[MOBY-dev] Error handling in Taverna (was Re: [MOBY-l]updatingMOBY Central with input/outputarticleNames)
Edward Kawas
edward.kawas at gmail.com
Fri May 19 13:38:57 UTC 2006
Hi Pieter,
I was wondering if you could send me a workflow where the parser doesn't work.
I am glad that you like the rest of the updates!
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: Thursday, May 18, 2006 10:57 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Error handling in Taverna (was Re:
> [MOBY-l]updatingMOBY Central with input/outputarticleNames)
>
> Hi Eddie,
>
> Wow, this is great! Especially the secondary parameter
> support rocks.
> Previously I used Taverna for simple tests and for creating
> nice flowcharts of my workflows, but for the real work I used
> custom Perl clients. Now that secondaries are supported as
> well, I guess those custom Perl clients will start catching dust...
>
> I tried a lot and so far I can not find bugs for the handling
> of Secondaries, serviceNotes and the "Parse moby data -
> updated (2006)"
> Local Java widget :). Just a few comments, see further down.
>
> The "other" BioMOBY Object parser that is available form the
> "Moby Service Details" contextual menu doesn't work very well
> though. I tried to dissect an object with two childs twice.
> In one case the processor is correctly added to the workflow.
> Hence the output from the corresponding BioMOBY service goes
> into this BioMOBY parser processor, but there is only one
> additional output port (for one of the child objects). For
> the other child object there's no output port. I ran the
> workflow this way and I do get the correct output for the
> cild for which there was an output port. In the second case
> the parser processor was not connected to the output of the
> service and there were no output ports for the two child
> objects. If I decompose objects without children the parser
> works perfectly, but in that case one might just as well use
> the Local Java widget. I guess I cheered a bit prematurely
> for this one and it is a bit more work in progress, but it
> looks very promising.
>
> On 16-May-2006, at 3:57 AM, Edward Kawas wrote:
>
> > Hi Pieter,
> >
> > I uploaded a new build of Taverna that hopefully addresses the
> > servicenote absences.
> >
> > Please try it and let me know how it goes. All ports should have
> > servicenotes if the service provides them.
>
> Works as advertised :). The services I use only provide
> "human readable" stuff in the notes section of the
> serviceNotes. If a service has multiple outputs then the same
> human readable notes are shown multiple times. That is a bit
> redundant. Unless the BioMOBY plugin handles the latest error
> handling specs and shows errors specifically for a certain
> output, maybe it would be better the have an additional
> output port for the serviceNotes instead. But for now I'm
> just very happy to see those notes.
>
> > The build is available at
> > http://bioinfo.icapture.ubc.ca/ekawas/jars/taverna-workbench-1.3.2-
> > RC1.zip
>
> (For those who want to tried this on Linux / Unix machines:
> make sure to "dos2unix" some of the flat text files in that build.)
>
> > As for secondarys, if you context click services that are
> configurable
> > from the 'advanced workflow ...' and choose 'Configure Moby
> Service'
> > you will be able to use secodaries.
>
> Works! And even the enumeration lists and default values are
> supported. There is one thing missing though: I couldn't
> fetch descriptions for the secondaries. For the secondaries
> of my own services I know what they are doing, but for a
> remote service I wouldn't have a clue on how to use them. One
> final comment about the name for the contextual menus. Now there is:
> * Moby Service Details: for info about the required input or
> output Simples and Collections.
> * Configure Moby Service: for the optional Secondaries.
> The names of the contextual menus are rather non-descriptive.
> Why would Secondaries not be part of Moby Service Details?
> From the contextual menu names I can not figure out that one
> of them is for required stuff and the other for optional parameters.
>
> So it could be a bit more user friendly, but the bottom line
> is that I have been playing with Taverna for 1,5 day now like
> a little kid that just got an invaluable Christmas present.
> (Imagine what happens here when the object decomposition
> parser works as well :)).
>
> > I was pleasantly surprised that you had found this build of
> Taverna on
> > the web.
> > I had originally put it there for mark to download and try
> out before
> > I committed my changes to the cvs. I did think of asking you to try
> > it, but I didn't want to bother you.
>
> I wouldn't mind of you'd bother me a bit more often with cool
> tools like this!
>
> Thanks,
>
> Pi
>
> > Thanks,
> >
> > 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
> >>>>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> MOBY-dev mailing list
> >>>>> MOBY-dev at lists.open-bio.org
> >>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
> >>>>
> >>>> _______________________________________________
> >>>> MOBY-dev mailing list
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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
> >>
> >>
> >>
> >> _______________________________________________
> >> 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
>
>
>
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