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

Tue Sep 13 15:58:51 UTC 2005

Great. I will be waiting ;-)

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 8:49 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Moby objects in Taverna. Where do
> they come from?
> 
> Hi,
> 
> On 13-Sep-2005, at 4:43 PM, Edward Kawas wrote:
> 
> > Hi,
> >
> > For the Taverna workbench, download it temporarily from
> > http://bioinfo.icapture.ubc.ca/ekawas/taverna-workbench-
> 1.2.
> > zip
> 
> I will...
> 
> > 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.
> 
> Ok, that sounds like a much more elegant solution :).
> 
> > 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.
> 
> Ok, I will start with tomcat tomorrow... and will request
> further
> advice one I have that one up and running...
> 
> 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 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
> >>
> >
> > _______________________________________________
> > 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