From ytanoh at cs.man.ac.uk  Mon Feb  2 11:48:07 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Mon, 2 Feb 2009 16:48:07 -0000
Subject: [BioCatalogue-developers] FW: bioinformatics service monitoring
Message-ID: <75BC3BFCB7354FD198C42F4772C6A6C3@franckPC>


Guys we need to follow this one closely... 
Should I arrange a meeting... probably Skype? 

Franck

-----Original Message-----
From: Francois Moreews [mailto:fmoreews at irisa.fr] 
Sent: 02 February 2009 16:36
To: Franck Tanoh
Subject: Re: bioinformatics service monitoring

Hi Franck,

Welcome in the father's club! I hope you sleep enough ;-)

The QBIOS taverna 1.7 plugin (SSO)  is available at
http://qbios.gforge.inria.fr/repository/
It is a functionnal prototype.

The SSFA command line is available at
http://qbios.gforge.inria.fr/SSFA_aggregator.zip
(it can generate report like 
http://lipm-bioinfo.toulouse.inra.fr/biomoby/QBIOS/output/report.html)
It is really easy to use.

If you and your collegues are interested in QBIOS API, you can ask for a 
gforge account at
https://gforge.inria.fr/account/register.php
 
I will be happy to present  our work to the biocatalogue developpers team.
I could be productive to merge our effort on service monitoring.

regards,

Francois



Franck Tanoh a ?crit :
> Hi Francois, 
>
> Happy New Year 2009!!!
>
> Sorry for the delayed response, I've been out on paternity leave for a
> while. 
> QBIOS is looking good; is the Taverna plugin ready for download? I'll be
> glad to test it. 
> Service quality is a key requirement of BioCatalogue. Looking at your
slides
> and demo, I can see that QBIOS addresses most of it. Do you have any API
> available I can point the BioCatalogue developer to? If you have a mailing
> list for the project I can sign up to for update, please let me know. 
>
>   
>> I'm following the evolution of the biocatalog project with the 
>> BIOCATALOGUE-FRIENDS list with interest.
>>     
> Cool, your comments, suggestions and feedbacks are welcome.
> We're aiming to release our first public beta in April. More information
> will be posted on the mailing list soon.  
>
> In case you haven't noticed it yet, Taverna 2 is out:
> http://www.mygrid.org.uk/ 
>
> Cheers, 
> Franck
>
>
>
> -----Original Message-----
> From: Francois Moreews INRA [mailto:fmoreews at irisa.fr] 
> Sent: 19 December 2008 09:22
> To: ytanoh at CS.MAN.AC.UK
> Cc: carole.goble at manchester.ac.uk
> Subject: bioinformatics service monitoring
>
> Hello Franck,
>
> I'm following the evolution of the biocatalog project with the 
> BIOCATALOGUE-FRIENDS list with interest.
>
> When we met us in Rennes, I told you that I was involved in a 
> bioinformatics service monitoring project (QBIOS).
> At BOSC 2008, I quickly explained to prof Goble the goal of this project.
> You can find more information about the QBIOS project  at
> http://qbios.gforge.inria.fr/
>
>
> best regards,
> Francois
>
>
>
>
>
>
>
>
>
>   



From jits at cs.man.ac.uk  Tue Feb  3 05:25:08 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 03 Feb 2009 10:25:08 +0000
Subject: [BioCatalogue-developers] [Fwd: [Myexperiment-topsecret] meetings
	this week]
Message-ID: <49881B84.4050901@cs.man.ac.uk>

Hi guys,

For tomorrow's chat, we will be doing it at 4pm.

Cheers,
Jits


-------- Original Message --------
Subject: 	[Myexperiment-topsecret] meetings this week
Date: 	Sun, 1 Feb 2009 21:17:05 +0000
From: 	David De Roure <dder at ecs.soton.ac.uk>
To: 	myexperiment-topsecret at nongnu.org <myexperiment-topsecret at nongnu.org>



I will be available for all meetings this week except for Tuesday at 4pm 
(teaching) and Wednesday at 4pm and 5pm (on plane to Manchester).

Can I suggest we stay with the 4pm chat and 5pm JISC regime? Jits ? is 
this ok with Biocat?

Thanks

-- Dave

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From jits at cs.man.ac.uk  Tue Feb  3 08:03:21 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 03 Feb 2009 13:03:21 +0000
Subject: [BioCatalogue-developers] FW: bioinformatics service monitoring
In-Reply-To: <75BC3BFCB7354FD198C42F4772C6A6C3@franckPC>
References: <75BC3BFCB7354FD198C42F4772C6A6C3@franckPC>
Message-ID: <49884099.7080105@cs.man.ac.uk>

How about we set up a skype voice chat next week sometime?

This could fit in very well with the service testing stuff.

Cheers,
Jits


Franck Tanoh wrote:
> Guys we need to follow this one closely... 
> Should I arrange a meeting... probably Skype? 
>
> Franck
>
> -----Original Message-----
> From: Francois Moreews [mailto:fmoreews at irisa.fr] 
> Sent: 02 February 2009 16:36
> To: Franck Tanoh
> Subject: Re: bioinformatics service monitoring
>
> Hi Franck,
>
> Welcome in the father's club! I hope you sleep enough ;-)
>
> The QBIOS taverna 1.7 plugin (SSO)  is available at
> http://qbios.gforge.inria.fr/repository/
> It is a functionnal prototype.
>
> The SSFA command line is available at
> http://qbios.gforge.inria.fr/SSFA_aggregator.zip
> (it can generate report like 
> http://lipm-bioinfo.toulouse.inra.fr/biomoby/QBIOS/output/report.html)
> It is really easy to use.
>
> If you and your collegues are interested in QBIOS API, you can ask for a 
> gforge account at
> https://gforge.inria.fr/account/register.php
>  
> I will be happy to present  our work to the biocatalogue developpers team.
> I could be productive to merge our effort on service monitoring.
>
> regards,
>
> Francois
>
>
>
> Franck Tanoh a ?crit :
>   
>> Hi Francois, 
>>
>> Happy New Year 2009!!!
>>
>> Sorry for the delayed response, I've been out on paternity leave for a
>> while. 
>> QBIOS is looking good; is the Taverna plugin ready for download? I'll be
>> glad to test it. 
>> Service quality is a key requirement of BioCatalogue. Looking at your
>>     
> slides
>   
>> and demo, I can see that QBIOS addresses most of it. Do you have any API
>> available I can point the BioCatalogue developer to? If you have a mailing
>> list for the project I can sign up to for update, please let me know. 
>>
>>   
>>     
>>> I'm following the evolution of the biocatalog project with the 
>>> BIOCATALOGUE-FRIENDS list with interest.
>>>     
>>>       
>> Cool, your comments, suggestions and feedbacks are welcome.
>> We're aiming to release our first public beta in April. More information
>> will be posted on the mailing list soon.  
>>
>> In case you haven't noticed it yet, Taverna 2 is out:
>> http://www.mygrid.org.uk/ 
>>
>> Cheers, 
>> Franck
>>
>>
>>
>> -----Original Message-----
>> From: Francois Moreews INRA [mailto:fmoreews at irisa.fr] 
>> Sent: 19 December 2008 09:22
>> To: ytanoh at CS.MAN.AC.UK
>> Cc: carole.goble at manchester.ac.uk
>> Subject: bioinformatics service monitoring
>>
>> Hello Franck,
>>
>> I'm following the evolution of the biocatalog project with the 
>> BIOCATALOGUE-FRIENDS list with interest.
>>
>> When we met us in Rennes, I told you that I was involved in a 
>> bioinformatics service monitoring project (QBIOS).
>> At BOSC 2008, I quickly explained to prof Goble the goal of this project.
>> You can find more information about the QBIOS project  at
>> http://qbios.gforge.inria.fr/
>>
>>
>> best regards,
>> Francois
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>   
>>     
>
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From noreply at rubyforge.org  Tue Feb  3 09:14:35 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  3 Feb 2009 09:14:35 -0500 (EST)
Subject: [BioCatalogue-developers] [403]
	trunk/app/views/soaplab_servers/_new_form.html.erb: typo correction
Message-ID: <20090203141435.A22491978545@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  4 05:49:07 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Feb 2009 05:49:07 -0500 (EST)
Subject: [BioCatalogue-developers] [404]
 trunk/vendor/plugins/annotations/RUNNING_UNIT_TESTS: Clarified
 documentation.
Message-ID: <20090204104908.9A6D218580FD@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  4 06:02:02 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Feb 2009 06:02:02 -0500 (EST)
Subject: [BioCatalogue-developers] [405] trunk/app: get listing for saoplab
	show from the relationship table
Message-ID: <20090204110202.D158418580FC@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  4 08:38:06 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Feb 2009 08:38:06 -0500 (EST)
Subject: [BioCatalogue-developers] [406] trunk/config: config update for
	soaplab.
Message-ID: <20090204133806.6ED4F18580FD@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  4 09:00:02 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Feb 2009 09:00:02 -0500 (EST)
Subject: [BioCatalogue-developers] [407]
 trunk/app/controllers/sessions_controller.rb: do not use HTTP_REFERER if
 session[:original_uri] is defined -> fix bug for 'wrong activation code'
 message
Message-ID: <20090204140006.CA2891858101@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  4 09:01:22 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Feb 2009 09:01:22 -0500 (EST)
Subject: [BioCatalogue-developers] [408]
 trunk/app/controllers/users_controller.rb: redirect user to its user page
 after succesful login folowing account activation
Message-ID: <20090204140122.2204718580F6@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  4 09:03:35 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Feb 2009 09:03:35 -0500 (EST)
Subject: [BioCatalogue-developers] [409]
 trunk/app/controllers/application.rb: does not need to set session[:
 original_uri] as it's always performed in the before_filter
Message-ID: <20090204140336.1A4F518580FD@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  4 09:41:49 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Feb 2009 09:41:49 -0500 (EST)
Subject: [BioCatalogue-developers] [410]
 trunk/app/views/layouts/_feed_link_tags.html.erb: autodetect service index
 feed
Message-ID: <20090204144149.7FE561858104@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  4 09:42:17 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Feb 2009 09:42:17 -0500 (EST)
Subject: [BioCatalogue-developers] [411]
 trunk/app/views/services/index.rss.builder: rss feed for services index
Message-ID: <20090204144217.D635418580FE@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  4 10:03:03 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Feb 2009 10:03:03 -0500 (EST)
Subject: [BioCatalogue-developers] [412] trunk/app: "Name" annotations from
 all subobjects of a Service are now shown collectively as aliases for the
 service .
Message-ID: <20090204150303.7C8E61779926@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  4 10:27:48 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Feb 2009 10:27:48 -0500 (EST)
Subject: [BioCatalogue-developers] [413]
 trunk/app/controllers/services_controller.rb: enable rss feed from the
 services index action
Message-ID: <20090204152748.27D6A18580FD@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  4 11:14:04 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Feb 2009 11:14:04 -0500 (EST)
Subject: [BioCatalogue-developers] [414] trunk/app: - Added documentation
 url annotations to service show page .
Message-ID: <20090204161404.2F6AE1858100@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Wed Feb  4 12:14:25 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 04 Feb 2009 17:14:25 +0000
Subject: [BioCatalogue-developers] rss feed for service listing enabled on
	the beta
Message-ID: <4989CCF1.3050502@ebi.ac.uk>


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From noreply at rubyforge.org  Wed Feb  4 12:39:40 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Feb 2009 12:39:40 -0500 (EST)
Subject: [BioCatalogue-developers] [415] trunk/public: Fixed centering issue
 with Redbox popups,
 and changed the close button to something more conventional.
Message-ID: <20090204173940.DC1021858105@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  4 13:18:17 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Feb 2009 13:18:17 -0500 (EST)
Subject: [BioCatalogue-developers] [416] trunk: - Tab code modified to now
 allow for setting of tab to show by anchor in the url (see:
 http://groups.google.com/group/barelyfitz/browse_thread/thread/
 03e8b0672238391a).
Message-ID: <20090204181817.C604B18580FF@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb  5 06:47:11 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  5 Feb 2009 06:47:11 -0500 (EST)
Subject: [BioCatalogue-developers] [417]
 trunk/app/views/services/new.html.erb: show soaplab in the new service view
Message-ID: <20090205114711.C4D20185810A@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb  5 06:48:46 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  5 Feb 2009 06:48:46 -0500 (EST)
Subject: [BioCatalogue-developers] [418]
 trunk/app/views/soaplab_servers/_new_form.html.erb: remove display of error
 messages which are already included in enclosing view
Message-ID: <20090205114846.1B715185810A@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb  5 09:21:47 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  5 Feb 2009 09:21:47 -0500 (EST)
Subject: [BioCatalogue-developers] [419]
 trunk/app/controllers/search_controller.rb: Ever so minor textual change in
 comment.
Message-ID: <20090205142147.DE84F18580F9@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb  5 11:00:55 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  5 Feb 2009 11:00:55 -0500 (EST)
Subject: [BioCatalogue-developers] [420] trunk: Implemented a search. xml
 API call so that search results can be returned in XML.
Message-ID: <20090205160055.A020118580F5@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb  5 17:41:58 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  5 Feb 2009 17:41:58 -0500 (EST)
Subject: [BioCatalogue-developers] [421] trunk: Initial implementation of
 the tags index (ie: main tag cloud) and tag show page.
Message-ID: <20090205224158.368C01978543@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  6 08:26:31 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  6 Feb 2009 08:26:31 -0500 (EST)
Subject: [BioCatalogue-developers] [422] trunk: - Refactored tag specific
 logic into a new /lib/tags. rb library.
Message-ID: <20090206132631.B344C1858108@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  6 09:54:19 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  6 Feb 2009 09:54:19 -0500 (EST)
Subject: [BioCatalogue-developers] [423]
 trunk/app/views/widgets/_action_bar.html.erb: Search query is not persisted
 in the search box.
Message-ID: <20090206145419.CD016167820F@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  6 09:57:00 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  6 Feb 2009 09:57:00 -0500 (EST)
Subject: [BioCatalogue-developers] [424] trunk: Refactored the grouping of
 disparate model objects into a generic method in the /lib/util.rb library.
Message-ID: <20090206145700.49CA31678211@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  6 11:40:06 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  6 Feb 2009 11:40:06 -0500 (EST)
Subject: [BioCatalogue-developers] [425] trunk: - Added "examples" section
 on soap inputs and soap outputs,
 to allow users to add example code/info as annotations.
Message-ID: <20090206164006.87C6718580FB@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  6 11:41:53 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  6 Feb 2009 11:41:53 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2514] Annotations: examples for
	inputs and outputs
Message-ID: <20090206164153.58F2218580FA@rubyforge.org>

Task #2514 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Annotations: examples for inputs and outputs
Complete: 100%
Status: Closed

Description: As requested by Franck and Katy - allow users to provide example inputs and output content for soap input and soap outputs.

Follow-Ups:

-------------------------------------------------------
Date: 2009-02-06 16:41
By: jits

Comment:
Done

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2514&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Fri Feb  6 11:55:30 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  6 Feb 2009 11:55:30 -0500 (EST)
Subject: [BioCatalogue-developers] [426] trunk/app: Added tag cloud to
 "browse" page (ie: services index page) .
Message-ID: <20090206165530.95E3718580F5@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  6 12:04:18 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  6 Feb 2009 12:04:18 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2515] Add delete options for tags
	when viewing tag clouds
Message-ID: <20090206170418.D9B5716781A6@rubyforge.org>

Task #2515 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Add delete options for tags when viewing tag clouds
Complete: 0%
Status: Open

Description: As usual, make sure only the creator of the tag can delete it.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2515&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Feb  9 03:35:33 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  9 Feb 2009 03:35:33 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2516] Implement
	messaging/networking and other such features
Message-ID: <20090209083533.C4B7D1858109@rubyforge.org>

Task #2516 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Implement messaging/networking and other such features
Complete: 0%
Status: Open

Description: As requested by Frnack:

---

Hi,

 

Yesterday, I wanted to contact a biocat user about a service he submitted ? but couldn?t.

I said to myself; how will a biocat user contact a provider about his services then?

Should he send us a mail first?  Not a good idea? we are not service providers.

We therefore need a way to enable communication between services provider/submitters/users/curators.

My solution is to have an internal messaging system (myExperiment style)? leverage on existing technology :-)

I know you guys have already a long list of requirements but I think we should have this system in place before the public release.

 

Cheers
Franck

---

Should be able to drop in a plugin to achieve this.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2516&group_id=6901&group_project_id=12540

From jits at cs.man.ac.uk  Mon Feb  9 04:38:49 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 09 Feb 2009 09:38:49 +0000
Subject: [BioCatalogue-developers] Working in branches
Message-ID: <498FF9A9.6050502@cs.man.ac.uk>

Morning guys,

Now that we have the beta site running, I suggest we all do any major 
new features/development in branches instead of trunk, and then when we 
are convinced they are ready we merge the branches back into trunk and 
release to beta site. This way we can do updates to the beta site in a 
more managed fashion and make sure we get bug fixes in asap.

I'm in the process of creating the following branches for the next 
pieces of work we need to tackle:
1. for REST/DAS/General services support.
2. for the annotations form that will be used post submission of services.
3. inital service monitoring work.
4. initial search discovery work.

Hope this is ok!

Also, I will be looking to add tests wherever I can, so just a reminder 
that we should all do so. One big step really is getting a large set of 
fixtures in. Though we can still write some basic tests without fixtures.

Cheers,
Jits

From noreply at rubyforge.org  Mon Feb  9 05:16:26 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  9 Feb 2009 05:16:26 -0500 (EST)
Subject: [BioCatalogue-developers] [427] trunk: Fixed loadpath to load up
 the various rails libraries so that they can be opened within RadRails
 /Eclipse.
Message-ID: <20090209101627.0DE26185810A@rubyforge.org>

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From noreply at rubyforge.org  Mon Feb  9 05:29:36 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  9 Feb 2009 05:29:36 -0500 (EST)
Subject: [BioCatalogue-developers] [428] branches/rest-support/: Branch to
 do the REST services support development in
Message-ID: <20090209102936.64F0918580FD@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Mon Feb  9 06:04:11 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 09 Feb 2009 11:04:11 +0000
Subject: [BioCatalogue-developers] [428] branches/rest-support/: Branch
 to do the REST services support development in
In-Reply-To: <20090209102936.64F0918580FD@rubyforge.org>
References: <20090209102936.64F0918580FD@rubyforge.org>
Message-ID: <49900DAB.4090009@ebi.ac.uk>

Thanks!


noreply at rubyforge.org wrote:
>
> Revision
>     428
> Author
>     jits
> Date
>     2009-02-09 05:29:35 -0500 (Mon, 09 Feb 2009)
>
>
>       Log Message
>
> Branch to do the REST services support development in
>
>
>       Added Paths
>
>     * branches/rest-support/
>
>
>       Diff
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   

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From ericnzuo at ebi.ac.uk  Mon Feb  9 06:08:08 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 09 Feb 2009 11:08:08 +0000
Subject: [BioCatalogue-developers] telcon Today?
Message-ID: <49900E98.5070203@ebi.ac.uk>

Hi Franck,

Where are we wrt moving the telcon to Mondays? Has Carole and everyone 
upthere agreed to the Monday slot? If so, when do we start? Personally I 
would rather not have any telcon today but I need to know in order to 
confirm or not the room reservations that I have made.

cheers,

Eric

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From tlaurent at ebi.ac.uk  Mon Feb  9 06:26:44 2009
From: tlaurent at ebi.ac.uk (Thomas Laurent)
Date: Mon, 09 Feb 2009 11:26:44 +0000
Subject: [BioCatalogue-developers] Working in branches
In-Reply-To: <498FF9A9.6050502@cs.man.ac.uk>
References: <498FF9A9.6050502@cs.man.ac.uk>
Message-ID: <499012F4.8040305@ebi.ac.uk>

Could you write quickly a "Working in branches" HOW-TO on the wiki, so 
that we are sure we al folow the same procedures for creation/merging of 
branches.

