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

Tue Sep 13 15:48:47 UTC 2005

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