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

[Edward Kawas]

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
;-).

By the way, do you think that you could send me a workflow
whenever you notice something fishy?

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
> >>
> 
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