Cheers,
Thomas

Jiten Bhagat wrote:
> Morning guys,
> 
> Now that we have the beta site running, I suggest we all do any major 
> new features/development in branches instead of trunk, and then when we 
> are convinced they are ready we merge the branches back into trunk and 
> release to beta site. This way we can do updates to the beta site in a 
> more managed fashion and make sure we get bug fixes in asap.
> 
> I'm in the process of creating the following branches for the next 
> pieces of work we need to tackle:
> 1. for REST/DAS/General services support.
> 2. for the annotations form that will be used post submission of services.
> 3. inital service monitoring work.
> 4. initial search discovery work.
> 
> Hope this is ok!
> 
> Also, I will be looking to add tests wherever I can, so just a reminder 
> that we should all do so. One big step really is getting a large set of 
> fixtures in. Though we can still write some basic tests without fixtures.
> 
> Cheers,
> Jits
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers

From jits at cs.man.ac.uk  Mon Feb  9 06:34:04 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 09 Feb 2009 11:34:04 +0000
Subject: [BioCatalogue-developers] Working in branches
In-Reply-To: <499012F4.8040305@ebi.ac.uk>
References: <498FF9A9.6050502@cs.man.ac.uk> <499012F4.8040305@ebi.ac.uk>
Message-ID: <499014AC.7020808@cs.man.ac.uk>

Ok, sure.


Thomas Laurent wrote:
> Could you write quickly a "Working in branches" HOW-TO on the wiki, so 
> that we are sure we al folow the same procedures for creation/merging 
> of branches.
>
> Cheers,
> Thomas
>
> Jiten Bhagat wrote:
>> Morning guys,
>>
>> Now that we have the beta site running, I suggest we all do any major 
>> new features/development in branches instead of trunk, and then when 
>> we are convinced they are ready we merge the branches back into trunk 
>> and release to beta site. This way we can do updates to the beta site 
>> in a more managed fashion and make sure we get bug fixes in asap.
>>
>> I'm in the process of creating the following branches for the next 
>> pieces of work we need to tackle:
>> 1. for REST/DAS/General services support.
>> 2. for the annotations form that will be used post submission of 
>> services.
>> 3. inital service monitoring work.
>> 4. initial search discovery work.
>>
>> Hope this is ok!
>>
>> Also, I will be looking to add tests wherever I can, so just a 
>> reminder that we should all do so. One big step really is getting a 
>> large set of fixtures in. Though we can still write some basic tests 
>> without fixtures.
>>
>> Cheers,
>> Jits
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From ytanoh at cs.man.ac.uk  Sun Feb  8 07:14:28 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Sun, 8 Feb 2009 12:14:28 -0000
Subject: [BioCatalogue-developers] telcon Today?
In-Reply-To: <49900E98.5070203@ebi.ac.uk>
Message-ID: <20090209121557.6848418580FD@rubyforge.org>

Eric, 

3-4pm on Monday is the best time for everyone.
Let's start it from next week.  

Franck 

-----Original Message-----
From: biocatalogue-developers-bounces at rubyforge.org
[mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
Nzuobontane
Sent: 09 February 2009 11:08
To: biocatalogue-developers at rubyforge.org
Subject: [BioCatalogue-developers] telcon Today?

Hi Franck,

Where are we wrt moving the telcon to Mondays? Has Carole and everyone 
upthere agreed to the Monday slot? If so, when do we start? Personally I 
would rather not have any telcon today but I need to know in order to 
confirm or not the room reservations that I have made.

cheers,

Eric



From jits at cs.man.ac.uk  Mon Feb  9 08:59:14 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 09 Feb 2009 13:59:14 +0000
Subject: [BioCatalogue-developers] Working in branches
In-Reply-To: <499012F4.8040305@ebi.ac.uk>
References: <498FF9A9.6050502@cs.man.ac.uk> <499012F4.8040305@ebi.ac.uk>
Message-ID: <499036B2.3010605@cs.man.ac.uk>

Here it is: 
http://www.ebi.ac.uk/ebiwiki/biocatalogue/doku.php?id=development:codebase_guidelines#developing_in_branches

Cheers,
Jits


Thomas Laurent wrote:
> Could you write quickly a "Working in branches" HOW-TO on the wiki, so 
> that we are sure we al folow the same procedures for creation/merging 
> of branches.
>
> Cheers,
> Thomas
>
> Jiten Bhagat wrote:
>> Morning guys,
>>
>> Now that we have the beta site running, I suggest we all do any major 
>> new features/development in branches instead of trunk, and then when 
>> we are convinced they are ready we merge the branches back into trunk 
>> and release to beta site. This way we can do updates to the beta site 
>> in a more managed fashion and make sure we get bug fixes in asap.
>>
>> I'm in the process of creating the following branches for the next 
>> pieces of work we need to tackle:
>> 1. for REST/DAS/General services support.
>> 2. for the annotations form that will be used post submission of 
>> services.
>> 3. inital service monitoring work.
>> 4. initial search discovery work.
>>
>> Hope this is ok!
>>
>> Also, I will be looking to add tests wherever I can, so just a 
>> reminder that we should all do so. One big step really is getting a 
>> large set of fixtures in. Though we can still write some basic tests 
>> without fixtures.
>>
>> Cheers,
>> Jits
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From jits at cs.man.ac.uk  Mon Feb  9 11:15:13 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 09 Feb 2009 16:15:13 +0000
Subject: [BioCatalogue-developers] Visa
Message-ID: <49905691.4000807@cs.man.ac.uk>

Hi guys,

I'm afraid to say that my visa got rejected today, so I will not be 
working on BioCatalogue until something else is sorted out :-(

Jits


From noreply at rubyforge.org  Wed Feb 11 05:02:45 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 11 Feb 2009 05:02:45 -0500 (EST)
Subject: [BioCatalogue-developers] [429] trunk/app: get data from both
 soaplab1 & soaplab2 servers and tag services with ' soaplab' and emboss
 group.
Message-ID: <20090211100245.803C31858100@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 11 05:03:39 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 11 Feb 2009 05:03:39 -0500 (EST)
Subject: [BioCatalogue-developers] [430] trunk/app/models/service.rb:
Message-ID: <20090211100339.29B7B1858100@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 11 06:38:13 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 11 Feb 2009 06:38:13 -0500 (EST)
Subject: [BioCatalogue-developers] [431] trunk/app/views/soaplab_servers:
 disable submit button if no services are found in soaplab server
Message-ID: <20090211113814.188E91858103@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 11 09:28:25 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 11 Feb 2009 09:28:25 -0500 (EST)
Subject: [BioCatalogue-developers] [432] trunk/lib/wsdl_parser.rb: bufgix
	for handling types
Message-ID: <20090211142825.BD4531858103@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 12 07:26:27 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Feb 2009 07:26:27 -0500 (EST)
Subject: [BioCatalogue-developers] [433]
 trunk/public/stylesheets/styles.css: added styles for content of flash
 messages
Message-ID: <20090212122627.F275A15B802D@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 12 07:30:19 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Feb 2009 07:30:19 -0500 (EST)
Subject: [BioCatalogue-developers] [434] trunk/app/models/user.rb: added the
 activate! action to active a user account
Message-ID: <20090212123019.B197E1858116@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 12 07:36:17 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Feb 2009 07:36:17 -0500 (EST)
Subject: [BioCatalogue-developers] [435]
 trunk/app/controllers/users_controller.rb: refactored the user account
 activation and changed some of the messages
Message-ID: <20090212123617.C3A451858101@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 12 10:53:13 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Feb 2009 10:53:13 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2533] add progress bar to soaplab
	services upload
Message-ID: <20090212155313.5B59D15B802E@rubyforge.org>

Task #2533 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: add progress bar to soaplab services upload
Complete: 0%
Status: Open

Description: Uploading hundreds of services from soaplab server can take a while. It will be useful to feedback to the user through a progress bar or some other mechanism

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2533&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Feb 12 11:34:10 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Feb 2009 11:34:10 -0500 (EST)
Subject: [BioCatalogue-developers] [436]
 trunk/app/controllers/users_controller.rb: simplified the error messages
 for user account activation
Message-ID: <20090212163410.39C2918580F8@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Fri Feb 13 06:48:03 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Fri, 13 Feb 2009 11:48:03 +0000
Subject: [BioCatalogue-developers] updating the beta site
Message-ID: <49955DF3.5090107@ebi.ac.uk>

Hi Guys,
I intend to update the beta site in the an hour or so. Is there 
something I need to do/know before I do that?
This current update will include:
  - tag cloud display
  - soaplab server registration
Though the new service page has no links to the soaplab server, it is 
available by direct url. Ideally I would have loved someone else to play 
with submitting a soaplab server locally before any exposure to public

cheers,

Eric

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From noreply at rubyforge.org  Fri Feb 13 08:12:08 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 13 Feb 2009 08:12:08 -0500 (EST)
Subject: [BioCatalogue-developers] [437]
 trunk/app/views/services/new.html.erb: don' t show soaplab in the new
 service view
Message-ID: <20090213131208.7AA4C18580FA@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 13 08:44:20 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 13 Feb 2009 08:44:20 -0500 (EST)
Subject: [BioCatalogue-developers] [438]
 trunk/app/views/services/index.html.erb: attempting bugfix for ' undefined
 method `h' for BioCatalogue::Tags:Module'
Message-ID: <20090213134420.5515918580FA@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 13 08:50:07 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 13 Feb 2009 08:50:07 -0500 (EST)
Subject: [BioCatalogue-developers] [439]
	trunk/app/views/services/index.html.erb:
Message-ID: <20090213135007.592BD18580FA@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Fri Feb 13 08:54:30 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Fri, 13 Feb 2009 13:54:30 +0000
Subject: [BioCatalogue-developers] updating the beta site
In-Reply-To: <49955DF3.5090107@ebi.ac.uk>
References: <49955DF3.5090107@ebi.ac.uk>
Message-ID: <49957B96.1020905@ebi.ac.uk>

Unfortunately there was bug in services index view which I was not able 
to figure right away. So I did the drastic thing of bring down the 
servers. Unfortunately my local installation works just fine and it 
seems to be the same code as the repository. So I am quite puzzled

Showing /app/views/services/index.html.erb/ where line *#19* raised:

|undefined method `h' for BioCatalogue::Tags:Module|

Extracted source (around line *#19*):

|16: 		<span style="font-size: 0.7em; margin-left: 1em;">[ <%= link_to("See All Tags", tags_index_path) -%> ]</span>
17: 	</h3>
18: 	
19: 	<%= generate_tag_cloud(@tags, :tag_cloud_style => "margin-top: 0.6em;") %>
20: </div>
21: 
22: <span style="float: right;">
|

|RAILS_ROOT: 
/net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue|

Application Trace <http://beta.biocatalogue.org/services#> | Framework 
Trace <http://beta.biocatalogue.org/services#> | Full Trace 
<http://beta.biocatalogue.org/services#>

|lib/tags.rb:129:in `tag_cloud'
lib/tags.rb:122:in `each'
lib/tags.rb:122:in `tag_cloud'
app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
app/views/services/index.html.erb:19

app/controllers/services_controller.rb:24:in `index'|

|/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.rb:39:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.rb:39:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb:73:in `render_template'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367:in `_render_with_layout'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:1174:in `render_for_file'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:905:in `render_without_benchmark'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:51:in `render'
/ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_ext/benchmark.rb:8:in `realtime'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:51:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:135:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:135:in `custom'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:164:in `call'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:164:in `respond'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:158:in `each'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:158:in `respond'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:107:in `respond_to'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:1253:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:1253:in `perform_action_without_filters'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filters.rb:617:in `call_filters'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filters.rb:610:in `perform_action_without_benchmark'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue'
/usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescue.rb:136:in `perform_action_without_caching'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/caching/sql_cache.rb:13:in `perform_action'
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in `cache'
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_cache.rb:8:in `cache'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/caching/sql_cache.rb:12:in `perform_action'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:524:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:524:in `process_without_filters'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filters.rb:606:in `process_without_session_management_support'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/session_management.rb:134:in `process'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:392:in `process'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:183:in `handle_request'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:110:in `dispatch_unlocked'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:123:in `dispatch'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:122:in `synchronize'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:122:in `dispatch'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:132:in `dispatch_cgi'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:39:in `dispatch'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in `process'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in `synchronize'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in `process'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in `process_client'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in `each'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in `process_client'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `initialize'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `new'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `initialize'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `new'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:282:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:281:in `each'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:281:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
/ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
/ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|

|lib/tags.rb:129:in `tag_cloud'
lib/tags.rb:122:in `each'
lib/tags.rb:122:in `tag_cloud'
app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
app/views/services/index.html.erb:19
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.rb:39:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.rb:39:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb:73:in `render_template'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367:in `_render_with_layout'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:1174:in `render_for_file'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:905:in `render_without_benchmark'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:51:in `render'
/ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_ext/benchmark.rb:8:in `realtime'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:51:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:135:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:135:in `custom'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:164:in `call'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:164:in `respond'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:158:in `each'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:158:in `respond'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:107:in `respond_to'
app/controllers/services_controller.rb:24:in `index'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:1253:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:1253:in `perform_action_without_filters'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filters.rb:617:in `call_filters'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filters.rb:610:in `perform_action_without_benchmark'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue'
/usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescue.rb:136:in `perform_action_without_caching'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/caching/sql_cache.rb:13:in `perform_action'
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in `cache'
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_cache.rb:8:in `cache'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/caching/sql_cache.rb:12:in `perform_action'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:524:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:524:in `process_without_filters'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filters.rb:606:in `process_without_session_management_support'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/session_management.rb:134:in `process'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:392:in `process'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:183:in `handle_request'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:110:in `dispatch_unlocked'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:123:in `dispatch'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:122:in `synchronize'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:122:in `dispatch'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:132:in `dispatch_cgi'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:39:in `dispatch'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in `process'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in `synchronize'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in `process'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in `process_client'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in `each'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in `process_client'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `initialize'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `new'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `initialize'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `new'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:282:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:281:in `each'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:281:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
/ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
/ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|


    Request



Eric Nzuobontane wrote:
> Hi Guys,
> I intend to update the beta site in the an hour or so. Is there 
> something I need to do/know before I do that?
> This current update will include:
>  - tag cloud display
>  - soaplab server registration
> Though the new service page has no links to the soaplab server, it is 
> available by direct url. Ideally I would have loved someone else to 
> play with submitting a soaplab server locally before any exposure to 
> public
>
> cheers,
>
> Eric
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   

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From jits at cs.man.ac.uk  Fri Feb 13 09:04:31 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 13 Feb 2009 14:04:31 +0000
Subject: [BioCatalogue-developers] updating the beta site
In-Reply-To: <49957B96.1020905@ebi.ac.uk>
References: <49955DF3.5090107@ebi.ac.uk> <49957B96.1020905@ebi.ac.uk>
Message-ID: <49957DEF.106@cs.man.ac.uk>

Hi Eric,

That is weird, I initially expected to have that error on my local set 
up but when it worked locally I thought the relevant method ('h' which 
is html encode) was included.

I think if you change the use of the h function in the Tags module to 
"CGI.escapeHTML(..)", this should work.

Jits



Eric Nzuobontane wrote:
> Unfortunately there was bug in services index view which I was not 
> able to figure right away. So I did the drastic thing of bring down 
> the servers. Unfortunately my local installation works just fine and 
> it seems to be the same code as the repository. So I am quite puzzled
>
> Showing /app/views/services/index.html.erb/ where line *#19* raised:
>
> |undefined method `h' for BioCatalogue::Tags:Module|
>
> Extracted source (around line *#19*):
>
> |16:         <span style="font-size: 0.7em; margin-left: 1em;">[ <%= 
> link_to("See All Tags", tags_index_path) -%> ]</span>
> 17:     </h3>
> 18:    
> 19:     <%= generate_tag_cloud(@tags, :tag_cloud_style => "margin-top: 
> 0.6em;") %>
> 20: </div>
> 21: 22: <span style="float: right;">
> |
>
> |RAILS_ROOT: 
> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue|
>
> Application Trace <http://beta.biocatalogue.org/services#> | Framework 
> Trace <http://beta.biocatalogue.org/services#> | Full Trace 
> <http://beta.biocatalogue.org/services#>
>
> |lib/tags.rb:129:in `tag_cloud'
> lib/tags.rb:122:in `each'
> lib/tags.rb:122:in `tag_cloud'
> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
> app/views/services/index.html.erb:19
>
> app/controllers/services_controller.rb:24:in `index'|
>
> |/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.rb:39:in 
> `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.rb:39:in 
> `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb:73:in 
> `render_template'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256:in 
> `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367:in 
> `_render_with_layout'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254:in 
> `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:1174:in 
> `render_for_file'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:905:in 
> `render_without_benchmark'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:51:in 
> `render'
> /ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_ext/benchmark.rb:8:in 
> `realtime'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:51:in 
> `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:135:in 
> `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:135:in 
> `custom'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:164:in 
> `call'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:164:in 
> `respond'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:158:in 
> `each'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:158:in 
> `respond'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:107:in 
> `respond_to'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:1253:in 
> `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:1253:in 
> `perform_action_without_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filters.rb:617:in 
> `call_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filters.rb:610:in 
> `perform_action_without_benchmark'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:68:in 
> `perform_action_without_rescue'
> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:68:in 
> `perform_action_without_rescue'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescue.rb:136:in 
> `perform_action_without_caching'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/caching/sql_cache.rb:13:in 
> `perform_action'
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in 
> `cache'
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_cache.rb:8:in 
> `cache'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/caching/sql_cache.rb:12:in 
> `perform_action'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:524:in 
> `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:524:in 
> `process_without_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filters.rb:606:in 
> `process_without_session_management_support'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/session_management.rb:134:in 
> `process'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:392:in 
> `process'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:183:in 
> `handle_request'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:110:in 
> `dispatch_unlocked'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:123:in 
> `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:122:in 
> `synchronize'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:122:in 
> `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:132:in 
> `dispatch_cgi'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:39:in 
> `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in 
> `process'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
> `synchronize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
> `process'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in 
> `process_client'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
> `each'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
> `process_client'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
> `initialize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `new'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
> `initialize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `new'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:282:in 
> `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:281:in 
> `each'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:281:in 
> `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in 
> `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in 
> `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>
> |lib/tags.rb:129:in `tag_cloud'
> lib/tags.rb:122:in `each'
> lib/tags.rb:122:in `tag_cloud'
> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
> app/views/services/index.html.erb:19
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.rb:39:in 
> `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.rb:39:in 
> `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb:73:in 
> `render_template'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256:in 
> `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367:in 
> `_render_with_layout'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254:in 
> `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:1174:in 
> `render_for_file'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:905:in 
> `render_without_benchmark'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:51:in 
> `render'
> /ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_ext/benchmark.rb:8:in 
> `realtime'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:51:in 
> `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:135:in 
> `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:135:in 
> `custom'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:164:in 
> `call'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:164:in 
> `respond'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:158:in 
> `each'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:158:in 
> `respond'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_responds.rb:107:in 
> `respond_to'
> app/controllers/services_controller.rb:24:in `index'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:1253:in 
> `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:1253:in 
> `perform_action_without_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filters.rb:617:in 
> `call_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filters.rb:610:in 
> `perform_action_without_benchmark'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:68:in 
> `perform_action_without_rescue'
> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/benchmarking.rb:68:in 
> `perform_action_without_rescue'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescue.rb:136:in 
> `perform_action_without_caching'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/caching/sql_cache.rb:13:in 
> `perform_action'
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in 
> `cache'
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_cache.rb:8:in 
> `cache'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/caching/sql_cache.rb:12:in 
> `perform_action'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:524:in 
> `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:524:in 
> `process_without_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filters.rb:606:in 
> `process_without_session_management_support'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/session_management.rb:134:in 
> `process'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.rb:392:in 
> `process'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:183:in 
> `handle_request'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:110:in 
> `dispatch_unlocked'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:123:in 
> `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:122:in 
> `synchronize'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:122:in 
> `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:132:in 
> `dispatch_cgi'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispatcher.rb:39:in 
> `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in 
> `process'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
> `synchronize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
> `process'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in 
> `process_client'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
> `each'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
> `process_client'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
> `initialize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `new'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
> `initialize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `new'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:282:in 
> `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:281:in 
> `each'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:281:in 
> `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in 
> `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in 
> `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>
>
>    Request
>
>
>
> Eric Nzuobontane wrote:
>> Hi Guys,
>> I intend to update the beta site in the an hour or so. Is there 
>> something I need to do/know before I do that?
>> This current update will include:
>>  - tag cloud display
>>  - soaplab server registration
>> Though the new service page has no links to the soaplab server, it is 
>> available by direct url. Ideally I would have loved someone else to 
>> play with submitting a soaplab server locally before any exposure to 
>> public
>>
>> cheers,
>>
>> Eric
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>   
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From noreply at rubyforge.org  Fri Feb 13 09:24:29 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 13 Feb 2009 09:24:29 -0500 (EST)
Subject: [BioCatalogue-developers] [440] trunk/lib/tags.rb: use CGI.escape
 and CGI. escapeHTML to escape html instead of h & URI.escape
Message-ID: <20090213142429.37FC018580FB@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 13 10:10:59 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 13 Feb 2009 10:10:59 -0500 (EST)
Subject: [BioCatalogue-developers] [441]
 trunk/app/controllers/tags_controller.rb: completing the change of using
 CGI for escaping - escape before finding tags
Message-ID: <20090213151100.0CAD6185810A@rubyforge.org>

