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

Wed Sep 14 11:04:53 UTC 2005

Ok, got Tomcat installed... Please tell me what to download from  
where and where to install it...

Thanks,

Pieter

On 13-Sep-2005, at 5:58 PM, Edward Kawas wrote:

> 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
>>
>
> _______________________________________________
> 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