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

[Pieter Neerincx]

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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>>
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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
>
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.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