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From ytanoh at cs.man.ac.uk  Fri Feb 13 09:20:41 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Fri, 13 Feb 2009 14:20:41 -0000
Subject: [BioCatalogue-developers] beta site is down
In-Reply-To: <49957B96.1020905@ebi.ac.uk>
Message-ID: <E1LXyuH-0003NF-T8@muffin>

Hi,
I can't access the beta site... <<error 500...>>

Please check

Cheers,
Franck

-----Original Message-----
From: biocatalogue-developers-bounces at rubyforge.org
[mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
Nzuobontane
Sent: 13 February 2009 13:55
To: biocatalogue-developers at rubyforge.org
Subject: Re: [BioCatalogue-developers] updating the beta site

Unfortunately there was bug in services index view which I was not able 
to figure right away. So I did the drastic thing of bring down the 
servers. Unfortunately my local installation works just fine and it 
seems to be the same code as the repository. So I am quite puzzled

Showing /app/views/services/index.html.erb/ where line *#19* raised:

|undefined method `h' for BioCatalogue::Tags:Module|

Extracted source (around line *#19*):

|16: 		<span style="font-size: 0.7em; margin-left: 1em;">[ <%=
link_to("See All Tags", tags_index_path) -%> ]</span>
17: 	</h3>
18: 	
19: 	<%= generate_tag_cloud(@tags, :tag_cloud_style => "margin-top:
0.6em;") %>
20: </div>
21: 
22: <span style="float: right;">
|

|RAILS_ROOT: 
/net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue|

Application Trace <http://beta.biocatalogue.org/services#> | Framework 
Trace <http://beta.biocatalogue.org/services#> | Full Trace 
<http://beta.biocatalogue.org/services#>

|lib/tags.rb:129:in `tag_cloud'
lib/tags.rb:122:in `each'
lib/tags.rb:122:in `tag_cloud'
app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
app/views/services/index.html.erb:19

app/controllers/services_controller.rb:24:in `index'|

|/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable
.rb:39:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.
rb:39:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb
:73:in `render_template'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256
:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367
:in `_render_with_layout'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254
:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
rb:1174:in `render_for_file'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
rb:905:in `render_without_benchmark'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
marking.rb:51:in `render'
/ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_
ext/benchmark.rb:8:in `realtime'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
marking.rb:51:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
responds.rb:135:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
responds.rb:135:in `custom'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
responds.rb:164:in `call'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
responds.rb:164:in `respond'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
responds.rb:158:in `each'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
responds.rb:158:in `respond'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
responds.rb:107:in `respond_to'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
rb:1253:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
rb:1253:in `perform_action_without_filters'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
rs.rb:617:in `call_filters'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
rs.rb:610:in `perform_action_without_benchmark'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
marking.rb:68:in `perform_action_without_rescue'
/usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
marking.rb:68:in `perform_action_without_rescue'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu
e.rb:136:in `perform_action_without_caching'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
ng/sql_cache.rb:13:in `perform_action'
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect
ion_adapters/abstract/query_cache.rb:34:in `cache'
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c
ache.rb:8:in `cache'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
ng/sql_cache.rb:12:in `perform_action'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
rb:524:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
rb:524:in `process_without_filters'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
rs.rb:606:in `process_without_session_management_support'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi
on_management.rb:134:in `process'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
rb:392:in `process'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
tcher.rb:183:in `handle_request'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
tcher.rb:110:in `dispatch_unlocked'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
tcher.rb:123:in `dispatch'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
tcher.rb:122:in `synchronize'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
tcher.rb:122:in `dispatch'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
tcher.rb:132:in `dispatch_cgi'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
tcher.rb:39:in `dispatch'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in
`process'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
`synchronize'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
`process'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
`process_client'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in `each'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
`process_client'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
`initialize'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `new'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
`initialize'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `new'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
2:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
1:in `each'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
1:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in
`run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
/ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
/ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|

|lib/tags.rb:129:in `tag_cloud'
lib/tags.rb:122:in `each'
lib/tags.rb:122:in `tag_cloud'
app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
app/views/services/index.html.erb:19
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.
rb:39:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.
rb:39:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb
:73:in `render_template'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256
:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367
:in `_render_with_layout'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254
:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
rb:1174:in `render_for_file'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
rb:905:in `render_without_benchmark'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
marking.rb:51:in `render'
/ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_
ext/benchmark.rb:8:in `realtime'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
marking.rb:51:in `render'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
responds.rb:135:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
responds.rb:135:in `custom'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
responds.rb:164:in `call'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
responds.rb:164:in `respond'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
responds.rb:158:in `each'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
responds.rb:158:in `respond'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
responds.rb:107:in `respond_to'
app/controllers/services_controller.rb:24:in `index'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
rb:1253:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
rb:1253:in `perform_action_without_filters'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
rs.rb:617:in `call_filters'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
rs.rb:610:in `perform_action_without_benchmark'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
marking.rb:68:in `perform_action_without_rescue'
/usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
marking.rb:68:in `perform_action_without_rescue'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu
e.rb:136:in `perform_action_without_caching'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
ng/sql_cache.rb:13:in `perform_action'
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect
ion_adapters/abstract/query_cache.rb:34:in `cache'
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c
ache.rb:8:in `cache'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
ng/sql_cache.rb:12:in `perform_action'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
rb:524:in `send'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
rb:524:in `process_without_filters'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
rs.rb:606:in `process_without_session_management_support'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi
on_management.rb:134:in `process'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
rb:392:in `process'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
tcher.rb:183:in `handle_request'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
tcher.rb:110:in `dispatch_unlocked'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
tcher.rb:123:in `dispatch'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
tcher.rb:122:in `synchronize'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
tcher.rb:122:in `dispatch'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
tcher.rb:132:in `dispatch_cgi'
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
tcher.rb:39:in `dispatch'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in
`process'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
`synchronize'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
`process'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
`process_client'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in `each'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
`process_client'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
`initialize'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `new'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
`initialize'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `new'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
2:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
1:in `each'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
1:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in `run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in
`run'
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
/ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
/ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|


    Request



Eric Nzuobontane wrote:
> Hi Guys,
> I intend to update the beta site in the an hour or so. Is there 
> something I need to do/know before I do that?
> This current update will include:
>  - tag cloud display
>  - soaplab server registration
> Though the new service page has no links to the soaplab server, it is 
> available by direct url. Ideally I would have loved someone else to 
> play with submitting a soaplab server locally before any exposure to 
> public
>
> cheers,
>
> Eric
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   



From ericnzuo at ebi.ac.uk  Fri Feb 13 10:31:27 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Fri, 13 Feb 2009 15:31:27 +0000
Subject: [BioCatalogue-developers] beta site is down
In-Reply-To: <E1LXyuH-0003NF-T8@muffin>
References: <E1LXyuH-0003NF-T8@muffin>
Message-ID: <4995924F.5050807@ebi.ac.uk>

should be back up now.
Please try again

Eric

Franck Tanoh wrote:
> Hi,
> I can't access the beta site... <<error 500...>>
>
> Please check
>
> Cheers,
> Franck
>
> -----Original Message-----
> From: biocatalogue-developers-bounces at rubyforge.org
> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
> Nzuobontane
> Sent: 13 February 2009 13:55
> To: biocatalogue-developers at rubyforge.org
> Subject: Re: [BioCatalogue-developers] updating the beta site
>
> Unfortunately there was bug in services index view which I was not able 
> to figure right away. So I did the drastic thing of bring down the 
> servers. Unfortunately my local installation works just fine and it 
> seems to be the same code as the repository. So I am quite puzzled
>
> Showing /app/views/services/index.html.erb/ where line *#19* raised:
>
> |undefined method `h' for BioCatalogue::Tags:Module|
>
> Extracted source (around line *#19*):
>
> |16: 		<span style="font-size: 0.7em; margin-left: 1em;">[ <%=
> link_to("See All Tags", tags_index_path) -%> ]</span>
> 17: 	</h3>
> 18: 	
> 19: 	<%= generate_tag_cloud(@tags, :tag_cloud_style => "margin-top:
> 0.6em;") %>
> 20: </div>
> 21: 
> 22: <span style="float: right;">
> |
>
> |RAILS_ROOT: 
> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue|
>
> Application Trace <http://beta.biocatalogue.org/services#> | Framework 
> Trace <http://beta.biocatalogue.org/services#> | Full Trace 
> <http://beta.biocatalogue.org/services#>
>
> |lib/tags.rb:129:in `tag_cloud'
> lib/tags.rb:122:in `each'
> lib/tags.rb:122:in `tag_cloud'
> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
> app/views/services/index.html.erb:19
>
> app/controllers/services_controller.rb:24:in `index'|
>
> |/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable
> .rb:39:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.
> rb:39:in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb
> :73:in `render_template'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256
> :in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367
> :in `_render_with_layout'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254
> :in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:1174:in `render_for_file'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:905:in `render_without_benchmark'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:51:in `render'
> /ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_
> ext/benchmark.rb:8:in `realtime'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:51:in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:135:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:135:in `custom'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:164:in `call'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:164:in `respond'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:158:in `each'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:158:in `respond'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:107:in `respond_to'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:1253:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:1253:in `perform_action_without_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
> rs.rb:617:in `call_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
> rs.rb:610:in `perform_action_without_benchmark'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:68:in `perform_action_without_rescue'
> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:68:in `perform_action_without_rescue'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu
> e.rb:136:in `perform_action_without_caching'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
> ng/sql_cache.rb:13:in `perform_action'
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect
> ion_adapters/abstract/query_cache.rb:34:in `cache'
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c
> ache.rb:8:in `cache'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
> ng/sql_cache.rb:12:in `perform_action'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:524:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:524:in `process_without_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
> rs.rb:606:in `process_without_session_management_support'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi
> on_management.rb:134:in `process'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:392:in `process'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:183:in `handle_request'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:110:in `dispatch_unlocked'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:123:in `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:122:in `synchronize'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:122:in `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:132:in `dispatch_cgi'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:39:in `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in
> `process'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
> `synchronize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
> `process'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
> `process_client'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in `each'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
> `process_client'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
> `initialize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `new'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
> `initialize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `new'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
> 2:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
> 1:in `each'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
> 1:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in
> `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>
> |lib/tags.rb:129:in `tag_cloud'
> lib/tags.rb:122:in `each'
> lib/tags.rb:122:in `tag_cloud'
> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
> app/views/services/index.html.erb:19
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.
> rb:39:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.
> rb:39:in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb
> :73:in `render_template'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256
> :in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367
> :in `_render_with_layout'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254
> :in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:1174:in `render_for_file'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:905:in `render_without_benchmark'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:51:in `render'
> /ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_
> ext/benchmark.rb:8:in `realtime'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:51:in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:135:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:135:in `custom'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:164:in `call'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:164:in `respond'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:158:in `each'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:158:in `respond'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:107:in `respond_to'
> app/controllers/services_controller.rb:24:in `index'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:1253:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:1253:in `perform_action_without_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
> rs.rb:617:in `call_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
> rs.rb:610:in `perform_action_without_benchmark'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:68:in `perform_action_without_rescue'
> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:68:in `perform_action_without_rescue'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu
> e.rb:136:in `perform_action_without_caching'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
> ng/sql_cache.rb:13:in `perform_action'
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect
> ion_adapters/abstract/query_cache.rb:34:in `cache'
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c
> ache.rb:8:in `cache'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
> ng/sql_cache.rb:12:in `perform_action'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:524:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:524:in `process_without_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
> rs.rb:606:in `process_without_session_management_support'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi
> on_management.rb:134:in `process'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:392:in `process'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:183:in `handle_request'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:110:in `dispatch_unlocked'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:123:in `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:122:in `synchronize'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:122:in `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:132:in `dispatch_cgi'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:39:in `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in
> `process'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
> `synchronize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
> `process'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
> `process_client'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in `each'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
> `process_client'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
> `initialize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `new'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
> `initialize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `new'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
> 2:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
> 1:in `each'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
> 1:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in
> `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>
>
>     Request
>
>
>
> Eric Nzuobontane wrote:
>   
>> Hi Guys,
>> I intend to update the beta site in the an hour or so. Is there 
>> something I need to do/know before I do that?
>> This current update will include:
>>  - tag cloud display
>>  - soaplab server registration
>> Though the new service page has no links to the soaplab server, it is 
>> available by direct url. Ideally I would have loved someone else to 
>> play with submitting a soaplab server locally before any exposure to 
>> public
>>
>> cheers,
>>
>> Eric
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>   
>>     
>
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   

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From tlaurent at ebi.ac.uk  Fri Feb 13 10:31:39 2009
From: tlaurent at ebi.ac.uk (Thomas Laurent)
Date: Fri, 13 Feb 2009 15:31:39 +0000
Subject: [BioCatalogue-developers] beta site is down
In-Reply-To: <E1LXyuH-0003NF-T8@muffin>
References: <E1LXyuH-0003NF-T8@muffin>
Message-ID: <4995925B.1010109@ebi.ac.uk>

Does somebody know anything about that ?

Am I the only one receiving the emails from the list 1 hour late ? 
That's kind of annoying, especially for urgent cases like this one...

Thomas

Franck Tanoh wrote:
> Hi,
> I can't access the beta site... <<error 500...>>
> 
> Please check
> 
> Cheers,
> Franck
> 
> -----Original Message-----
> From: biocatalogue-developers-bounces at rubyforge.org
> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
> Nzuobontane
> Sent: 13 February 2009 13:55
> To: biocatalogue-developers at rubyforge.org
> Subject: Re: [BioCatalogue-developers] updating the beta site
> 
> Unfortunately there was bug in services index view which I was not able 
> to figure right away. So I did the drastic thing of bring down the 
> servers. Unfortunately my local installation works just fine and it 
> seems to be the same code as the repository. So I am quite puzzled
> 
> Showing /app/views/services/index.html.erb/ where line *#19* raised:
> 
> |undefined method `h' for BioCatalogue::Tags:Module|
> 
> Extracted source (around line *#19*):
> 
> |16: 		<span style="font-size: 0.7em; margin-left: 1em;">[ <%=
> link_to("See All Tags", tags_index_path) -%> ]</span>
> 17: 	</h3>
> 18: 	
> 19: 	<%= generate_tag_cloud(@tags, :tag_cloud_style => "margin-top:
> 0.6em;") %>
> 20: </div>
> 21: 
> 22: <span style="float: right;">
> |
> 
> |RAILS_ROOT: 
> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue|
> 
> Application Trace <http://beta.biocatalogue.org/services#> | Framework 
> Trace <http://beta.biocatalogue.org/services#> | Full Trace 
> <http://beta.biocatalogue.org/services#>
> 
> |lib/tags.rb:129:in `tag_cloud'
> lib/tags.rb:122:in `each'
> lib/tags.rb:122:in `tag_cloud'
> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
> app/views/services/index.html.erb:19
> 
> app/controllers/services_controller.rb:24:in `index'|
> 
> |/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable
> .rb:39:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.
> rb:39:in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb
> :73:in `render_template'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256
> :in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367
> :in `_render_with_layout'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254
> :in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:1174:in `render_for_file'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:905:in `render_without_benchmark'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:51:in `render'
> /ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_
> ext/benchmark.rb:8:in `realtime'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:51:in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:135:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:135:in `custom'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:164:in `call'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:164:in `respond'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:158:in `each'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:158:in `respond'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:107:in `respond_to'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:1253:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:1253:in `perform_action_without_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
> rs.rb:617:in `call_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
> rs.rb:610:in `perform_action_without_benchmark'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:68:in `perform_action_without_rescue'
> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:68:in `perform_action_without_rescue'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu
> e.rb:136:in `perform_action_without_caching'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
> ng/sql_cache.rb:13:in `perform_action'
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect
> ion_adapters/abstract/query_cache.rb:34:in `cache'
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c
> ache.rb:8:in `cache'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
> ng/sql_cache.rb:12:in `perform_action'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:524:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:524:in `process_without_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
> rs.rb:606:in `process_without_session_management_support'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi
> on_management.rb:134:in `process'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:392:in `process'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:183:in `handle_request'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:110:in `dispatch_unlocked'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:123:in `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:122:in `synchronize'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:122:in `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:132:in `dispatch_cgi'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:39:in `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in
> `process'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
> `synchronize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
> `process'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
> `process_client'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in `each'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
> `process_client'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
> `initialize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `new'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
> `initialize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `new'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
> 2:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
> 1:in `each'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
> 1:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in
> `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
> 
> |lib/tags.rb:129:in `tag_cloud'
> lib/tags.rb:122:in `each'
> lib/tags.rb:122:in `tag_cloud'
> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
> app/views/services/index.html.erb:19
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.
> rb:39:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.
> rb:39:in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb
> :73:in `render_template'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256
> :in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367
> :in `_render_with_layout'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254
> :in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:1174:in `render_for_file'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:905:in `render_without_benchmark'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:51:in `render'
> /ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_
> ext/benchmark.rb:8:in `realtime'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:51:in `render'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:135:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:135:in `custom'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:164:in `call'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:164:in `respond'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:158:in `each'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:158:in `respond'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
> responds.rb:107:in `respond_to'
> app/controllers/services_controller.rb:24:in `index'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:1253:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:1253:in `perform_action_without_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
> rs.rb:617:in `call_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
> rs.rb:610:in `perform_action_without_benchmark'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:68:in `perform_action_without_rescue'
> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
> marking.rb:68:in `perform_action_without_rescue'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu
> e.rb:136:in `perform_action_without_caching'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
> ng/sql_cache.rb:13:in `perform_action'
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect
> ion_adapters/abstract/query_cache.rb:34:in `cache'
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c
> ache.rb:8:in `cache'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
> ng/sql_cache.rb:12:in `perform_action'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:524:in `send'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:524:in `process_without_filters'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
> rs.rb:606:in `process_without_session_management_support'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi
> on_management.rb:134:in `process'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
> rb:392:in `process'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:183:in `handle_request'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:110:in `dispatch_unlocked'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:123:in `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:122:in `synchronize'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:122:in `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:132:in `dispatch_cgi'
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
> tcher.rb:39:in `dispatch'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in
> `process'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
> `synchronize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
> `process'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
> `process_client'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in `each'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
> `process_client'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
> `initialize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `new'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
> `initialize'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `new'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
> 2:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
> 1:in `each'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
> 1:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in
> `run'
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
> 
> 
>     Request
> 
> 
> 
> Eric Nzuobontane wrote:
>> Hi Guys,
>> I intend to update the beta site in the an hour or so. Is there 
>> something I need to do/know before I do that?
>> This current update will include:
>>  - tag cloud display
>>  - soaplab server registration
>> Though the new service page has no links to the soaplab server, it is 
>> available by direct url. Ideally I would have loved someone else to 
>> play with submitting a soaplab server locally before any exposure to 
>> public
>>
>> cheers,
>>
>> Eric
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>   
> 
> 
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers

From ericnzuo at ebi.ac.uk  Fri Feb 13 12:29:18 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Fri, 13 Feb 2009 17:29:18 +0000
Subject: [BioCatalogue-developers] beta site is down
In-Reply-To: <4995925B.1010109@ebi.ac.uk>
References: <E1LXyuH-0003NF-T8@muffin> <4995925B.1010109@ebi.ac.uk>
Message-ID: <4995ADEE.40709@ebi.ac.uk>

