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

Fri Sep 16 13:37:33 UTC 2005

Hi Eddie,

Thanks for the tools! Here's my feedback:

On 15-Sep-2005, at 8:17 PM, Edward Kawas wrote:

> Hi Pieter,
>
>
>
> I am sending you a link to a java based installer (GUI) that should  
> make installation very easy. If this is not useful for you, I will  
> create 3 war files and send you the links to them.
>
> http://bioinfo.icapture.ubc.ca/ekawas/servlets/install.jar
>
>
>
> Some people can run the jar file by double clicking it. If that  
> doesn’t work, then type at the command prompt
>
> java –jar install.jar
This gave me:

     The java class is not found: -jar

Works fine though without the -jar :) So 'java install.jar' was enough.
>
>
> If that doesn’t work, then email me back and I will send you 3 war  
> files and let you know what to do with them.
>
>
>
> Assuming that all goes well, there are a few things for you to do,  
> configuration wise.
>
>
>
> You will have to edit the biomoby.properties file in 3 different  
> locations:
>
>
>
> /tomcat/webapps/RESOURCES/WEB-INF/classes/org/BioMoby/registry/ 
> properties
>
> /tomcat/webapps/types/WEB-INF/classes/org/BioMoby/registry/properties
>
> /tomcat/webapps/authority/WEB-INF/classes/org/BioMoby/registry/ 
> properties
Close, but the installer created ..../biomoby/.... instead of ..../ 
BioMoby/.... .
>
> Open this file in any one of the locations and modify the properties:
>
> ‘config’  - this property points to mobycentral.conf(ig)
>
> ‘lsid_port’  -  this is the port that tomcat is running on
Ok, that is a bit confusing though. Shouldn't it be labelled  
'tomcat_port' port then?
> ‘lsid_domain’ – the domain that you would like your lsids to have
> ‘resources_script_domain’ – the domain that the RESOURCES script (a  
> servlet you have installed) uses.
>
>  Save this file in the 3 above stated locations.
Ok, done. Editing one file and copying it 2 times was fast enough. So  
it's not a big deal, but I do wonder you why you would want to have  
this redundancy. Are people ever going to use different settings in  
these 3 locations? If not, then why not have just one file to rule 'm  
all?
>  Restart tomcat and let me know what happens! My fingers are  
> crossed ;-)
Well, nothing yet. At least Tomcat doesn't complain. Seems to be Ok.  
But in Taverna I see my custom services from my local central as  
before and my custom objects are missing as before. You didn't  
mention it, but I assume I need to update my BioMOBY API stuff as  
well. So I tried an cvs up -d of moby-live. When I try make test for  
the Perl stuff I see a lot of tests failing.... Can I safely ignore  
them for now?

Pieter

> Eddie
>
>
>
> From: Pieter Neerincx [mailto:Pieter.Neerincx at wur.nl]
> Sent: Thursday, September 15, 2005 10:19 AM
> To: Edward Kawas
> Subject: Fwd: [MOBY-dev] Moby objects in Taverna. Where do they  
> come from?
>
>
>
> Hi Eddie,
>
>
>
> I suspect some problems with the mailinglist. I send the mail below  
> to the mailinglist yesterday, but so I haven't received it back  
> yet. Haven't received any other mails from the list anymore and one  
> of your mails of on 13-Sep-2005 was the last one showing up in the  
> online archive....
>
>
>
> Anyway, Tomcat is up and running so I'm awaiting further  
> instructions :).
>
>
>
> Cheers,
>
>
>
> Pieter
>
>
>
> Begin forwarded message:
>
>
>
>
> From: Pieter Neerincx <Pieter.Neerincx at wur.nl>
>
> Date: 14-September-2005 1:04:53 PM GMT+02:00
>
> To: Core developer announcements <moby-dev at portal.open-bio.org>
>
> Subject: Re: [MOBY-dev] Moby objects in Taverna. Where do they come  
> from?
>
>
>
>
>
> 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
>
>
>
>
>
>
>
>
>
>
>
>
>
> 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
>
>
>
>
>
>
>
>
>

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