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

Tue Sep 13 14:17:46 UTC 2005

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
>>
>
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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