No, you are not alone Thomas! I think ruby forge mailing is unliable. 
Sometimes mails simply do not get delivered if they are not late. For 
something as important as that, I should have sent the mail directly...sorry

cheers,
Eric


Thomas Laurent wrote:
> Does somebody know anything about that ?
>
> Am I the only one receiving the emails from the list 1 hour late ? 
> That's kind of annoying, especially for urgent cases like this one...
>
> Thomas
>
> Franck Tanoh wrote:
>> Hi,
>> I can't access the beta site... <<error 500...>>
>>
>> Please check
>>
>> Cheers,
>> Franck
>>
>> -----Original Message-----
>> From: biocatalogue-developers-bounces at rubyforge.org
>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
>> Nzuobontane
>> Sent: 13 February 2009 13:55
>> To: biocatalogue-developers at rubyforge.org
>> Subject: Re: [BioCatalogue-developers] updating the beta site
>>
>> Unfortunately there was bug in services index view which I was not 
>> able to figure right away. So I did the drastic thing of bring down 
>> the servers. Unfortunately my local installation works just fine and 
>> it seems to be the same code as the repository. So I am quite puzzled
>>
>> Showing /app/views/services/index.html.erb/ where line *#19* raised:
>>
>> |undefined method `h' for BioCatalogue::Tags:Module|
>>
>> Extracted source (around line *#19*):
>>
>> |16:         <span style="font-size: 0.7em; margin-left: 1em;">[ <%=
>> link_to("See All Tags", tags_index_path) -%> ]</span>
>> 17:     </h3>
>> 18:    
>> 19:     <%= generate_tag_cloud(@tags, :tag_cloud_style => "margin-top:
>> 0.6em;") %>
>> 20: </div>
>> 21: 22: <span style="float: right;">
>> |
>>
>> |RAILS_ROOT: 
>> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue|
>>
>> Application Trace <http://beta.biocatalogue.org/services#> | 
>> Framework Trace <http://beta.biocatalogue.org/services#> | Full Trace 
>> <http://beta.biocatalogue.org/services#>
>>
>> |lib/tags.rb:129:in `tag_cloud'
>> lib/tags.rb:122:in `each'
>> lib/tags.rb:122:in `tag_cloud'
>> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
>> app/views/services/index.html.erb:19
>>
>> app/controllers/services_controller.rb:24:in `index'|
>>
>> |/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable 
>>
>> .rb:39:in `send'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable. 
>>
>> rb:39:in `render'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb 
>>
>> :73:in `render_template'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256 
>>
>> :in `render'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367 
>>
>> :in `_render_with_layout'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254 
>>
>> :in `render'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>
>> rb:1174:in `render_for_file'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>
>> rb:905:in `render_without_benchmark'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>
>> marking.rb:51:in `render'
>> /ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_ 
>>
>> ext/benchmark.rb:8:in `realtime'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>
>> marking.rb:51:in `render'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>
>> responds.rb:135:in `send'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>
>> responds.rb:135:in `custom'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>
>> responds.rb:164:in `call'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>
>> responds.rb:164:in `respond'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>
>> responds.rb:158:in `each'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>
>> responds.rb:158:in `respond'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>
>> responds.rb:107:in `respond_to'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>
>> rb:1253:in `send'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>
>> rb:1253:in `perform_action_without_filters'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>
>> rs.rb:617:in `call_filters'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>
>> rs.rb:610:in `perform_action_without_benchmark'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>
>> marking.rb:68:in `perform_action_without_rescue'
>> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>
>> marking.rb:68:in `perform_action_without_rescue'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu 
>>
>> e.rb:136:in `perform_action_without_caching'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi 
>>
>> ng/sql_cache.rb:13:in `perform_action'
>> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect 
>>
>> ion_adapters/abstract/query_cache.rb:34:in `cache'
>> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c 
>>
>> ache.rb:8:in `cache'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi 
>>
>> ng/sql_cache.rb:12:in `perform_action'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>
>> rb:524:in `send'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>
>> rb:524:in `process_without_filters'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>
>> rs.rb:606:in `process_without_session_management_support'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi 
>>
>> on_management.rb:134:in `process'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>
>> rb:392:in `process'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>
>> tcher.rb:183:in `handle_request'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>
>> tcher.rb:110:in `dispatch_unlocked'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>
>> tcher.rb:123:in `dispatch'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>
>> tcher.rb:122:in `synchronize'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>
>> tcher.rb:122:in `dispatch'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>
>> tcher.rb:132:in `dispatch_cgi'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>
>> tcher.rb:39:in `dispatch'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in
>> `process'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
>> `synchronize'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
>> `process'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
>> `process_client'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
>> `each'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
>> `process_client'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
>> `initialize'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>> `new'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
>> `initialize'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>> `new'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>
>> 2:in `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>
>> 1:in `each'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>
>> 1:in `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in 
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in 
>>
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>>
>> |lib/tags.rb:129:in `tag_cloud'
>> lib/tags.rb:122:in `each'
>> lib/tags.rb:122:in `tag_cloud'
>> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
>> app/views/services/index.html.erb:19
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable. 
>>
>> rb:39:in `send'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable. 
>>
>> rb:39:in `render'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb 
>>
>> :73:in `render_template'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256 
>>
>> :in `render'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367 
>>
>> :in `_render_with_layout'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254 
>>
>> :in `render'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>
>> rb:1174:in `render_for_file'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>
>> rb:905:in `render_without_benchmark'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>
>> marking.rb:51:in `render'
>> /ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_ 
>>
>> ext/benchmark.rb:8:in `realtime'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>
>> marking.rb:51:in `render'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>
>> responds.rb:135:in `send'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>
>> responds.rb:135:in `custom'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>
>> responds.rb:164:in `call'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>
>> responds.rb:164:in `respond'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>
>> responds.rb:158:in `each'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>
>> responds.rb:158:in `respond'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>
>> responds.rb:107:in `respond_to'
>> app/controllers/services_controller.rb:24:in `index'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>
>> rb:1253:in `send'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>
>> rb:1253:in `perform_action_without_filters'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>
>> rs.rb:617:in `call_filters'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>
>> rs.rb:610:in `perform_action_without_benchmark'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>
>> marking.rb:68:in `perform_action_without_rescue'
>> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>
>> marking.rb:68:in `perform_action_without_rescue'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu 
>>
>> e.rb:136:in `perform_action_without_caching'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi 
>>
>> ng/sql_cache.rb:13:in `perform_action'
>> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect 
>>
>> ion_adapters/abstract/query_cache.rb:34:in `cache'
>> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c 
>>
>> ache.rb:8:in `cache'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi 
>>
>> ng/sql_cache.rb:12:in `perform_action'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>
>> rb:524:in `send'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>
>> rb:524:in `process_without_filters'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>
>> rs.rb:606:in `process_without_session_management_support'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi 
>>
>> on_management.rb:134:in `process'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>
>> rb:392:in `process'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>
>> tcher.rb:183:in `handle_request'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>
>> tcher.rb:110:in `dispatch_unlocked'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>
>> tcher.rb:123:in `dispatch'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>
>> tcher.rb:122:in `synchronize'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>
>> tcher.rb:122:in `dispatch'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>
>> tcher.rb:132:in `dispatch_cgi'
>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>
>> tcher.rb:39:in `dispatch'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in
>> `process'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
>> `synchronize'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
>> `process'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
>> `process_client'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
>> `each'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
>> `process_client'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
>> `initialize'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>> `new'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
>> `initialize'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>> `new'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>
>> 2:in `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>
>> 1:in `each'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>
>> 1:in `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in 
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in 
>>
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>>
>>
>>     Request
>>
>>
>>
>> Eric Nzuobontane wrote:
>>> Hi Guys,
>>> I intend to update the beta site in the an hour or so. Is there 
>>> something I need to do/know before I do that?
>>> This current update will include:
>>>  - tag cloud display
>>>  - soaplab server registration
>>> Though the new service page has no links to the soaplab server, it 
>>> is available by direct url. Ideally I would have loved someone else 
>>> to play with submitting a soaplab server locally before any exposure 
>>> to public
>>>
>>> cheers,
>>>
>>> Eric
>>>
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>   
>>
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers

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From ytanoh at cs.man.ac.uk  Fri Feb 13 12:34:25 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Fri, 13 Feb 2009 17:34:25 -0000
Subject: [BioCatalogue-developers] beta site is down
In-Reply-To: <4995ADEE.40709@ebi.ac.uk>
Message-ID: <E1LY1vl-0003cq-Un@muffin>

Can we find an alternative to ruby mailing list or making behave faster?
People may think that we don't answer their mails... hope none of mail sent
so far has been lost. 

Franck 

-----Original Message-----
From: Eric Nzuobontane [mailto:ericnzuo at ebi.ac.uk] 
Sent: 13 February 2009 17:29
To: Thomas Laurent
Cc: Franck Tanoh; biocatalogue-developers at rubyforge.org
Subject: Re: [BioCatalogue-developers] beta site is down

No, you are not alone Thomas! I think ruby forge mailing is unliable. 
Sometimes mails simply do not get delivered if they are not late. For 
something as important as that, I should have sent the mail directly...sorry

cheers,
Eric


Thomas Laurent wrote:
> Does somebody know anything about that ?
>
> Am I the only one receiving the emails from the list 1 hour late ? 
> That's kind of annoying, especially for urgent cases like this one...
>
> Thomas
>
> Franck Tanoh wrote:
>> Hi,
>> I can't access the beta site... <<error 500...>>
>>
>> Please check
>>
>> Cheers,
>> Franck
>>
>> -----Original Message-----
>> From: biocatalogue-developers-bounces at rubyforge.org
>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
>> Nzuobontane
>> Sent: 13 February 2009 13:55
>> To: biocatalogue-developers at rubyforge.org
>> Subject: Re: [BioCatalogue-developers] updating the beta site
>>
>> Unfortunately there was bug in services index view which I was not 
>> able to figure right away. So I did the drastic thing of bring down 
>> the servers. Unfortunately my local installation works just fine and 
>> it seems to be the same code as the repository. So I am quite puzzled
>>
>> Showing /app/views/services/index.html.erb/ where line *#19* raised:
>>
>> |undefined method `h' for BioCatalogue::Tags:Module|
>>
>> Extracted source (around line *#19*):
>>
>> |16:         <span style="font-size: 0.7em; margin-left: 1em;">[ <%=
>> link_to("See All Tags", tags_index_path) -%> ]</span>
>> 17:     </h3>
>> 18:    
>> 19:     <%= generate_tag_cloud(@tags, :tag_cloud_style => "margin-top:
>> 0.6em;") %>
>> 20: </div>
>> 21: 22: <span style="float: right;">
>> |
>>
>> |RAILS_ROOT: 
>> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue|
>>
>> Application Trace <http://beta.biocatalogue.org/services#> | 
>> Framework Trace <http://beta.biocatalogue.org/services#> | Full Trace 
>> <http://beta.biocatalogue.org/services#>
>>
>> |lib/tags.rb:129:in `tag_cloud'
>> lib/tags.rb:122:in `each'
>> lib/tags.rb:122:in `tag_cloud'
>> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
>> app/views/services/index.html.erb:19
>>
>> app/controllers/services_controller.rb:24:in `index'|
>>
>>
|/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable

>>
>> .rb:39:in `send'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.

>>
>> rb:39:in `render'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb

>>
>> :73:in `render_template'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256

>>
>> :in `render'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367

>>
>> :in `_render_with_layout'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254

>>
>> :in `render'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>
>> rb:1174:in `render_for_file'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>
>> rb:905:in `render_without_benchmark'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>
>> marking.rb:51:in `render'
>>
/ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_

>>
>> ext/benchmark.rb:8:in `realtime'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>
>> marking.rb:51:in `render'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>
>> responds.rb:135:in `send'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>
>> responds.rb:135:in `custom'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>
>> responds.rb:164:in `call'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>
>> responds.rb:164:in `respond'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>
>> responds.rb:158:in `each'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>
>> responds.rb:158:in `respond'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>
>> responds.rb:107:in `respond_to'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>
>> rb:1253:in `send'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>
>> rb:1253:in `perform_action_without_filters'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte

>>
>> rs.rb:617:in `call_filters'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte

>>
>> rs.rb:610:in `perform_action_without_benchmark'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>
>> marking.rb:68:in `perform_action_without_rescue'
>> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>
>> marking.rb:68:in `perform_action_without_rescue'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu

>>
>> e.rb:136:in `perform_action_without_caching'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi

>>
>> ng/sql_cache.rb:13:in `perform_action'
>>
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect

>>
>> ion_adapters/abstract/query_cache.rb:34:in `cache'
>>
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c

>>
>> ache.rb:8:in `cache'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi

>>
>> ng/sql_cache.rb:12:in `perform_action'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>
>> rb:524:in `send'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>
>> rb:524:in `process_without_filters'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte

>>
>> rs.rb:606:in `process_without_session_management_support'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi

>>
>> on_management.rb:134:in `process'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>
>> rb:392:in `process'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>
>> tcher.rb:183:in `handle_request'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>
>> tcher.rb:110:in `dispatch_unlocked'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>
>> tcher.rb:123:in `dispatch'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>
>> tcher.rb:122:in `synchronize'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>
>> tcher.rb:122:in `dispatch'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>
>> tcher.rb:132:in `dispatch_cgi'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>
>> tcher.rb:39:in `dispatch'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in
>> `process'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
>> `synchronize'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
>> `process'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
>> `process_client'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
>> `each'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
>> `process_client'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
>> `initialize'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>> `new'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
>> `initialize'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>> `new'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>> `run'
>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28

>>
>> 2:in `run'
>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28

>>
>> 1:in `each'
>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28

>>
>> 1:in `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in 
>> `run'
>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in 
>>
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>>
>> |lib/tags.rb:129:in `tag_cloud'
>> lib/tags.rb:122:in `each'
>> lib/tags.rb:122:in `tag_cloud'
>> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
>> app/views/services/index.html.erb:19
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.

>>
>> rb:39:in `send'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.

>>
>> rb:39:in `render'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb

>>
>> :73:in `render_template'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256

>>
>> :in `render'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367

>>
>> :in `_render_with_layout'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254

>>
>> :in `render'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>
>> rb:1174:in `render_for_file'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>
>> rb:905:in `render_without_benchmark'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>
>> marking.rb:51:in `render'
>>
/ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_

>>
>> ext/benchmark.rb:8:in `realtime'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>
>> marking.rb:51:in `render'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>
>> responds.rb:135:in `send'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>
>> responds.rb:135:in `custom'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>
>> responds.rb:164:in `call'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>
>> responds.rb:164:in `respond'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>
>> responds.rb:158:in `each'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>
>> responds.rb:158:in `respond'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>
>> responds.rb:107:in `respond_to'
>> app/controllers/services_controller.rb:24:in `index'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>
>> rb:1253:in `send'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>
>> rb:1253:in `perform_action_without_filters'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte

>>
>> rs.rb:617:in `call_filters'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte

>>
>> rs.rb:610:in `perform_action_without_benchmark'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>
>> marking.rb:68:in `perform_action_without_rescue'
>> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>
>> marking.rb:68:in `perform_action_without_rescue'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu

>>
>> e.rb:136:in `perform_action_without_caching'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi

>>
>> ng/sql_cache.rb:13:in `perform_action'
>>
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect

>>
>> ion_adapters/abstract/query_cache.rb:34:in `cache'
>>
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c

>>
>> ache.rb:8:in `cache'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi

>>
>> ng/sql_cache.rb:12:in `perform_action'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>
>> rb:524:in `send'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>
>> rb:524:in `process_without_filters'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte

>>
>> rs.rb:606:in `process_without_session_management_support'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi

>>
>> on_management.rb:134:in `process'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>
>> rb:392:in `process'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>
>> tcher.rb:183:in `handle_request'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>
>> tcher.rb:110:in `dispatch_unlocked'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>
>> tcher.rb:123:in `dispatch'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>
>> tcher.rb:122:in `synchronize'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>
>> tcher.rb:122:in `dispatch'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>
>> tcher.rb:132:in `dispatch_cgi'
>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>
>> tcher.rb:39:in `dispatch'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in
>> `process'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
>> `synchronize'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in
>> `process'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
>> `process_client'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
>> `each'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
>> `process_client'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
>> `initialize'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>> `new'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
>> `initialize'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>> `new'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>> `run'
>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28

>>
>> 2:in `run'
>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28

>>
>> 1:in `each'
>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28

>>
>> 1:in `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in 
>> `run'
>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in 
>>
>> `run'
>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>>
>>
>>     Request
>>
>>
>>
>> Eric Nzuobontane wrote:
>>> Hi Guys,
>>> I intend to update the beta site in the an hour or so. Is there 
>>> something I need to do/know before I do that?
>>> This current update will include:
>>>  - tag cloud display
>>>  - soaplab server registration
>>> Though the new service page has no links to the soaplab server, it 
>>> is available by direct url. Ideally I would have loved someone else 
>>> to play with submitting a soaplab server locally before any exposure 
>>> to public
>>>
>>> cheers,
>>>
>>> Eric
>>>
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>   
>>
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers



From jits at cs.man.ac.uk  Fri Feb 13 13:00:03 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 13 Feb 2009 18:00:03 +0000
Subject: [BioCatalogue-developers] beta site is down
In-Reply-To: <4995ADEE.40709@ebi.ac.uk>
References: <E1LXyuH-0003NF-T8@muffin> <4995925B.1010109@ebi.ac.uk>
	<4995ADEE.40709@ebi.ac.uk>
Message-ID: <4995B523.7070403@cs.man.ac.uk>

I agree, we need to change the lists to something more reliable....

