.open-bio.org
> [mailto:moby-
> >> dev-bounces at portal.open-bio.org] On Behalf Of Pieter
> >> Neerincx
> >> Sent: Friday, October 07, 2005 10:25 AM
> >> To: Core developer announcements
> >> Subject: Re: [MOBY-dev] Taverna plugin bug?: elements
> >> missing in BioMOBYobjects
> >>
> >> Hi Eddie,
> >>
> >> Sorry, I cheered premature :(. For one of my services I
> >> use the
> >> articleName attribute of two String objects to know
> which
> >> one
> >> contains which data. Hence I have something like:
> >>
> >> <SomeObject id="" namespace="some.ns">
> >>      <String id="" namespace="another.ns"
> >> articleName="this.one">
> >>          Bla bla
> >>      </String>
> >>      <String id="" namespace="another.ns"
> >> articleName="the.other.one">
> >>          Alb alb
> >>      </String>
> >> <SomeObject>
> >>
> >> The Object my service receives in Taverna lacks the
> >> articleName
> >> attributes for it's String childs :(. Hence it becomes
> >> this:
> >>
> >> <SomeObject id="" namespace="some.ns">
> >>      <String id="" namespace="another.ns">
> >>          Bla bla
> >>      </String>
> >>      <String id="" namespace="another.ns">
> >>          Alb alb
> >>      </String>
> >> <SomeObject>
> >>
> >> Looks like the fix introduced a new bug as well...
> >>
> >> Pieter
> >>
> >> On  07Oct2005, at 11:30, Pieter Neerincx wrote:
> >>
> >>
> >>> Hi Eddie,
> >>>
> >>> On 5-Oct-2005, at 2:52 AM, Edward Kawas wrote:
> >>>
> >>>
> >>>
> >>>> Hi Pieter!
> >>>>
> >>>> I tracked down the bug and I fixed it (*fingers
> >>>>
> >> crossed*).
> >>
> >>>>
> >>>> I am placing 2 jar files at the following links that
> >>>>
> >> need to
> >>
> >>>> replace the ones in your /taverna-workbench-1.3/lib/
> >>>> directory:
> >>>> http://bioinfo.icapture.ubc.ca/ekawas/jars/taverna-
> >>>>
> >> 1.3.jar
> >>
> >>>> http://bioinfo.icapture.ubc.ca/ekawas/jars/jmoby.jar
> >>>>
> >>>> Be sure to backup the 2 files you are about to
> replace,
> >>>>
> >> just
> >>
> >>>> in case!
> >>>>
> >>>> Then try out your workflows and let me know what
> >>>>
> >> happens.
> >>
> >>>>
> >>>>
> >>>
> >>> I did some simple tests with the objects that failed
> >>>
> >> previously and
> >>
> >>> so far so good :)
> >>>
> >>> Thanks for the quick fix!
> >>>
> >>>
> >>>
> >>>>
> >>>> Also, if all is well, do you think that you could
> send
> >>>>
> >> me
> >>
> >>>> one of those workflows so I can use it as an example?
> >>>>
> >>>>
> >>>
> >>> After a lot of trail and error playing with a local
> >>>
> >> central I think
> >>
> >>> it's about time I register my services and objects at
> >>>
> >> the central
> >>
> >>> Central as well. Will do so once the central Central
> >>>
> >> databases are
> >>
> >>> migrated to the new API...
> >>>
> >>> Cheers,
> >>>
> >>> Pi
> >>>
> >>>
> >>>
> >>>> Thanks a lot,
> >>>>
> >>>> Eddie
> >>>>
> >>>>
> >>
> >> _______________________________________________
> >> MOBY-dev mailing list
> >> MOBY-dev at biomoby.org
> >> http://www.biomoby.org/mailman/listinfo/moby-dev
> >>
> >
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at biomoby.org
> > http://www.biomoby.org/mailman/listinfo/moby-dev
> >
> 
> 
> Wageningen University and Research centre (WUR)
> Laboratory of Bioinformatics
> Transitorium (building 312) room 1034
> Dreijenlaan 3
> 6703 HA Wageningen
> The Netherlands
> phone: 0317-483 060
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> mobile: 06-143 66 783
> pieter.neerincx at wur.nl
> 
> 
> 
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