[MOBY-dev] Moby objects in Taverna. Where do they come from?

Tue Sep 13 14:43:32 UTC 2005

Hi,

For the Taverna workbench, download it temporarily from
http://bioinfo.icapture.ubc.ca/ekawas/taverna-workbench-1.2.
zip
This version contains my changes (the ones that are in the
Taverna CVS).

The Moby api actually now has a method in it called
getResources (or something similar to that) that returns the
locations of these documents for a registry. So in the newly
updated version of the plugin, I have removed the textbox
that asks for this url and replaced it with an api call.
(a description on the Moby plugin can be found at
http://bioinfo.icapture.ubc.ca/ekawas/guide/biomobyworker.ht
ml but is being changed to reflect the api calling).

You are correct in saying that we are moving towards having
Services and datatypes described by RDF.

Finally, as for the servlet installation, if you are
interested, I can guide you through this relatively painless
procedure. I would just need to update certain files that
you need to download and you would have to install tomcat.

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, September 13, 2005 7:18 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Moby objects in Taverna. Where do
> they come from?
> 
> Hi Eddie,
> 
> On 13-Sep-2005, at 3:08 PM, Edward Kawas wrote:
> 
> > Hi,
> >
> > Objects aren't hard coded. They just have to be
> registered
> > in Mobycentral.
> 
> Today I fetched the source code for Taverna and 'grep'ed
> over the
> files. There are several instances where the path to the
> central
> biomoby central and an RDF file are hardcoded outside the
> files in
> conf/. Sometime ago I started to work with Taverna and the
> user
> manual only mentions the path to a biomoby central in the
> conf/
> mygrid.properties file. So I appended my local biomoby
> central to
> this conf file and expected this would allow me to use
> both services
> and objects registered in my local central. I think that
> the current
> situation where service info is fetched from a URL in the
> conf/
> mygrid.properties file and object info is fetched from a
> RDF file at
> a different location is very confusing and needlessly
> complex.
> Especially since I cannot supply an URL to a custom RDF
> file for my
> objects in the conf/mygrid.properties file. I did see
> though that I
> can right-click in Taverna to add a scavenger and than I
> can supply
> both an URL to my local central and an URL to this RDF
> file for the
> objects.
> 
> I also browsed the mailinglist and wiki. Did I understand
> correctly
> that the current situation is a temporary solution and
> that
> eventually all info (hence services and objects) will be
> described
> using RDF? Please correct me if I'm wrong...
> 
> > I am not sure if you are up for it, but you could always
> > install the servlets
> 
> Are those servlets generating this RDF file from the info
> in a central?
> Is this documented somewhere? I couldn't find any
> reference to
> servlets at
> http://www.biomoby.org/InstallingMOBYCentral.html ...
> 
> > (I could help you).
> 
> Your help is much appreciated! Thanks,
> 
> Pieter
> 
> >
> > 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, September 13, 2005 1:35 AM
> >> To: Core developer announcements
> >> Subject: Re: [MOBY-dev] Moby objects in Taverna. Where
> do
> >> they come from?
> >>
> >> Hi Eddie,
> >>
> >> On 12-Sep-2005, at 5:10 PM, Edward Kawas wrote:
> >>
> >>
> >>> Hi,
> >>>
> >>> The answer basically is that you also need to set up
> >>>
> >> some
> >>
> >>> servlets (RESOURCES script, types, etc), if you have a
> >>> custom registry.
> >>>
> >>
> >> Thanks for the quick feedback. I was already afraid it
> >> would be
> >> something like that :(.
> >>
> >>
> >>> So Taverna is basically reading in your services, and
> >>>
> >> cannot
> >>
> >>> find the objects, so it probably defaults to the
> >>>
> >> Mobycentral
> >>
> >>> registry.
> >>>
> >>
> >> Would it help if I register my objects at THE central
> >> mobycentral
> >> instead of in my local central? Or are the objects
> >> hardcoded in some
> >> jar file (like lib/jmoby.jar perhaps)?
> >>
> >> Pieter
> >>
> >>
> >>>
> >>> 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: Monday, September 12, 2005 8:06 AM
> >>>> To: Core developer announcements
> >>>> Subject: [MOBY-dev] Moby objects in Taverna. Where do
> >>>>
> >> they
> >>
> >>>> come from?
> >>>>
> >>>> Hi all,
> >>>>
> >>>> I'm having some trouble to make BioMOBY work with
> >>>>
> >> Taverna.
> >>
> >>>> I have a
> >>>> local development Moby central. When I register both
> >>>>
> >> new
> >>
> >>>> services and
> >>>> new objects I notice that only my custom services are
> >>>> listed in
> >>>> Taverna. The list of moby objects is not in sync with
> >>>>
> >> what
> >>
> >>>> is
> >>>> registered in my central. So where does Taverna get
> >>>>
> >> those
> >>
> >>>> objects
> >>>> from and how do I get my own objects in there? Does
> >>>>
> >> anyone
> >>
> >>>> have a clue?
> >>>>
> >>>> Cheers,
> >>>>
> >>>> Pieter
> >>>>
> >>>> 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
> >>
> >>
> >>
> >> _______________________________________________
> >> 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
> 
> 
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at biomoby.org
> http://www.biomoby.org/mailman/listinfo/moby-dev