Jits


Eric Nzuobontane wrote:
> No, you are not alone Thomas! I think ruby forge mailing is unliable. 
> Sometimes mails simply do not get delivered if they are not late. For 
> something as important as that, I should have sent the mail 
> directly...sorry
>
> cheers,
> Eric
>
>
> Thomas Laurent wrote:
>> Does somebody know anything about that ?
>>
>> Am I the only one receiving the emails from the list 1 hour late ? 
>> That's kind of annoying, especially for urgent cases like this one...
>>
>> Thomas
>>
>> Franck Tanoh wrote:
>>> Hi,
>>> I can't access the beta site... <<error 500...>>
>>>
>>> Please check
>>>
>>> Cheers,
>>> Franck
>>>
>>> -----Original Message-----
>>> From: biocatalogue-developers-bounces at rubyforge.org
>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of 
>>> Eric
>>> Nzuobontane
>>> Sent: 13 February 2009 13:55
>>> To: biocatalogue-developers at rubyforge.org
>>> Subject: Re: [BioCatalogue-developers] updating the beta site
>>>
>>> Unfortunately there was bug in services index view which I was not 
>>> able to figure right away. So I did the drastic thing of bring down 
>>> the servers. Unfortunately my local installation works just fine and 
>>> it seems to be the same code as the repository. So I am quite puzzled
>>>
>>> Showing /app/views/services/index.html.erb/ where line *#19* raised:
>>>
>>> |undefined method `h' for BioCatalogue::Tags:Module|
>>>
>>> Extracted source (around line *#19*):
>>>
>>> |16:         <span style="font-size: 0.7em; margin-left: 1em;">[ <%=
>>> link_to("See All Tags", tags_index_path) -%> ]</span>
>>> 17:     </h3>
>>> 18:    19:     <%= generate_tag_cloud(@tags, :tag_cloud_style => 
>>> "margin-top:
>>> 0.6em;") %>
>>> 20: </div>
>>> 21: 22: <span style="float: right;">
>>> |
>>>
>>> |RAILS_ROOT: 
>>> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue|
>>>
>>> Application Trace <http://beta.biocatalogue.org/services#> | 
>>> Framework Trace <http://beta.biocatalogue.org/services#> | Full 
>>> Trace <http://beta.biocatalogue.org/services#>
>>>
>>> |lib/tags.rb:129:in `tag_cloud'
>>> lib/tags.rb:122:in `each'
>>> lib/tags.rb:122:in `tag_cloud'
>>> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
>>> app/views/services/index.html.erb:19
>>>
>>> app/controllers/services_controller.rb:24:in `index'|
>>>
>>> |/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable 
>>>
>>> .rb:39:in `send'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable. 
>>>
>>> rb:39:in `render'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb 
>>>
>>> :73:in `render_template'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256 
>>>
>>> :in `render'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367 
>>>
>>> :in `_render_with_layout'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254 
>>>
>>> :in `render'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>
>>> rb:1174:in `render_for_file'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>
>>> rb:905:in `render_without_benchmark'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>
>>> marking.rb:51:in `render'
>>> /ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_ 
>>>
>>> ext/benchmark.rb:8:in `realtime'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>
>>> marking.rb:51:in `render'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>
>>> responds.rb:135:in `send'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>
>>> responds.rb:135:in `custom'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>
>>> responds.rb:164:in `call'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>
>>> responds.rb:164:in `respond'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>
>>> responds.rb:158:in `each'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>
>>> responds.rb:158:in `respond'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>
>>> responds.rb:107:in `respond_to'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>
>>> rb:1253:in `send'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>
>>> rb:1253:in `perform_action_without_filters'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>>
>>> rs.rb:617:in `call_filters'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>>
>>> rs.rb:610:in `perform_action_without_benchmark'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>
>>> marking.rb:68:in `perform_action_without_rescue'
>>> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>
>>> marking.rb:68:in `perform_action_without_rescue'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu 
>>>
>>> e.rb:136:in `perform_action_without_caching'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi 
>>>
>>> ng/sql_cache.rb:13:in `perform_action'
>>> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect 
>>>
>>> ion_adapters/abstract/query_cache.rb:34:in `cache'
>>> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c 
>>>
>>> ache.rb:8:in `cache'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi 
>>>
>>> ng/sql_cache.rb:12:in `perform_action'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>
>>> rb:524:in `send'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>
>>> rb:524:in `process_without_filters'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>>
>>> rs.rb:606:in `process_without_session_management_support'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi 
>>>
>>> on_management.rb:134:in `process'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>
>>> rb:392:in `process'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>
>>> tcher.rb:183:in `handle_request'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>
>>> tcher.rb:110:in `dispatch_unlocked'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>
>>> tcher.rb:123:in `dispatch'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>
>>> tcher.rb:122:in `synchronize'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>
>>> tcher.rb:122:in `dispatch'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>
>>> tcher.rb:132:in `dispatch_cgi'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>
>>> tcher.rb:39:in `dispatch'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in 
>>>
>>> `process'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>>>
>>> `synchronize'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>>>
>>> `process'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
>>> `process_client'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
>>> `each'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
>>> `process_client'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>> `run'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
>>> `initialize'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>> `new'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>> `run'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
>>> `initialize'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>> `new'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>> `run'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>>
>>> 2:in `run'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>>
>>> 1:in `each'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>>
>>> 1:in `run'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in 
>>> `run'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in 
>>>
>>> `run'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>>>
>>> |lib/tags.rb:129:in `tag_cloud'
>>> lib/tags.rb:122:in `each'
>>> lib/tags.rb:122:in `tag_cloud'
>>> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
>>> app/views/services/index.html.erb:19
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable. 
>>>
>>> rb:39:in `send'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable. 
>>>
>>> rb:39:in `render'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb 
>>>
>>> :73:in `render_template'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256 
>>>
>>> :in `render'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367 
>>>
>>> :in `_render_with_layout'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254 
>>>
>>> :in `render'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>
>>> rb:1174:in `render_for_file'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>
>>> rb:905:in `render_without_benchmark'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>
>>> marking.rb:51:in `render'
>>> /ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_ 
>>>
>>> ext/benchmark.rb:8:in `realtime'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>
>>> marking.rb:51:in `render'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>
>>> responds.rb:135:in `send'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>
>>> responds.rb:135:in `custom'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>
>>> responds.rb:164:in `call'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>
>>> responds.rb:164:in `respond'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>
>>> responds.rb:158:in `each'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>
>>> responds.rb:158:in `respond'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>
>>> responds.rb:107:in `respond_to'
>>> app/controllers/services_controller.rb:24:in `index'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>
>>> rb:1253:in `send'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>
>>> rb:1253:in `perform_action_without_filters'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>>
>>> rs.rb:617:in `call_filters'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>>
>>> rs.rb:610:in `perform_action_without_benchmark'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>
>>> marking.rb:68:in `perform_action_without_rescue'
>>> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>
>>> marking.rb:68:in `perform_action_without_rescue'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu 
>>>
>>> e.rb:136:in `perform_action_without_caching'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi 
>>>
>>> ng/sql_cache.rb:13:in `perform_action'
>>> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect 
>>>
>>> ion_adapters/abstract/query_cache.rb:34:in `cache'
>>> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c 
>>>
>>> ache.rb:8:in `cache'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi 
>>>
>>> ng/sql_cache.rb:12:in `perform_action'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>
>>> rb:524:in `send'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>
>>> rb:524:in `process_without_filters'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>>
>>> rs.rb:606:in `process_without_session_management_support'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi 
>>>
>>> on_management.rb:134:in `process'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>
>>> rb:392:in `process'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>
>>> tcher.rb:183:in `handle_request'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>
>>> tcher.rb:110:in `dispatch_unlocked'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>
>>> tcher.rb:123:in `dispatch'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>
>>> tcher.rb:122:in `synchronize'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>
>>> tcher.rb:122:in `dispatch'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>
>>> tcher.rb:132:in `dispatch_cgi'
>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>
>>> tcher.rb:39:in `dispatch'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in 
>>>
>>> `process'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>>>
>>> `synchronize'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>>>
>>> `process'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
>>> `process_client'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
>>> `each'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
>>> `process_client'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>> `run'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
>>> `initialize'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>> `new'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>> `run'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
>>> `initialize'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>> `new'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>> `run'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>>
>>> 2:in `run'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>>
>>> 1:in `each'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>>
>>> 1:in `run'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in 
>>> `run'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in 
>>>
>>> `run'
>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>>>
>>>
>>>     Request
>>>
>>>
>>>
>>> Eric Nzuobontane wrote:
>>>> Hi Guys,
>>>> I intend to update the beta site in the an hour or so. Is there 
>>>> something I need to do/know before I do that?
>>>> This current update will include:
>>>>  - tag cloud display
>>>>  - soaplab server registration
>>>> Though the new service page has no links to the soaplab server, it 
>>>> is available by direct url. Ideally I would have loved someone else 
>>>> to play with submitting a soaplab server locally before any 
>>>> exposure to public
>>>>
>>>> cheers,
>>>>
>>>> Eric
>>>>
>>>> _______________________________________________
>>>> BioCatalogue-developers mailing list
>>>> BioCatalogue-developers at rubyforge.org
>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>>   
>>>
>>>
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From noreply at rubyforge.org  Sun Feb 15 05:39:19 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 15 Feb 2009 05:39:19 -0500 (EST)
Subject: [BioCatalogue-developers] [442] branches/annotations-form/: Created
 branch to work on the annotations form ( this will probably involve
 changing the service submission pages into a wizard like thing ).
Message-ID: <20090215103920.2AC3D18580E4@rubyforge.org>

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From tlaurent at ebi.ac.uk  Mon Feb 16 05:57:21 2009
From: tlaurent at ebi.ac.uk (Thomas Laurent)
Date: Mon, 16 Feb 2009 10:57:21 +0000
Subject: [BioCatalogue-developers] beta site is down
In-Reply-To: <4995B523.7070403@cs.man.ac.uk>
References: <E1LXyuH-0003NF-T8@muffin> <4995925B.1010109@ebi.ac.uk>
	<4995ADEE.40709@ebi.ac.uk> <4995B523.7070403@cs.man.ac.uk>
Message-ID: <49994691.6060804@ebi.ac.uk>

Until we find an more reliable list, can we just email directly Eric, 
Jits, Franck and I (in addition to the list) for matters as urgent as 
the site being down ? For less urgent matters, the list is probably fine.

Thomas

Jiten Bhagat wrote:
> I agree, we need to change the lists to something more reliable....
> 
> Jits
> 
> 
> Eric Nzuobontane wrote:
>> No, you are not alone Thomas! I think ruby forge mailing is unliable. 
>> Sometimes mails simply do not get delivered if they are not late. For 
>> something as important as that, I should have sent the mail 
>> directly...sorry
>>
>> cheers,
>> Eric
>>
>>
>> Thomas Laurent wrote:
>>> Does somebody know anything about that ?
>>>
>>> Am I the only one receiving the emails from the list 1 hour late ? 
>>> That's kind of annoying, especially for urgent cases like this one...
>>>
>>> Thomas
>>>
>>> Franck Tanoh wrote:
>>>> Hi,
>>>> I can't access the beta site... <<error 500...>>
>>>>
>>>> Please check
>>>>
>>>> Cheers,
>>>> Franck
>>>>
>>>> -----Original Message-----
>>>> From: biocatalogue-developers-bounces at rubyforge.org
>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of 
>>>> Eric
>>>> Nzuobontane
>>>> Sent: 13 February 2009 13:55
>>>> To: biocatalogue-developers at rubyforge.org
>>>> Subject: Re: [BioCatalogue-developers] updating the beta site
>>>>
>>>> Unfortunately there was bug in services index view which I was not 
>>>> able to figure right away. So I did the drastic thing of bring down 
>>>> the servers. Unfortunately my local installation works just fine and 
>>>> it seems to be the same code as the repository. So I am quite puzzled
>>>>
>>>> Showing /app/views/services/index.html.erb/ where line *#19* raised:
>>>>
>>>> |undefined method `h' for BioCatalogue::Tags:Module|
>>>>
>>>> Extracted source (around line *#19*):
>>>>
>>>> |16:         <span style="font-size: 0.7em; margin-left: 1em;">[ <%=
>>>> link_to("See All Tags", tags_index_path) -%> ]</span>
>>>> 17:     </h3>
>>>> 18:    19:     <%= generate_tag_cloud(@tags, :tag_cloud_style => 
>>>> "margin-top:
>>>> 0.6em;") %>
>>>> 20: </div>
>>>> 21: 22: <span style="float: right;">
>>>> |
>>>>
>>>> |RAILS_ROOT: 
>>>> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue|
>>>>
>>>> Application Trace <http://beta.biocatalogue.org/services#> | 
>>>> Framework Trace <http://beta.biocatalogue.org/services#> | Full 
>>>> Trace <http://beta.biocatalogue.org/services#>
>>>>
>>>> |lib/tags.rb:129:in `tag_cloud'
>>>> lib/tags.rb:122:in `each'
>>>> lib/tags.rb:122:in `tag_cloud'
>>>> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
>>>> app/views/services/index.html.erb:19
>>>>
>>>> app/controllers/services_controller.rb:24:in `index'|
>>>>
>>>> |/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable 
>>>>
>>>> .rb:39:in `send'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable. 
>>>>
>>>> rb:39:in `render'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb 
>>>>
>>>> :73:in `render_template'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256 
>>>>
>>>> :in `render'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367 
>>>>
>>>> :in `_render_with_layout'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254 
>>>>
>>>> :in `render'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>>
>>>> rb:1174:in `render_for_file'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>>
>>>> rb:905:in `render_without_benchmark'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>>
>>>> marking.rb:51:in `render'
>>>> /ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_ 
>>>>
>>>> ext/benchmark.rb:8:in `realtime'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>>
>>>> marking.rb:51:in `render'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>>
>>>> responds.rb:135:in `send'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>>
>>>> responds.rb:135:in `custom'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>>
>>>> responds.rb:164:in `call'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>>
>>>> responds.rb:164:in `respond'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>>
>>>> responds.rb:158:in `each'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>>
>>>> responds.rb:158:in `respond'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>>
>>>> responds.rb:107:in `respond_to'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>>
>>>> rb:1253:in `send'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>>
>>>> rb:1253:in `perform_action_without_filters'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>>>
>>>> rs.rb:617:in `call_filters'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>>>
>>>> rs.rb:610:in `perform_action_without_benchmark'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>>
>>>> marking.rb:68:in `perform_action_without_rescue'
>>>> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>>
>>>> marking.rb:68:in `perform_action_without_rescue'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu 
>>>>
>>>> e.rb:136:in `perform_action_without_caching'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi 
>>>>
>>>> ng/sql_cache.rb:13:in `perform_action'
>>>> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect 
>>>>
>>>> ion_adapters/abstract/query_cache.rb:34:in `cache'
>>>> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c 
>>>>
>>>> ache.rb:8:in `cache'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi 
>>>>
>>>> ng/sql_cache.rb:12:in `perform_action'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>>
>>>> rb:524:in `send'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>>
>>>> rb:524:in `process_without_filters'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>>>
>>>> rs.rb:606:in `process_without_session_management_support'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi 
>>>>
>>>> on_management.rb:134:in `process'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>>
>>>> rb:392:in `process'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>>
>>>> tcher.rb:183:in `handle_request'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>>
>>>> tcher.rb:110:in `dispatch_unlocked'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>>
>>>> tcher.rb:123:in `dispatch'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>>
>>>> tcher.rb:122:in `synchronize'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>>
>>>> tcher.rb:122:in `dispatch'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>>
>>>> tcher.rb:132:in `dispatch_cgi'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>>
>>>> tcher.rb:39:in `dispatch'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in 
>>>>
>>>> `process'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>>>>
>>>> `synchronize'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>>>>
>>>> `process'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
>>>> `process_client'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
>>>> `each'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
>>>> `process_client'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
>>>> `initialize'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>> `new'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
>>>> `initialize'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>>> `new'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>>>
>>>> 2:in `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>>>
>>>> 1:in `each'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>>>
>>>> 1:in `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in 
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in 
>>>>
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
>>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
>>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>>>>
>>>> |lib/tags.rb:129:in `tag_cloud'
>>>> lib/tags.rb:122:in `each'
>>>> lib/tags.rb:122:in `tag_cloud'
>>>> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
>>>> app/views/services/index.html.erb:19
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable. 
>>>>
>>>> rb:39:in `send'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable. 
>>>>
>>>> rb:39:in `render'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb 
>>>>
>>>> :73:in `render_template'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256 
>>>>
>>>> :in `render'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367 
>>>>
>>>> :in `_render_with_layout'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254 
>>>>
>>>> :in `render'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>>
>>>> rb:1174:in `render_for_file'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>>
>>>> rb:905:in `render_without_benchmark'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>>
>>>> marking.rb:51:in `render'
>>>> /ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_ 
>>>>
>>>> ext/benchmark.rb:8:in `realtime'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>>
>>>> marking.rb:51:in `render'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>>
>>>> responds.rb:135:in `send'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>>
>>>> responds.rb:135:in `custom'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>>
>>>> responds.rb:164:in `call'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>>
>>>> responds.rb:164:in `respond'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>>
>>>> responds.rb:158:in `each'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>>
>>>> responds.rb:158:in `respond'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_ 
>>>>
>>>> responds.rb:107:in `respond_to'
>>>> app/controllers/services_controller.rb:24:in `index'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>>
>>>> rb:1253:in `send'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>>
>>>> rb:1253:in `perform_action_without_filters'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>>>
>>>> rs.rb:617:in `call_filters'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>>>
>>>> rs.rb:610:in `perform_action_without_benchmark'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>>
>>>> marking.rb:68:in `perform_action_without_rescue'
>>>> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench 
>>>>
>>>> marking.rb:68:in `perform_action_without_rescue'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu 
>>>>
>>>> e.rb:136:in `perform_action_without_caching'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi 
>>>>
>>>> ng/sql_cache.rb:13:in `perform_action'
>>>> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect 
>>>>
>>>> ion_adapters/abstract/query_cache.rb:34:in `cache'
>>>> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c 
>>>>
>>>> ache.rb:8:in `cache'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi 
>>>>
>>>> ng/sql_cache.rb:12:in `perform_action'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>>
>>>> rb:524:in `send'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>>
>>>> rb:524:in `process_without_filters'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte 
>>>>
>>>> rs.rb:606:in `process_without_session_management_support'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi 
>>>>
>>>> on_management.rb:134:in `process'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base. 
>>>>
>>>> rb:392:in `process'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>>
>>>> tcher.rb:183:in `handle_request'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>>
>>>> tcher.rb:110:in `dispatch_unlocked'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>>
>>>> tcher.rb:123:in `dispatch'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>>
>>>> tcher.rb:122:in `synchronize'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>>
>>>> tcher.rb:122:in `dispatch'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>>
>>>> tcher.rb:132:in `dispatch_cgi'
>>>> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa 
>>>>
>>>> tcher.rb:39:in `dispatch'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in 
>>>>
>>>> `process'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>>>>
>>>> `synchronize'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>>>>
>>>> `process'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
>>>> `process_client'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
>>>> `each'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
>>>> `process_client'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
>>>> `initialize'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>> `new'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
>>>> `initialize'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>>> `new'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>>>
>>>> 2:in `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>>>
>>>> 1:in `each'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28 
>>>>
>>>> 1:in `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in 
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in 
>>>>
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
>>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
>>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>>>>
>>>>
>>>>     Request
>>>>
>>>>
>>>>
>>>> Eric Nzuobontane wrote:
>>>>> Hi Guys,
>>>>> I intend to update the beta site in the an hour or so. Is there 
>>>>> something I need to do/know before I do that?
>>>>> This current update will include:
>>>>>  - tag cloud display
>>>>>  - soaplab server registration
>>>>> Though the new service page has no links to the soaplab server, it 
>>>>> is available by direct url. Ideally I would have loved someone else 
>>>>> to play with submitting a soaplab server locally before any 
>>>>> exposure to public
>>>>>
>>>>> cheers,
>>>>>
>>>>> Eric
>>>>>
>>>>> _______________________________________________
>>>>> BioCatalogue-developers mailing list
>>>>> BioCatalogue-developers at rubyforge.org
>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>>>   
>>>>
>>>>
>>>> _______________________________________________
>>>> BioCatalogue-developers mailing list
>>>> BioCatalogue-developers at rubyforge.org
>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>   

From ytanoh at cs.man.ac.uk  Mon Feb 16 06:18:31 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Mon, 16 Feb 2009 11:18:31 -0000
Subject: [BioCatalogue-developers] beta site is down
In-Reply-To: <49994691.6060804@ebi.ac.uk>
Message-ID: <E1LZ1Ue-00007N-24@muffin>

That's a good point but I'm concerned about the people out there trying to
email us on biocat support. We definitively need to get it sorted before the
April release. 
Why not use the same mailing system as our 'friend list'? 

Franck  

-----Original Message-----
From: Thomas Laurent [mailto:tlaurent at ebi.ac.uk] 
Sent: 16 February 2009 10:57
To: Jiten Bhagat
Cc: Eric Nzuobontane; biocatalogue-developers at rubyforge.org; Franck Tanoh
Subject: Re: [BioCatalogue-developers] beta site is down

Until we find an more reliable list, can we just email directly Eric, 
Jits, Franck and I (in addition to the list) for matters as urgent as 
the site being down ? For less urgent matters, the list is probably fine.

Thomas

Jiten Bhagat wrote:
> I agree, we need to change the lists to something more reliable....
> 
> Jits
> 
> 
> Eric Nzuobontane wrote:
>> No, you are not alone Thomas! I think ruby forge mailing is unliable. 
>> Sometimes mails simply do not get delivered if they are not late. For 
>> something as important as that, I should have sent the mail 
>> directly...sorry
>>
>> cheers,
>> Eric
>>
>>
>> Thomas Laurent wrote:
>>> Does somebody know anything about that ?
>>>
>>> Am I the only one receiving the emails from the list 1 hour late ? 
>>> That's kind of annoying, especially for urgent cases like this one...
>>>
>>> Thomas
>>>
>>> Franck Tanoh wrote:
>>>> Hi,
>>>> I can't access the beta site... <<error 500...>>
>>>>
>>>> Please check
>>>>
>>>> Cheers,
>>>> Franck
>>>>
>>>> -----Original Message-----
>>>> From: biocatalogue-developers-bounces at rubyforge.org
>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of 
>>>> Eric
>>>> Nzuobontane
>>>> Sent: 13 February 2009 13:55
>>>> To: biocatalogue-developers at rubyforge.org
>>>> Subject: Re: [BioCatalogue-developers] updating the beta site
>>>>
>>>> Unfortunately there was bug in services index view which I was not 
>>>> able to figure right away. So I did the drastic thing of bring down 
>>>> the servers. Unfortunately my local installation works just fine and 
>>>> it seems to be the same code as the repository. So I am quite puzzled
>>>>
>>>> Showing /app/views/services/index.html.erb/ where line *#19* raised:
>>>>
>>>> |undefined method `h' for BioCatalogue::Tags:Module|
>>>>
>>>> Extracted source (around line *#19*):
>>>>
>>>> |16:         <span style="font-size: 0.7em; margin-left: 1em;">[ <%=
>>>> link_to("See All Tags", tags_index_path) -%> ]</span>
>>>> 17:     </h3>
>>>> 18:    19:     <%= generate_tag_cloud(@tags, :tag_cloud_style => 
>>>> "margin-top:
>>>> 0.6em;") %>
>>>> 20: </div>
>>>> 21: 22: <span style="float: right;">
>>>> |
>>>>
>>>> |RAILS_ROOT: 
>>>> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue|
>>>>
>>>> Application Trace <http://beta.biocatalogue.org/services#> | 
>>>> Framework Trace <http://beta.biocatalogue.org/services#> | Full 
>>>> Trace <http://beta.biocatalogue.org/services#>
>>>>
>>>> |lib/tags.rb:129:in `tag_cloud'
>>>> lib/tags.rb:122:in `each'
>>>> lib/tags.rb:122:in `tag_cloud'
>>>> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
>>>> app/views/services/index.html.erb:19
>>>>
>>>> app/controllers/services_controller.rb:24:in `index'|
>>>>
>>>>
|/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable

>>>>
>>>> .rb:39:in `send'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.

