[MOBY-dev] Error handling in Taverna (was Re: [MOBY-l] updatingMOBY Central with input/outputarticleNames)

Mon May 15 13:28:54 UTC 2006

Hi Pieter,

Putting the service notes into the the other ports is actually on my todo list.

My current objectives were to create the parser processor and support
secondarys. These tasks are done, but I am still testing the parser. 

I am glad that you liked the parser (which must have been hard to find,
considering it isnt documented yet).

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org 
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of 
> Pieter Neerincx
> Sent: Monday, May 15, 2006 5:18 AM
> To: Core developer announcements
> Subject: [MOBY-dev] Error handling in Taverna (was Re: 
> [MOBY-l] updatingMOBY Central with input/outputarticleNames)
> 
> Hi Eddie,
> 
> I tried the latest Taverna version today and I really enjoyed it :).  
> Automatic addition of articleNames works perfectly and the 
> new "Parse moby data" processor makes decomposing BioMOBY 
> objects a breeze.
> 
> I also browsed the online documentation again and noticed 
> that the "output" and "input" ports are depreciated and only 
> meant to be used for backwards compatibility. I used them to 
> get the full output from BioMOBY services. This allowed me to 
> have a look at the serviceNotes section in addition to the 
> mobyData section. In Taverna 1.3.2RC1 (with updated *.jar 
> from the BioMOBY site) this behaviour has changed and the 
> legacy input and output ports only return the mobyData block.  
> I realise now that I've been abusing those legacy ports for 
> something they were never made for, but it was the only way 
> to have a peek at diagnostic error massages from the 
> serviceNotes. (Or is there another
> way?) I'd love to see that kind of functionality return one day...
> 
> Thanks,
> 
> Pi
> 
> 
> On 2-May-2006, at 6:51 PM, Pieter Neerincx wrote:
> 
> > Hi Eddie,
> >
> > Super, I'll update.
> >
> > Thanks,
> >
> > Pi
> >
> > On 2-May-2006, at 3:16 PM, Edward Kawas wrote:
> >
> >> Hi Pieter,
> >>
> >> If you update your version of Taverna, you no longer have 
> to fill in 
> >> the article name as it is filled in automatically.
> >>
> >> Eddie
> >>
> >>
> >>> -----Original Message-----
> >>> From: moby-dev-bounces at lists.open-bio.org
> >>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter 
> >>> Neerincx
> >>> Sent: Tuesday, May 02, 2006 2:56 AM
> >>> To: mobydev
> >>> Subject: Re: [MOBY-dev] [MOBY-l] updating MOBY Central with 
> >>> input/outputarticleNames
> >>>
> >>> Hi all,
> >>>
> >>> On 25-Apr-2006, at 4:53 PM, Mark Wilkinson wrote:
> >>>
> >>>> Hi all,
> >>>>
> >>>> A few months ago the spec for service registration was
> >>> tightened such
> >>>> that all inputs and outputs require an articleName.  This is now 
> >>>> required also in Taverna workflows, and as such, many
> >>> "illegitimate"
> >>>> services currently in the registry will not function with
> >>> Taverna even
> >>>> though they are perfectly functional in reality.
> >>>>
> >>>> Given that these services are not looking for an
> >>> articleName, it will
> >>>> do no harm to them if one were added.  Thus the fastest way
> >>> to bring
> >>>> all service registrations back into compliance with the API
> >>> would be
> >>>> for me to manipulate the MOBY Central database directly and add 
> >>>> "dummy"
> >>>> articleNames
> >>>> ("input", "output") to all inputs and outputs that are
> >>> currently un-
> >>>> named.
> >>>>
> >>>> Would this bother anyone?
> >>>
> >>> It's fine with me. Actually I already registered most of 
> my services 
> >>> to use "input" and "output" as dummy articleNames to make 
> sure they 
> >>> worked in Taverna :). I was wondering the following though. Maybe 
> >>> this is a question for Eddie. If
> >>> * articleName attributes are required for input and 
> output articles 
> >>> and
> >>> * every service is registered with certain articleNames for their 
> >>> inputs and outputs,
> >>> * wouldn't it be possible to let Taverna fill in those 
> articleName 
> >>> attributes automatically?
> >>>
> >>> Currently I have to fill them in manually all the time 
> and that is a 
> >>> bit boring :(. Furthermore I already spent quite a bit of time 
> >>> staring at XML wondering why something didn't work ... and in the 
> >>> end it was a missing articleName or one with a typo.
> >>>
> >>> Cheers,
> >>>
> >>> Pi
> >>>
> >>>> Please let me know ASAP.
> >>>>
> >>>> Mark
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> moby-l mailing list
> >>>> moby-l at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/moby-l
> >>>
> >>>
> >>> 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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> >>> http://lists.open-bio.org/mailman/listinfo/moby-dev
> >>
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> >
> >
> > 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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> 
> 
> 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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