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

[Edward Kawas]

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.

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?

Thanks a lot,

Eddie

> -----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: Tuesday, October 04, 2005 9:04 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Taverna plugin bug?: elements
> missing in BioMOBYobjects
> 
> 
> On 4-Oct-2005, at 5:12 PM, Edward Kawas wrote:
> 
> > No you are on to something! When I first created the
> plugin,
> > I used a certain xml parser based on w3c dom. I had to
> > switch to another parser and it seems that I was unaware
> of
> > its limitations (getChildren only gets the direct
> children
> > of an element).
> >
> > I will have this fixed fairly soon.
> 
> I'm looking forward to "testdrive" it :)
> 
> Thanks,
> 
> Pieter
> 
> >
> > Thanks,
> >
> > Eddie
> >
> >> -----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: Tuesday, October 04, 2005 8:07 AM
> >> To: Core developer announcements
> >> Subject: Re: [MOBY-dev] Taverna plugin bug?: elements
> >> missing in BioMOBYobjects
> >>
> >>
> >> On 4-Oct-2005, at 3:44 PM, Edward Kawas wrote:
> >>
> >>
> >>>> moby:MOBY
> >>>>      moby:Content
> >>>>          moby:Data
> >>>>              moby:Simple
> >>>>                      moby:My_Child_Level_1B
> >>>>                          moby:My_Child_Level_2A
> >>>>                          moby:My_Child_Level_2B
> >>>>
> >>>>
> >>>>
> >>>
> >>> Do you have an example of an object that has this type
> >>>
> >> of
> >>
> >>> structure?
> >>>
> >>
> >> Yes, try for example DnaSequenceHolder from the BioMOBY
> >> Central.
> >>
> >> I have been running some other tests in the mean time
> and
> >> so far
> >> almost every object I tried lacks child elements at
> level
> >> 2 or
> >> further down. The only one that does have an element at
> >> level 2 is
> >> the BlastJob object I have in my local Central. This
> one
> >> has Strings,
> >> Objects and a DataTime at level 2 or further down.
> >> Everything is
> >> missing except the DataTime primitive... I noticed that
> >> hardly anyone
> >> is using the DataTime primitive if I'm not the only one
> >> using. It is
> >> also hardly documented. Maybe it's just random noise in
> my
> >> testing or
> >> maybe I'm onto something....
> >>
> >> If you want to try the BlastJob object my local
> registry
> >> should still
> >> be accessible from outside at:
> >> http://137.224.52.237/phenolink/biomoby/central/cgi-
> >> bin/MOBY-Central.pl
> >>
> >> Hope this helps,
> >>
> >> Pi
> >>
> >>
> >>> Thanks,
> >>>
> >>> Eddie
> >>>
> >>> _______________________________________________
> >>> 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
> >> fax: 0317-483 584
> >> mobile: 06-143 66 783
> >> pieter.neerincx at wur.nl
> >>
> >>
> >>
> >> _______________________________________________
> >> 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
> fax: 0317-483 584
> mobile: 06-143 66 783
> pieter.neerincx at wur.nl
> 
> 
> 
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