>>>>
>>>> rb:39:in `render'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb

>>>>
>>>> :73:in `render_template'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256

>>>>
>>>> :in `render'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367

>>>>
>>>> :in `_render_with_layout'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254

>>>>
>>>> :in `render'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>>>
>>>> rb:1174:in `render_for_file'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>>>
>>>> rb:905:in `render_without_benchmark'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>>>
>>>> marking.rb:51:in `render'
>>>>
/ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_

>>>>
>>>> ext/benchmark.rb:8:in `realtime'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>>>
>>>> marking.rb:51:in `render'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>>>
>>>> responds.rb:135:in `send'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>>>
>>>> responds.rb:135:in `custom'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>>>
>>>> responds.rb:164:in `call'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>>>
>>>> responds.rb:164:in `respond'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>>>
>>>> responds.rb:158:in `each'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>>>
>>>> responds.rb:158:in `respond'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>>>
>>>> responds.rb:107:in `respond_to'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>>>
>>>> rb:1253:in `send'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>>>
>>>> rb:1253:in `perform_action_without_filters'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte

>>>>
>>>> rs.rb:617:in `call_filters'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte

>>>>
>>>> rs.rb:610:in `perform_action_without_benchmark'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>>>
>>>> marking.rb:68:in `perform_action_without_rescue'
>>>> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>>>
>>>> marking.rb:68:in `perform_action_without_rescue'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu

>>>>
>>>> e.rb:136:in `perform_action_without_caching'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi

>>>>
>>>> ng/sql_cache.rb:13:in `perform_action'
>>>>
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect

>>>>
>>>> ion_adapters/abstract/query_cache.rb:34:in `cache'
>>>>
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c

>>>>
>>>> ache.rb:8:in `cache'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi

>>>>
>>>> ng/sql_cache.rb:12:in `perform_action'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>>>
>>>> rb:524:in `send'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>>>
>>>> rb:524:in `process_without_filters'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte

>>>>
>>>> rs.rb:606:in `process_without_session_management_support'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi

>>>>
>>>> on_management.rb:134:in `process'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>>>
>>>> rb:392:in `process'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>>>
>>>> tcher.rb:183:in `handle_request'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>>>
>>>> tcher.rb:110:in `dispatch_unlocked'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>>>
>>>> tcher.rb:123:in `dispatch'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>>>
>>>> tcher.rb:122:in `synchronize'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>>>
>>>> tcher.rb:122:in `dispatch'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>>>
>>>> tcher.rb:132:in `dispatch_cgi'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>>>
>>>> tcher.rb:39:in `dispatch'
>>>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in 
>>>>
>>>> `process'
>>>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>>>>
>>>> `synchronize'
>>>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>>>>
>>>> `process'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
>>>> `process_client'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
>>>> `each'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
>>>> `process_client'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
>>>> `initialize'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>> `new'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
>>>> `initialize'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>>> `new'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>>> `run'
>>>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28

>>>>
>>>> 2:in `run'
>>>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28

>>>>
>>>> 1:in `each'
>>>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28

>>>>
>>>> 1:in `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in 
>>>> `run'
>>>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in 
>>>>
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
>>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
>>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>>>>
>>>> |lib/tags.rb:129:in `tag_cloud'
>>>> lib/tags.rb:122:in `each'
>>>> lib/tags.rb:122:in `tag_cloud'
>>>> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
>>>> app/views/services/index.html.erb:19
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.

>>>>
>>>> rb:39:in `send'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.

>>>>
>>>> rb:39:in `render'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb

>>>>
>>>> :73:in `render_template'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256

>>>>
>>>> :in `render'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367

>>>>
>>>> :in `_render_with_layout'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254

>>>>
>>>> :in `render'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>>>
>>>> rb:1174:in `render_for_file'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>>>
>>>> rb:905:in `render_without_benchmark'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>>>
>>>> marking.rb:51:in `render'
>>>>
/ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_

>>>>
>>>> ext/benchmark.rb:8:in `realtime'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>>>
>>>> marking.rb:51:in `render'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>>>
>>>> responds.rb:135:in `send'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>>>
>>>> responds.rb:135:in `custom'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>>>
>>>> responds.rb:164:in `call'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>>>
>>>> responds.rb:164:in `respond'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>>>
>>>> responds.rb:158:in `each'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>>>
>>>> responds.rb:158:in `respond'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_

>>>>
>>>> responds.rb:107:in `respond_to'
>>>> app/controllers/services_controller.rb:24:in `index'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>>>
>>>> rb:1253:in `send'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>>>
>>>> rb:1253:in `perform_action_without_filters'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte

>>>>
>>>> rs.rb:617:in `call_filters'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte

>>>>
>>>> rs.rb:610:in `perform_action_without_benchmark'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>>>
>>>> marking.rb:68:in `perform_action_without_rescue'
>>>> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench

>>>>
>>>> marking.rb:68:in `perform_action_without_rescue'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu

>>>>
>>>> e.rb:136:in `perform_action_without_caching'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi

>>>>
>>>> ng/sql_cache.rb:13:in `perform_action'
>>>>
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect

>>>>
>>>> ion_adapters/abstract/query_cache.rb:34:in `cache'
>>>>
/ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c

>>>>
>>>> ache.rb:8:in `cache'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi

>>>>
>>>> ng/sql_cache.rb:12:in `perform_action'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>>>
>>>> rb:524:in `send'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>>>
>>>> rb:524:in `process_without_filters'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte

>>>>
>>>> rs.rb:606:in `process_without_session_management_support'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi

>>>>
>>>> on_management.rb:134:in `process'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.

>>>>
>>>> rb:392:in `process'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>>>
>>>> tcher.rb:183:in `handle_request'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>>>
>>>> tcher.rb:110:in `dispatch_unlocked'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>>>
>>>> tcher.rb:123:in `dispatch'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>>>
>>>> tcher.rb:122:in `synchronize'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>>>
>>>> tcher.rb:122:in `dispatch'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>>>
>>>> tcher.rb:132:in `dispatch_cgi'
>>>>
/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa

>>>>
>>>> tcher.rb:39:in `dispatch'
>>>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in 
>>>>
>>>> `process'
>>>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>>>>
>>>> `synchronize'
>>>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>>>>
>>>> `process'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
>>>> `process_client'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
>>>> `each'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
>>>> `process_client'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
>>>> `initialize'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>> `new'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
>>>> `initialize'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>>> `new'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>>> `run'
>>>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28

>>>>
>>>> 2:in `run'
>>>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28

>>>>
>>>> 1:in `each'
>>>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28

>>>>
>>>> 1:in `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in 
>>>> `run'
>>>>
/ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in 
>>>>
>>>> `run'
>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
>>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
>>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>>>>
>>>>
>>>>     Request
>>>>
>>>>
>>>>
>>>> Eric Nzuobontane wrote:
>>>>> Hi Guys,
>>>>> I intend to update the beta site in the an hour or so. Is there 
>>>>> something I need to do/know before I do that?
>>>>> This current update will include:
>>>>>  - tag cloud display
>>>>>  - soaplab server registration
>>>>> Though the new service page has no links to the soaplab server, it 
>>>>> is available by direct url. Ideally I would have loved someone else 
>>>>> to play with submitting a soaplab server locally before any 
>>>>> exposure to public
>>>>>
>>>>> cheers,
>>>>>
>>>>> Eric
>>>>>
>>>>> _______________________________________________
>>>>> BioCatalogue-developers mailing list
>>>>> BioCatalogue-developers at rubyforge.org
>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>>>   
>>>>
>>>>
>>>> _______________________________________________
>>>> BioCatalogue-developers mailing list
>>>> BioCatalogue-developers at rubyforge.org
>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>   


From jits at cs.man.ac.uk  Mon Feb 16 16:33:02 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 16 Feb 2009 21:33:02 +0000
Subject: [BioCatalogue-developers] beta site is down
In-Reply-To: <E1LZ1Ue-00007N-24@muffin>
References: <E1LZ1Ue-00007N-24@muffin>
Message-ID: <4999DB8E.8080009@cs.man.ac.uk>

Could do. I'd need to look into whether the University of Manchester's 
mailing list software (the one used for the main list and friends) 
allows non members to send to a list. Should be able to with some 
configuration.

I'll try and start this process tomorrow, at least for the support list. 
Please remind me.

Thanks,
Jits


Franck Tanoh wrote:
> That's a good point but I'm concerned about the people out there trying to
> email us on biocat support. We definitively need to get it sorted before the
> April release. 
> Why not use the same mailing system as our 'friend list'? 
>
> Franck  
>
> -----Original Message-----
> From: Thomas Laurent [mailto:tlaurent at ebi.ac.uk] 
> Sent: 16 February 2009 10:57
> To: Jiten Bhagat
> Cc: Eric Nzuobontane; biocatalogue-developers at rubyforge.org; Franck Tanoh
> Subject: Re: [BioCatalogue-developers] beta site is down
>
> Until we find an more reliable list, can we just email directly Eric, 
> Jits, Franck and I (in addition to the list) for matters as urgent as 
> the site being down ? For less urgent matters, the list is probably fine.
>
> Thomas
>
> Jiten Bhagat wrote:
>   
>> I agree, we need to change the lists to something more reliable....
>>
>> Jits
>>
>>
>> Eric Nzuobontane wrote:
>>     
>>> No, you are not alone Thomas! I think ruby forge mailing is unliable. 
>>> Sometimes mails simply do not get delivered if they are not late. For 
>>> something as important as that, I should have sent the mail 
>>> directly...sorry
>>>
>>> cheers,
>>> Eric
>>>
>>>
>>> Thomas Laurent wrote:
>>>       
>>>> Does somebody know anything about that ?
>>>>
>>>> Am I the only one receiving the emails from the list 1 hour late ? 
>>>> That's kind of annoying, especially for urgent cases like this one...
>>>>
>>>> Thomas
>>>>
>>>> Franck Tanoh wrote:
>>>>         
>>>>> Hi,
>>>>> I can't access the beta site... <<error 500...>>
>>>>>
>>>>> Please check
>>>>>
>>>>> Cheers,
>>>>> Franck
>>>>>
>>>>> -----Original Message-----
>>>>> From: biocatalogue-developers-bounces at rubyforge.org
>>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of 
>>>>> Eric
>>>>> Nzuobontane
>>>>> Sent: 13 February 2009 13:55
>>>>> To: biocatalogue-developers at rubyforge.org
>>>>> Subject: Re: [BioCatalogue-developers] updating the beta site
>>>>>
>>>>> Unfortunately there was bug in services index view which I was not 
>>>>> able to figure right away. So I did the drastic thing of bring down 
>>>>> the servers. Unfortunately my local installation works just fine and 
>>>>> it seems to be the same code as the repository. So I am quite puzzled
>>>>>
>>>>> Showing /app/views/services/index.html.erb/ where line *#19* raised:
>>>>>
>>>>> |undefined method `h' for BioCatalogue::Tags:Module|
>>>>>
>>>>> Extracted source (around line *#19*):
>>>>>
>>>>> |16:         <span style="font-size: 0.7em; margin-left: 1em;">[ <%=
>>>>> link_to("See All Tags", tags_index_path) -%> ]</span>
>>>>> 17:     </h3>
>>>>> 18:    19:     <%= generate_tag_cloud(@tags, :tag_cloud_style => 
>>>>> "margin-top:
>>>>> 0.6em;") %>
>>>>> 20: </div>
>>>>> 21: 22: <span style="float: right;">
>>>>> |
>>>>>
>>>>> |RAILS_ROOT: 
>>>>> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue|
>>>>>
>>>>> Application Trace <http://beta.biocatalogue.org/services#> | 
>>>>> Framework Trace <http://beta.biocatalogue.org/services#> | Full 
>>>>> Trace <http://beta.biocatalogue.org/services#>
>>>>>
>>>>> |lib/tags.rb:129:in `tag_cloud'
>>>>> lib/tags.rb:122:in `each'
>>>>> lib/tags.rb:122:in `tag_cloud'
>>>>> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
>>>>> app/views/services/index.html.erb:19
>>>>>
>>>>> app/controllers/services_controller.rb:24:in `index'|
>>>>>
>>>>>
>>>>>           
> |/ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable
>
>   
>>>>> .rb:39:in `send'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.
>
>   
>>>>> rb:39:in `render'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb
>
>   
>>>>> :73:in `render_template'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256
>
>   
>>>>> :in `render'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367
>
>   
>>>>> :in `_render_with_layout'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254
>
>   
>>>>> :in `render'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
>
>   
>>>>> rb:1174:in `render_for_file'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
>
>   
>>>>> rb:905:in `render_without_benchmark'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
>
>   
>>>>> marking.rb:51:in `render'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_
>
>   
>>>>> ext/benchmark.rb:8:in `realtime'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
>
>   
>>>>> marking.rb:51:in `render'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
>
>   
>>>>> responds.rb:135:in `send'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
>
>   
>>>>> responds.rb:135:in `custom'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
>
>   
>>>>> responds.rb:164:in `call'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
>
>   
>>>>> responds.rb:164:in `respond'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
>
>   
>>>>> responds.rb:158:in `each'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
>
>   
>>>>> responds.rb:158:in `respond'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
>
>   
>>>>> responds.rb:107:in `respond_to'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
>
>   
>>>>> rb:1253:in `send'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
>
>   
>>>>> rb:1253:in `perform_action_without_filters'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
>
>   
>>>>> rs.rb:617:in `call_filters'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
>
>   
>>>>> rs.rb:610:in `perform_action_without_benchmark'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
>
>   
>>>>> marking.rb:68:in `perform_action_without_rescue'
>>>>> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
>
>   
>>>>> marking.rb:68:in `perform_action_without_rescue'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu
>
>   
>>>>> e.rb:136:in `perform_action_without_caching'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
>
>   
>>>>> ng/sql_cache.rb:13:in `perform_action'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect
>
>   
>>>>> ion_adapters/abstract/query_cache.rb:34:in `cache'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c
>
>   
>>>>> ache.rb:8:in `cache'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
>
>   
>>>>> ng/sql_cache.rb:12:in `perform_action'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
>
>   
>>>>> rb:524:in `send'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
>
>   
>>>>> rb:524:in `process_without_filters'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
>
>   
>>>>> rs.rb:606:in `process_without_session_management_support'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi
>
>   
>>>>> on_management.rb:134:in `process'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
>
>   
>>>>> rb:392:in `process'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
>
>   
>>>>> tcher.rb:183:in `handle_request'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
>
>   
>>>>> tcher.rb:110:in `dispatch_unlocked'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
>
>   
>>>>> tcher.rb:123:in `dispatch'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
>
>   
>>>>> tcher.rb:122:in `synchronize'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
>
>   
>>>>> tcher.rb:122:in `dispatch'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
>
>   
>>>>> tcher.rb:132:in `dispatch_cgi'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
>
>   
>>>>> tcher.rb:39:in `dispatch'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in 
>   
>>>>> `process'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>   
>>>>> `synchronize'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>   
>>>>> `process'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
>>>>> `process_client'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
>>>>> `each'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
>>>>> `process_client'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>>> `run'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
>>>>> `initialize'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>>> `new'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>>> `run'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
>>>>> `initialize'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>>>> `new'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>>>> `run'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
>
>   
>>>>> 2:in `run'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
>
>   
>>>>> 1:in `each'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
>
>   
>>>>> 1:in `run'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in 
>>>>> `run'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in 
>   
>>>>> `run'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
>>>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
>>>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>>>>>
>>>>> |lib/tags.rb:129:in `tag_cloud'
>>>>> lib/tags.rb:122:in `each'
>>>>> lib/tags.rb:122:in `tag_cloud'
>>>>> app/helpers/tags_helper.rb:9:in `generate_tag_cloud'
>>>>> app/views/services/index.html.erb:19
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.
>
>   
>>>>> rb:39:in `send'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/renderable.
>
>   
>>>>> rb:39:in `render'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/template.rb
>
>   
>>>>> :73:in `render_template'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:256
>
>   
>>>>> :in `render'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:367
>
>   
>>>>> :in `_render_with_layout'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_view/base.rb:254
>
>   
>>>>> :in `render'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
>
>   
>>>>> rb:1174:in `render_for_file'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
>
>   
>>>>> rb:905:in `render_without_benchmark'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
>
>   
>>>>> marking.rb:51:in `render'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/activesupport-2.2.2/lib/active_support/core_
>
>   
>>>>> ext/benchmark.rb:8:in `realtime'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
>
>   
>>>>> marking.rb:51:in `render'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
>
>   
>>>>> responds.rb:135:in `send'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
>
>   
>>>>> responds.rb:135:in `custom'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
>
>   
>>>>> responds.rb:164:in `call'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
>
>   
>>>>> responds.rb:164:in `respond'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
>
>   
>>>>> responds.rb:158:in `each'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
>
>   
>>>>> responds.rb:158:in `respond'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/mime_
>
>   
>>>>> responds.rb:107:in `respond_to'
>>>>> app/controllers/services_controller.rb:24:in `index'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
>
>   
>>>>> rb:1253:in `send'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
>
>   
>>>>> rb:1253:in `perform_action_without_filters'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
>
>   
>>>>> rs.rb:617:in `call_filters'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
>
>   
>>>>> rs.rb:610:in `perform_action_without_benchmark'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
>
>   
>>>>> marking.rb:68:in `perform_action_without_rescue'
>>>>> /usr/lib/ruby/1.8/benchmark.rb:293:in `measure'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/bench
>
>   
>>>>> marking.rb:68:in `perform_action_without_rescue'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/rescu
>
>   
>>>>> e.rb:136:in `perform_action_without_caching'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
>
>   
>>>>> ng/sql_cache.rb:13:in `perform_action'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/connect
>
>   
>>>>> ion_adapters/abstract/query_cache.rb:34:in `cache'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/activerecord-2.2.2/lib/active_record/query_c
>
>   
>>>>> ache.rb:8:in `cache'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/cachi
>
>   
>>>>> ng/sql_cache.rb:12:in `perform_action'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
>
>   
>>>>> rb:524:in `send'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
>
>   
>>>>> rb:524:in `process_without_filters'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/filte
>
>   
>>>>> rs.rb:606:in `process_without_session_management_support'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/sessi
>
>   
>>>>> on_management.rb:134:in `process'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/base.
>
>   
>>>>> rb:392:in `process'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
>
>   
>>>>> tcher.rb:183:in `handle_request'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
>
>   
>>>>> tcher.rb:110:in `dispatch_unlocked'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
>
>   
>>>>> tcher.rb:123:in `dispatch'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
>
>   
>>>>> tcher.rb:122:in `synchronize'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
>
>   
>>>>> tcher.rb:122:in `dispatch'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
>
>   
>>>>> tcher.rb:132:in `dispatch_cgi'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/actionpack-2.2.2/lib/action_controller/dispa
>
>   
>>>>> tcher.rb:39:in `dispatch'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:76:in 
>   
>>>>> `process'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>   
>>>>> `synchronize'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/rails.rb:74:in 
>   
>>>>> `process'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:159:in
>>>>> `process_client'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in 
>>>>> `each'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:158:in
>>>>> `process_client'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>>> `run'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in
>>>>> `initialize'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>>> `new'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:285:in 
>>>>> `run'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in
>>>>> `initialize'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>>>> `new'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel.rb:268:in 
>>>>> `run'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
>
>   
>>>>> 2:in `run'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
>
>   
>>>>> 1:in `each'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/configurator.rb:28
>
>   
>>>>> 1:in `run'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:128:in 
>>>>> `run'
>>>>>
>>>>>           
> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/lib/mongrel/command.rb:212:in 
>   
>>>>> `run'
>>>>> /ebi/extserv/bin/ruby_gems/gems/mongrel-1.1.5/bin/mongrel_rails:281
>>>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19:in `load'
>>>>> /ebi/extserv/bin/ruby_gems/bin/mongrel_rails:19|
>>>>>
>>>>>
>>>>>     Request
>>>>>
>>>>>
>>>>>
>>>>> Eric Nzuobontane wrote:
>>>>>           
>>>>>> Hi Guys,
>>>>>> I intend to update the beta site in the an hour or so. Is there 
>>>>>> something I need to do/know before I do that?
>>>>>> This current update will include:
>>>>>>  - tag cloud display
>>>>>>  - soaplab server registration
>>>>>> Though the new service page has no links to the soaplab server, it 
>>>>>> is available by direct url. Ideally I would have loved someone else 
>>>>>> to play with submitting a soaplab server locally before any 
>>>>>> exposure to public
>>>>>>
>>>>>> cheers,
>>>>>>
>>>>>> Eric
>>>>>>
>>>>>> _______________________________________________
>>>>>> BioCatalogue-developers mailing list
>>>>>> BioCatalogue-developers at rubyforge.org
>>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>>>>   
>>>>>>             
>>>>> _______________________________________________
>>>>> BioCatalogue-developers mailing list
>>>>> BioCatalogue-developers at rubyforge.org
>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>>>           
>>>> _______________________________________________
>>>> BioCatalogue-developers mailing list
>>>> BioCatalogue-developers at rubyforge.org
>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>>         
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>   
>>>       
>
>   


From noreply at rubyforge.org  Tue Feb 17 11:28:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 17 Feb 2009 11:28:09 -0500 (EST)
Subject: [BioCatalogue-developers] [443] branches/social/: Experimental
 branch to add social networking functionality.
Message-ID: <20090217162809.970CB1858109@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 18 05:07:29 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 18 Feb 2009 05:07:29 -0500 (EST)
Subject: [BioCatalogue-developers] [444]
 trunk/public/stylesheets/styles.css: reduced slightly font size for links
 in login box to avoid a line wrap in linux
Message-ID: <20090218100730.194A51858103@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 18 06:30:57 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 18 Feb 2009 06:30:57 -0500 (EST)
Subject: [BioCatalogue-developers] [445]
 trunk/app/views/user_mailer/reset_password.html.erb: body for reset
 password email
Message-ID: <20090218113057.45EB218580FB@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 18 06:48:49 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 18 Feb 2009 06:48:49 -0500 (EST)
Subject: [BioCatalogue-developers] [446] trunk/app/models/user_mailer.rb:
	add reset_pasword email
Message-ID: <20090218114849.2FF581858108@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 18 07:03:50 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 18 Feb 2009 07:03:50 -0500 (EST)
Subject: [BioCatalogue-developers] [447] trunk/app/views/users: add view for
	password reset functionality
Message-ID: <20090218120350.E1F2F1858103@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 18 07:06:22 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 18 Feb 2009 07:06:22 -0500 (EST)
Subject: [BioCatalogue-developers] [448]
 trunk/app/views/users/activate_account.html.erb: display log in link only
 if user not already logged in
Message-ID: <20090218120622.7B0951858103@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 18 07:11:10 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 18 Feb 2009 07:11:10 -0500 (EST)
Subject: [BioCatalogue-developers] [449] trunk: add reset password
	functionality
Message-ID: <20090218121110.C86E018580F9@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 18 10:34:24 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 18 Feb 2009 10:34:24 -0500 (EST)
Subject: [BioCatalogue-developers] [450]
 trunk/app/controllers/users_controller.rb: redirect user to the user page
 after successful change of password
Message-ID: <20090218153424.79BD7185810C@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 19 06:58:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 19 Feb 2009 06:58:09 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2549] Error 500 when you submit a
	service
Message-ID: <20090219115809.9F6C8185810E@rubyforge.org>

Task #2549 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Error 500 when you submit a service
Complete: 0%
Status: Open

Description: when you submit a service you are presented with a server error message << error 500 the request cannot be carried out by the server>> as if the service was not successfully submitted. 
However when you browse the list of services, the newly submitted service is there.



-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2549&group_id=6901&group_project_id=12540

From ericnzuo at ebi.ac.uk  Thu Feb 19 12:20:07 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 19 Feb 2009 17:20:07 +0000
Subject: [BioCatalogue-developers] uploaded test data
Message-ID: <499D94C7.6050408@ebi.ac.uk>

Hi Steve,
Just a quick question on how you how you store the test data that is 
uploaded to the embrace registry. Essentially to disk or db? Reasons for 
the choice made?

cheers,
Eric

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From jits at cs.man.ac.uk  Fri Feb 20 06:28:41 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 20 Feb 2009 11:28:41 +0000
Subject: [BioCatalogue-developers] uploaded test data
In-Reply-To: <499D94C7.6050408@ebi.ac.uk>
References: <499D94C7.6050408@ebi.ac.uk>
Message-ID: <499E93E9.4060509@cs.man.ac.uk>

You should contact that guy we spoke to (forgot his name) who provided 
us with the test scripts etc.

 From what he said I gathered they are using the Drupal file upload 
mechanisms for the test script uploads.

For Biocat, we should use a plugin like Milton or Paperclip to handle 
file uploads.

Cheers,
Jits (enjoying the Malawian sun)


Eric Nzuobontane wrote:
> Hi Steve,
> Just a quick question on how you how you store the test data that is 
> uploaded to the embrace registry. Essentially to disk or db? Reasons 
> for the choice made?
>
> cheers,
> Eric
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From ericnzuo at ebi.ac.uk  Fri Feb 20 07:06:15 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Fri, 20 Feb 2009 12:06:15 +0000
Subject: [BioCatalogue-developers] uploaded test data
In-Reply-To: <499E93E9.4060509@cs.man.ac.uk>
References: <499D94C7.6050408@ebi.ac.uk> <499E93E9.4060509@cs.man.ac.uk>
Message-ID: <499E9CB7.9030600@ebi.ac.uk>

Hi Jits,
Good to know you arrived safely and have some connection
> You should contact that guy we spoke to (forgot his name) who provided 
> us with the test scripts etc.
Joachim is his name, I guess
>
> From what he said I gathered they are using the Drupal file upload 
> mechanisms for the test script uploads.
>
> For Biocat, we should use a plugin like Milton or Paperclip to handle 
> file uploads.
As far as I know, these plugins use one or the other mechanism. I have 
looked into milton for example I think it saves the files on disk. So 
even if we are using a plugin, which one we chose depends on how we 
would like to keep the data.

Hope you do not get burnt in the sun!

Eric


>
> Eric Nzuobontane wrote:
>> Hi Steve,
>> Just a quick question on how you how you store the test data that is 
>> uploaded to the embrace registry. Essentially to disk or db? Reasons 
>> for the choice made?
>>
>> cheers,
>> Eric
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>   

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From ericnzuo at ebi.ac.uk  Fri Feb 20 07:14:27 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Fri, 20 Feb 2009 12:14:27 +0000
Subject: [BioCatalogue-developers] uploaded test data
In-Reply-To: <499E9CB7.9030600@ebi.ac.uk>
References: <499D94C7.6050408@ebi.ac.uk> <499E93E9.4060509@cs.man.ac.uk>
	<499E9CB7.9030600@ebi.ac.uk>
Message-ID: <499E9EA3.6060901@ebi.ac.uk>

looking at the test_harness and wrapper scripts from Joachim, I guess 
they only have the executable name in the db and all the require tests 
files are on disk. So they just go to the test directory and call the 
executable...

Eric


Eric Nzuobontane wrote:
> Hi Jits,
> Good to know you arrived safely and have some connection
>> You should contact that guy we spoke to (forgot his name) who 
>> provided us with the test scripts etc.
> Joachim is his name, I guess
>>
>> From what he said I gathered they are using the Drupal file upload 
>> mechanisms for the test script uploads.
>>
>> For Biocat, we should use a plugin like Milton or Paperclip to handle 
>> file uploads.
> As far as I know, these plugins use one or the other mechanism. I have 
> looked into milton for example I think it saves the files on disk. So 
> even if we are using a plugin, which one we chose depends on how we 
> would like to keep the data.
>
> Hope you do not get burnt in the sun!
>
> Eric
>
>
>>
>> Eric Nzuobontane wrote:
>>> Hi Steve,
>>> Just a quick question on how you how you store the test data that is 
>>> uploaded to the embrace registry. Essentially to disk or db? Reasons 
>>> for the choice made?
>>>
>>> cheers,
>>> Eric
>>>
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>   
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   

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From jits at cs.man.ac.uk  Fri Feb 20 07:20:01 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 20 Feb 2009 12:20:01 +0000
Subject: [BioCatalogue-developers] uploaded test data
In-Reply-To: <499E9EA3.6060901@ebi.ac.uk>
References: <499D94C7.6050408@ebi.ac.uk> <499E93E9.4060509@cs.man.ac.uk>
	<499E9CB7.9030600@ebi.ac.uk> <499E9EA3.6060901@ebi.ac.uk>
Message-ID: <499E9FF1.9020003@cs.man.ac.uk>

Ahh ok.

We could easily write our own file upload mechanism that reuses the 
content_blobs table for the actual storage of files. Personally I would 
prefer this mechanism as it would mean backing up the DB backs up 
everything, without having to worry about files and so on.

 From a performance point of view we can introduce an intermediate 
memcache layer in the future.

Cheers,
Jits

PS: will try and stay a lightly roasted crimson brown ;-)


Eric Nzuobontane wrote:
> looking at the test_harness and wrapper scripts from Joachim, I guess 
> they only have the executable name in the db and all the require tests 
> files are on disk. So they just go to the test directory and call the 
> executable...
>
> Eric
>
>
> Eric Nzuobontane wrote:
>> Hi Jits,
>> Good to know you arrived safely and have some connection
>>> You should contact that guy we spoke to (forgot his name) who 
>>> provided us with the test scripts etc.
>> Joachim is his name, I guess
>>>
>>> From what he said I gathered they are using the Drupal file upload 
>>> mechanisms for the test script uploads.
>>>
>>> For Biocat, we should use a plugin like Milton or Paperclip to 
>>> handle file uploads.
>> As far as I know, these plugins use one or the other mechanism. I 
>> have looked into milton for example I think it saves the files on 
>> disk. So even if we are using a plugin, which one we chose depends on 
>> how we would like to keep the data.
>>
>> Hope you do not get burnt in the sun!
>>
>> Eric
>>
>>
>>>
>>> Eric Nzuobontane wrote:
>>>> Hi Steve,
>>>> Just a quick question on how you how you store the test data that 
>>>> is uploaded to the embrace registry. Essentially to disk or db? 
>>>> Reasons for the choice made?
>>>>
>>>> cheers,
>>>> Eric
>>>>
>>>> _______________________________________________
>>>> BioCatalogue-developers mailing list
>>>> BioCatalogue-developers at rubyforge.org
>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>>   
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>   
>


From ericnzuo at ebi.ac.uk  Fri Feb 20 08:10:28 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Fri, 20 Feb 2009 13:10:28 +0000
Subject: [BioCatalogue-developers] uploaded test data
In-Reply-To: <FF5D74DD-F6FF-42A1-A20E-4A22FC4A9312@manchester.ac.uk>
References: <499D94C7.6050408@ebi.ac.uk>
	<FF5D74DD-F6FF-42A1-A20E-4A22FC4A9312@manchester.ac.uk>
Message-ID: <499EABC4.2030508@ebi.ac.uk>


>
> At the moment, you upload a zip of the files required for a test. This 
> should include the entry point (i.e. the command you'd type on a 
> command line to run the test) as well as any auxilliary files you may 
> need, such as support libraries that aren't installed on the server, 
> or other modules etc.
>
> The zip file gets put in to the database as a blog, in case we need to 
> restore the system, then also gets unzipped in to a safe bit of the 
> filestore, which is where the tests get executed from.
I think that is quite reasonable and do not see why biocatalogue could 
not use the same technique.

cheers,

Eric


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From jits at cs.man.ac.uk  Fri Feb 20 09:03:22 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 20 Feb 2009 14:03:22 +0000
Subject: [BioCatalogue-developers] uploaded test data
In-Reply-To: <499EABC4.2030508@ebi.ac.uk>
References: <499D94C7.6050408@ebi.ac.uk>	<FF5D74DD-F6FF-42A1-A20E-4A22FC4A9312@manchester.ac.uk>
	<499EABC4.2030508@ebi.ac.uk>
Message-ID: <499EB82A.3030203@cs.man.ac.uk>

Eric Nzuobontane wrote:
>
>>
>> At the moment, you upload a zip of the files required for a test. 
>> This should include the entry point (i.e. the command you'd type on a 
>> command line to run the test) as well as any auxilliary files you may 
>> need, such as support libraries that aren't installed on the server, 
>> or other modules etc.
>>
>> The zip file gets put in to the database as a blog, in case we need 
>> to restore the system, then also gets unzipped in to a safe bit of 
>> the filestore, which is where the tests get executed from.
> I think that is quite reasonable and do not see why biocatalogue could 
> not use the same technique.

Ok. Assuming he meant "blob" and not "blog".

So, taking my previous suggestion, I think we should use the existing 
content_blobs table to store the actual files, with another table acting 
as the 'registry' for the test files*. Then the test system can fetch 
these files from the db when required and store them locally in order to 
execute them.

How does this sound?

* It's important to separate out the binary blob from the other metadata 
otherwise Rails, by default, loads up all data in a record which for 
many records means loading up all the test scripts just to show an index 
in the UI, which is a big perf hit. (We learnt the hard way in 
myExperiment, and I assume Drupal has a similar mechanism of splitting 
out metadata and actual blob storage).

Cheers,
Jits


>
> cheers,
>
> Eric
>
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From ericnzuo at ebi.ac.uk  Fri Feb 20 09:29:56 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Fri, 20 Feb 2009 14:29:56 +0000
Subject: [BioCatalogue-developers] uploaded test data
In-Reply-To: <499EB82A.3030203@cs.man.ac.uk>
References: <499D94C7.6050408@ebi.ac.uk>	<FF5D74DD-F6FF-42A1-A20E-4A22FC4A9312@manchester.ac.uk>
	<499EABC4.2030508@ebi.ac.uk> <499EB82A.3030203@cs.man.ac.uk>
Message-ID: <499EBE64.2030307@ebi.ac.uk>


>
>
> So, taking my previous suggestion, I think we should use the existing 
> content_blobs table to store the actual files, with another table 
> acting as the 'registry' for the test files*. Then the test system can 
> fetch these files from the db when required and store them locally in 
> order to execute them.
>
> How does this sound?
that sounds good. Though I would like to add some meta data fields to 
the current content blob like the content_type and the file name that is 
being stored.

>
> * It's important to separate out the binary blob from the other 
> metadata otherwise Rails, by default, loads up all data in a record 
> which for many records means loading up all the test scripts just to 
> show an index in the UI, which is a big perf hit. (We learnt the hard 
> way in myExperiment, and I assume Drupal has a similar mechanism of 
> splitting out metadata and actual blob storage).
>
I see the performance problem...

cheers,

Eric

>
>>
>> cheers,
>>
>> Eric
>>
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>   

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From jits at cs.man.ac.uk  Fri Feb 20 09:36:21 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 20 Feb 2009 14:36:21 +0000
Subject: [BioCatalogue-developers] uploaded test data
In-Reply-To: <499EBE64.2030307@ebi.ac.uk>
References: <499D94C7.6050408@ebi.ac.uk>	<FF5D74DD-F6FF-42A1-A20E-4A22FC4A9312@manchester.ac.uk>
	<499EABC4.2030508@ebi.ac.uk> <499EB82A.3030203@cs.man.ac.uk>
	<499EBE64.2030307@ebi.ac.uk>
Message-ID: <499EBFE5.3020109@cs.man.ac.uk>

Eric Nzuobontane wrote:
>
>>
>>
>> So, taking my previous suggestion, I think we should use the existing 
>> content_blobs table to store the actual files, with another table 
>> acting as the 'registry' for the test files*. Then the test system 
>> can fetch these files from the db when required and store them 
>> locally in order to execute them.
>>
>> How does this sound?
> that sounds good. Though I would like to add some meta data fields to 
> the current content blob like the content_type and the file name that 
> is being stored.

Sounds reasonable. Though is this something that can be stored in the 
metadata place instead. Because imagine, every time you need to display 
the content type or filename you have to load up the blob (hence the 
perf problem mentioned before and defeating the point). The 
content_blobs is essentially just a blob store. Not sure if this is the 
best...

If you do decide to add these into content_blobs, please could you 
provide a script to update the columns for the existing wsdls stored?

Thanks,
Jits


>
>>
>> * It's important to separate out the binary blob from the other 
>> metadata otherwise Rails, by default, loads up all data in a record 
>> which for many records means loading up all the test scripts just to 
>> show an index in the UI, which is a big perf hit. (We learnt the hard 
>> way in myExperiment, and I assume Drupal has a similar mechanism of 
>> splitting out metadata and actual blob storage).
>>
> I see the performance problem...
>
> cheers,
>
> Eric
>
>>
>>>
>>> cheers,
>>>
>>> Eric
>>>
>>>
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>   
>


From noreply at rubyforge.org  Fri Feb 20 11:41:30 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 20 Feb 2009 11:41:30 -0500 (EST)
Subject: [BioCatalogue-developers] [451]
 trunk/app/controllers/search_controller.rb: minimal change removing white
 space that is generating syntax warnings
Message-ID: <20090220164130.46FDE18580EB@rubyforge.org>

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From steve.pettifer at manchester.ac.uk  Fri Feb 20 07:20:10 2009
From: steve.pettifer at manchester.ac.uk (Steve Pettifer)
Date: Fri, 20 Feb 2009 12:20:10 +0000
Subject: [BioCatalogue-developers] uploaded test data
In-Reply-To: <499D94C7.6050408@ebi.ac.uk>
References: <499D94C7.6050408@ebi.ac.uk>
Message-ID: <FF5D74DD-F6FF-42A1-A20E-4A22FC4A9312@manchester.ac.uk>

Hi Eric

At the moment, you upload a zip of the files required for a test. This  
should include the entry point (i.e. the command you'd type on a  
command line to run the test) as well as any auxilliary files you may  
need, such as support libraries that aren't installed on the server,  
or other modules etc.

The zip file gets put in to the database as a blog, in case we need to  
restore the system, then also gets unzipped in to a safe bit of the  
filestore, which is where the tests get executed from.

So we store them both on the disk (to execute) and in the db (for  
safety).

Steve

On 19 Feb 2009, at 17:20, Eric Nzuobontane wrote:

> Hi Steve,
> Just a quick question on how you how you store the test data that is  
> uploaded to the embrace registry. Essentially to disk or db? Reasons  
> for the choice made?
>
> cheers,
> Eric
>
> <ericnzuo.vcf>


From noreply at rubyforge.org  Mon Feb 23 11:24:45 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 23 Feb 2009 11:24:45 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2439] seekDa simple api
Message-ID: <20090223162445.9113618580FF@rubyforge.org>

Task #2439 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: seekDa simple api
Complete: 100%
Status: Open

Description: Agree on simple api for harvesting data from seekda

Follow-Ups:

-------------------------------------------------------
Date: 2009-02-23 16:24
By: jits

Comment:
As provided by Holgar (see emails)

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2439&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Feb 23 11:28:08 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 23 Feb 2009 11:28:08 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2428] Mention new
	biocatalogue-support email address
Message-ID: <20090223162808.67DBE18580FB@rubyforge.org>

Task #2428 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Mention new biocatalogue-support email address
Complete: 100%
Status: Closed

Description: 1st: send an email out to the main biocatalogue liast (the internal) one saying we have set this mailing list up? just to let Carole/Rodrigo/Franck know

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2428&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Feb 23 11:28:23 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 23 Feb 2009 11:28:23 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2439] seekDa simple api
Message-ID: <20090223162823.C4EC518580FC@rubyforge.org>

Task #2439 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: seekDa simple api
Complete: 100%
Status: Closed

Description: Agree on simple api for harvesting data from seekda

Follow-Ups:

-------------------------------------------------------
Date: 2009-02-23 16:24
By: jits

Comment:
As provided by Holgar (see emails)

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2439&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Feb 23 11:29:00 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 23 Feb 2009 11:29:00 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2443] Redo resolr scripts to
	proper ruby scripts
Message-ID: <20090223162900.97E3718580F6@rubyforge.org>

Task #2443 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Redo resolr scripts to proper ruby scripts
Complete: 100%
Status: Closed

Description: Like for regeolocate

Follow-Ups:

-------------------------------------------------------
Date: 2009-02-23 16:29
By: jits

Comment:
Done

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2443&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Feb 24 07:33:33 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 24 Feb 2009 07:33:33 -0500 (EST)
Subject: [BioCatalogue-developers] [452] trunk/db/migrate/
 20090224104138_add_indexes_for_soapservice_substructure.rb: DB migrate
 script to add indexes for soap_operations, soap_inputs and soap_outputs,
 all on parent foreign keys.
Message-ID: <20090224123333.CDF3818580F0@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 24 09:54:37 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 24 Feb 2009 09:54:37 -0500 (EST)
Subject: [BioCatalogue-developers] [453] branches/rest-support: REST + DAS
 Support: updated rest_service schema and implemented migration script for
 REST substructure tables and created blank model files for these .
Message-ID: <20090224145437.8949115B801E@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 24 11:02:26 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 24 Feb 2009 11:02:26 -0500 (EST)
Subject: [BioCatalogue-developers] [454]
 branches/rest-support/test/fixtures/annotations.yml: Removed annotations
 fixture as all testing for annotations is done in the annotations plugin .
Message-ID: <20090224160226.5D4E41858118@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 24 12:25:33 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 24 Feb 2009 12:25:33 -0500 (EST)
Subject: [BioCatalogue-developers] [455] branches/rest-support/app/models:
 REST + DAS support: Initial work on the models,
 defining the main associations and validations .
Message-ID: <20090224172533.5E68E1978561@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 25 04:59:34 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 25 Feb 2009 04:59:34 -0500 (EST)
Subject: [BioCatalogue-developers] [456]
 trunk/app/views/services/new.html.erb: show soaplab server in new service
 view
Message-ID: <20090225095934.90B2315B8021@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Wed Feb 25 05:58:12 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 25 Feb 2009 10:58:12 +0000
Subject: [BioCatalogue-developers] [Fwd: question about biocatalogue]
Message-ID: <49A52444.6030703@ebi.ac.uk>

Hi Guys,
I just got this request from one DDBJ person. I think they are accessing
the embrace registry as we have a link to it on our main page.

Eric

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From ytanoh at cs.man.ac.uk  Wed Feb 25 06:23:55 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 25 Feb 2009 11:23:55 -0000
Subject: [BioCatalogue-developers] [Fwd: question about biocatalogue]
In-Reply-To: <49A52444.6030703@ebi.ac.uk>
Message-ID: <E1LcHrn-0000Zo-GD@muffin>

It looks like they are trying to submit their REST services to the Embrace
registry. Do you know how? Otherwise, I can email Steve for that. I've
looked around the site but no documentation available. 

Franck

Ps: who is the other developer of the Embrace Registry Steve mentioned a
while ago?


-----Original Message-----
From: biocatalogue-developers-bounces at rubyforge.org
[mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
Nzuobontane
Sent: 25 February 2009 10:58
To: biocatalogue-developers at rubyforge.org
Subject: [BioCatalogue-developers] [Fwd: question about biocatalogue]

Hi Guys,
I just got this request from one DDBJ person. I think they are accessing
the embrace registry as we have a link to it on our main page.

Eric



From ytanoh at cs.man.ac.uk  Wed Feb 25 06:42:25 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 25 Feb 2009 11:42:25 -0000
Subject: [BioCatalogue-developers] [Fwd: question about biocatalogue]
In-Reply-To: <E1LcHrn-0000Zo-GD@muffin>
Message-ID: <E1LcI9h-0000bX-SF@muffin>

I can see that they've submitted one of their soap services: 
http://www.embraceregistry.net/  (GetEntry -- Data retrieval by accession
numbers etc -- (DDBJ)

Franck 

-----Original Message-----
From: biocatalogue-developers-bounces at rubyforge.org
[mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Franck
Tanoh
Sent: 25 February 2009 11:24
To: 'Eric Nzuobontane'; biocatalogue-developers at rubyforge.org
Subject: Re: [BioCatalogue-developers] [Fwd: question about biocatalogue]

It looks like they are trying to submit their REST services to the Embrace
registry. Do you know how? Otherwise, I can email Steve for that. I've
looked around the site but no documentation available. 

Franck

Ps: who is the other developer of the Embrace Registry Steve mentioned a
while ago?


-----Original Message-----
From: biocatalogue-developers-bounces at rubyforge.org
[mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
Nzuobontane
Sent: 25 February 2009 10:58
To: biocatalogue-developers at rubyforge.org
Subject: [BioCatalogue-developers] [Fwd: question about biocatalogue]

Hi Guys,
I just got this request from one DDBJ person. I think they are accessing
the embrace registry as we have a link to it on our main page.

Eric


_______________________________________________
BioCatalogue-developers mailing list
BioCatalogue-developers at rubyforge.org
http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From jits at cs.man.ac.uk  Wed Feb 25 07:15:11 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 25 Feb 2009 12:15:11 +0000
Subject: [BioCatalogue-developers] [Fwd: question about biocatalogue]
In-Reply-To: <E1LcHrn-0000Zo-GD@muffin>
References: <E1LcHrn-0000Zo-GD@muffin>
Message-ID: <49A5364F.2070205@cs.man.ac.uk>

You could tell this:

The usual blurb about how the BioCatalogue is superseding the EMBRACE 
registry...

and then mention that EMBRACE registry has basic support for REST 
services, ie: just register the endpoint and then describe it....

then tell them that BioCatalogue, in April, will have better support for 
REST services, being able to describe the exact Resources, Methods, 
Parameters and Representations.

Hope that helps...

Jits

PS: I GOT MY VISA TODAY :-D Should be back there on 6th March.



Franck Tanoh wrote:
> It looks like they are trying to submit their REST services to the Embrace
> registry. Do you know how? Otherwise, I can email Steve for that. I've
> looked around the site but no documentation available. 
>
> Franck
>
> Ps: who is the other developer of the Embrace Registry Steve mentioned a
> while ago?
>
>
> -----Original Message-----
> From: biocatalogue-developers-bounces at rubyforge.org
> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
> Nzuobontane
> Sent: 25 February 2009 10:58
> To: biocatalogue-developers at rubyforge.org
> Subject: [BioCatalogue-developers] [Fwd: question about biocatalogue]
>
> Hi Guys,
> I just got this request from one DDBJ person. I think they are accessing
> the embrace registry as we have a link to it on our main page.
>
> Eric
>
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From ericnzuo at ebi.ac.uk  Wed Feb 25 07:43:24 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 25 Feb 2009 12:43:24 +0000
Subject: [BioCatalogue-developers] [Fwd: question about biocatalogue]
In-Reply-To: <49A5364F.2070205@cs.man.ac.uk>
References: <E1LcHrn-0000Zo-GD@muffin> <49A5364F.2070205@cs.man.ac.uk>
Message-ID: <49A53CEC.5060807@ebi.ac.uk>


>
>
> PS: I GOT MY VISA TODAY :-D Should be back there on 6th March.
Excellent... Now have a good basking before u return :)

>
>
>
> Franck Tanoh wrote:
>> It looks like they are trying to submit their REST services to the 
>> Embrace
>> registry. Do you know how? Otherwise, I can email Steve for that. I've
>> looked around the site but no documentation available.
>> Franck
>>
>> Ps: who is the other developer of the Embrace Registry Steve mentioned a
>> while ago?
>>
>>
>> -----Original Message-----
>> From: biocatalogue-developers-bounces at rubyforge.org
>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
>> Nzuobontane
>> Sent: 25 February 2009 10:58
>> To: biocatalogue-developers at rubyforge.org
>> Subject: [BioCatalogue-developers] [Fwd: question about biocatalogue]
>>
>> Hi Guys,
>> I just got this request from one DDBJ person. I think they are accessing
>> the embrace registry as we have a link to it on our main page.
>>
>> Eric
>>
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>   

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From noreply at rubyforge.org  Thu Feb 26 09:35:04 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Feb 2009 09:35:04 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2557] Annotations plugin:
	implement curation assertions
Message-ID: <20090226143504.5004418580EB@rubyforge.org>

Task #2557 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Annotations plugin: implement curation assertions
Complete: 0%
Status: Open

Description: Make it generic, but for now the real use case is users being able to give a thumbs up or thumbs down for things.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2557&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Feb 26 11:04:55 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Feb 2009 11:04:55 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2558] User profiles: allow users
	to link to their myExp profiles
Message-ID: <20090226160455.27AD418580EE@rubyforge.org>

Task #2558 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: User profiles: allow users to link to their myExp profiles
Complete: 0%
Status: Open

Description: For now, at the very least we should allow users to submit their myExp user profile url or user id and then we fetch all the public info about them and cache it and show it in BioCatalogue

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2558&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Feb 26 11:07:47 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Feb 2009 11:07:47 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2558] User profiles: allow users
	to link to their myExp profiles
Message-ID: <20090226160747.6005C18580F5@rubyforge.org>

Task #2558 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: User profiles: allow users to link to their myExp profiles
Complete: 0%
Status: Open

Description: For now, at the very least we should allow users to submit their myExp user profile url or user id and then we fetch all the public info about them and cache it and show it in BioCatalogue

Follow-Ups:

-------------------------------------------------------
Date: 2009-02-26 16:07
By: jits

Comment:
Also, when displaying this info, make sure to mention that it comes from their myExp profile and provide a link back to it.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2558&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Feb 26 11:10:52 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Feb 2009 11:10:52 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2559] User profiles: allow users
	to register links to other things
Message-ID: <20090226161052.AB50618580F0@rubyforge.org>

Task #2559 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: User profiles: allow users to register links to other things
Complete: 0%
Status: Open

Description: Marco specifically wants to be able to link to his LinkedIn profile and such. 

So in the meantime we can allow users to register the URL to your LinkedIn etc profiles and any other links, which will then get shown on their profile.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2559&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Feb 26 11:13:18 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Feb 2009 11:13:18 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2560] Show user name in all places
	instead of email address
Message-ID: <20090226161319.0DB7518580EE@rubyforge.org>

Task #2560 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Show user name in all places instead of email address
Complete: 0%
Status: Open

Description: ... like in the welcome messages.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2560&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Feb 26 11:16:23 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Feb 2009 11:16:23 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2561] Scraping for services from a
	web page
Message-ID: <20090226161624.0C63518580EE@rubyforge.org>

Task #2561 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Scraping for services from a web page
Complete: 0%
Status: Open

Description: Look into possibly doing some page scraping of services.

Is this worth it?

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2561&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Feb 26 11:33:15 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Feb 2009 11:33:15 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2562] Add hints to service
	submission page
Message-ID: <20090226163315.7CBF318580EE@rubyforge.org>

Task #2562 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Add hints to service submission page
Complete: 0%
Status: Open

Description: From Marco:

# It would be very helpful if there would be little hints on the page (little pieces of text and mouse-over info).

    * E.g. How will a 'name alias' be used?

# Can I provide more than one alias?

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2562&group_id=6901&group_project_id=12540

From ericnzuo at ebi.ac.uk  Thu Feb 26 11:38:46 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 26 Feb 2009 16:38:46 +0000
Subject: [BioCatalogue-developers] [Fwd: question about biocatalogue]
In-Reply-To: <49A5364F.2070205@cs.man.ac.uk>
References: <E1LcHrn-0000Zo-GD@muffin> <49A5364F.2070205@cs.man.ac.uk>
Message-ID: <49A6C596.3000205@ebi.ac.uk>

Ok, I will respond to this mail now, since I have not seen a copy of a 
reply to these guys. They sent the mail to me so I will get the stick of 
nothing gets done.

Eric


Jiten Bhagat wrote:
> You could tell this:
>
> The usual blurb about how the BioCatalogue is superseding the EMBRACE 
> registry...
>
> and then mention that EMBRACE registry has basic support for REST 
> services, ie: just register the endpoint and then describe it....
>
> then tell them that BioCatalogue, in April, will have better support 
> for REST services, being able to describe the exact Resources, 
> Methods, Parameters and Representations.
>
> Hope that helps...
>
> Jits
>
> PS: I GOT MY VISA TODAY :-D Should be back there on 6th March.
>
>
>
> Franck Tanoh wrote:
>> It looks like they are trying to submit their REST services to the 
>> Embrace
>> registry. Do you know how? Otherwise, I can email Steve for that. I've
>> looked around the site but no documentation available.
>> Franck
>>
>> Ps: who is the other developer of the Embrace Registry Steve mentioned a
>> while ago?
>>
>>
>> -----Original Message-----
>> From: biocatalogue-developers-bounces at rubyforge.org
>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
>> Nzuobontane
>> Sent: 25 February 2009 10:58
>> To: biocatalogue-developers at rubyforge.org
>> Subject: [BioCatalogue-developers] [Fwd: question about biocatalogue]
>>
>> Hi Guys,
>> I just got this request from one DDBJ person. I think they are accessing
>> the embrace registry as we have a link to it on our main page.
>>
>> Eric
>>
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>   

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From jits at cs.man.ac.uk  Thu Feb 26 11:42:31 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Thu, 26 Feb 2009 16:42:31 +0000
Subject: [BioCatalogue-developers] [Fwd: question about biocatalogue]
In-Reply-To: <49A6C596.3000205@ebi.ac.uk>
References: <E1LcHrn-0000Zo-GD@muffin> <49A5364F.2070205@cs.man.ac.uk>
	<49A6C596.3000205@ebi.ac.uk>
Message-ID: <49A6C677.7090802@cs.man.ac.uk>

Ok, fair enough!

Franck, you should have responded to this!!!!! :-)

Jits


Eric Nzuobontane wrote:
> Ok, I will respond to this mail now, since I have not seen a copy of a 
> reply to these guys. They sent the mail to me so I will get the stick 
> of nothing gets done.
>
> Eric
>
>
> Jiten Bhagat wrote:
>> You could tell this:
>>
>> The usual blurb about how the BioCatalogue is superseding the EMBRACE 
>> registry...
>>
>> and then mention that EMBRACE registry has basic support for REST 
>> services, ie: just register the endpoint and then describe it....
>>
>> then tell them that BioCatalogue, in April, will have better support 
>> for REST services, being able to describe the exact Resources, 
>> Methods, Parameters and Representations.
>>
>> Hope that helps...
>>
>> Jits
>>
>> PS: I GOT MY VISA TODAY :-D Should be back there on 6th March.
>>
>>
>>
>> Franck Tanoh wrote:
>>> It looks like they are trying to submit their REST services to the 
>>> Embrace
>>> registry. Do you know how? Otherwise, I can email Steve for that. I've
>>> looked around the site but no documentation available.
>>> Franck
>>>
>>> Ps: who is the other developer of the Embrace Registry Steve 
>>> mentioned a
>>> while ago?
>>>
>>>
>>> -----Original Message-----
>>> From: biocatalogue-developers-bounces at rubyforge.org
>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of 
>>> Eric
>>> Nzuobontane
>>> Sent: 25 February 2009 10:58
>>> To: biocatalogue-developers at rubyforge.org
>>> Subject: [BioCatalogue-developers] [Fwd: question about biocatalogue]
>>>
>>> Hi Guys,
>>> I just got this request from one DDBJ person. I think they are 
>>> accessing
>>> the embrace registry as we have a link to it on our main page.
>>>
>>> Eric
>>>
>>>
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>   
>


From ericnzuo at ebi.ac.uk  Fri Feb 27 04:56:35 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Fri, 27 Feb 2009 09:56:35 +0000
Subject: [BioCatalogue-developers] question about biocatalogue
In-Reply-To: <49A519DB.50601@genes.nig.ac.jp>
References: <49A519DB.50601@genes.nig.ac.jp>
Message-ID: <49A7B8D3.2090006@ebi.ac.uk>

Dear Yasumasa

Thank you for your mail and for registering your services into the
embrace registry. The current embrace registry will be merge with the
BioCatalogue in April. BioCatalogue will offer more possibilities than
the current embrace registry does.
>
> 1. URL to REST collection
>    What does "What does "URL to REST collection"?mean ? Is the
> following page is suitable?
>
> http://xml.nig.ac.jp/wabi/Method?serviceName=GetEntry&mode=methodList&lang=en
>   
The URL to REST collection simple means the endpoint to the rest
services without the parameters
ie http://xml.nig.ac.jp/wabi/
Then please describe the service and you can add the url

http://xml.nig.ac.jp/wabi/Method?serviceName=GetEntry&mode=methodList&lang=en

as an example of how to invoke the service

> 2. Vocabularies
>    Do you intend to control the vocabularies of the Web service
> description ?
>   
Not directly at this point. But we intend to leverage existing
vocabularies like the myGrid ontology so that people can associate
service discriptions with ontologies
> 3. Rating
>    What algorithm is "Your rating" estimated based on ?
>   
This is a simple 5-star rating system. So the user determines the rating
rather than it being computed using an algorithm

I hope that helps. If there are any questions, please do not hesitate to
contact us


Regards,

BioCatalogue Team

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From noreply at rubyforge.org  Fri Feb 27 04:56:40 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 27 Feb 2009 04:56:40 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2564] Add index/contents table on
	operations tab for easy navigation
Message-ID: <20090227095641.67DC518580E4@rubyforge.org>

Task #2564 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Add index/contents table on operations tab for easy navigation
Complete: 0%
Status: Open

Description: ... with full anchor links

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2564&group_id=6901&group_project_id=12540

From ericnzuo at ebi.ac.uk  Fri Feb 27 05:37:31 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Fri, 27 Feb 2009 10:37:31 +0000
Subject: [BioCatalogue-developers] question about biocatalogue
In-Reply-To: <49A519DB.50601@genes.nig.ac.jp>
References: <49A519DB.50601@genes.nig.ac.jp>
Message-ID: <49A7C26B.2090809@ebi.ac.uk>

Dear Yasumasa

Thank you for your mail and for registering your services into the
embrace registry. The current embrace registry will be merge with the
BioCatalogue in April. BioCatalogue will offer more possibilities than
the current embrace registry does.

> >
> > 1. URL to REST collection
> >    What does "What does "URL to REST collection"?mean ? Is the
> > following page is suitable?
> >
> > http://xml.nig.ac.jp/wabi/Method?serviceName=GetEntry&mode=methodList&lang=en
> >   
>   
The URL to REST collection simple means the endpoint to the rest
services without the parameters
ie http://xml.nig.ac.jp/wabi/
Then please describe the service and you can add the url

http://xml.nig.ac.jp/wabi/Method?serviceName=GetEntry&mode=methodList&lang=en

as an example of how to invoke the service


> > 2. Vocabularies
> >    Do you intend to control the vocabularies of the Web service
> > description ?
> >   
>   
Not directly at this point. But we intend to leverage existing
vocabularies like the myGrid ontology so that people can associate
service descriptions with ontologies

> > 3. Rating
> >    What algorithm is "Your rating" estimated based on ?
> >   
>   
This is a simple 5-star rating system. So the user determines the rating
rather than it being computed using an algorithm

I hope that helps. If there are any questions, please do not hesitate to
contact us


Regards,

BioCatalogue Team


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From yshigemo at genes.nig.ac.jp  Fri Feb 27 07:43:28 2009
From: yshigemo at genes.nig.ac.jp (Yasumasa Shigemoto)
Date: Fri, 27 Feb 2009 21:43:28 +0900
Subject: [BioCatalogue-developers] question about biocatalogue
In-Reply-To: <49A7C26B.2090809@ebi.ac.uk>
References: <49A519DB.50601@genes.nig.ac.jp> <49A7C26B.2090809@ebi.ac.uk>
Message-ID: <49A7DFF0.6050104@genes.nig.ac.jp>

Dear Eric,

Thank you for your mail.

> The URL to REST collection simple means the endpoint to the rest
> services without the parameters
> ie http://xml.nig.ac.jp/wabi/
> Then please describe the service and you can add the url
>
>
http://xml.nig.ac.jp/wabi/Method?serviceName=GetEntry&mode=methodList&lang=en
>
> as an example of how to invoke the service

The example of the REST URL is as follows.

http://xml.nig.ac.jp/rest/Invoke?service=GetEntry&method=getDDBJEntry&accession=AB000100

The above URL provides DDBJ entry with specified accession number.
Then, the URL to REST collection is 'http://xml.nig.ac.jp/rest/' ?

However if the user access the above URL, there is no information
in the page. Because the API document is provided in the following
another page.
'http://xml.nig.ac.jp/wabi/Method?serviceName=GetEntry&mode=methodList&lang=en'

I appreciate very much if you could give us more advice.

Regards,
Yasumasa

> Dear Yasumasa
> 
> Thank you for your mail and for registering your services into the
> embrace registry. The current embrace registry will be merge with the
> BioCatalogue in April. BioCatalogue will offer more possibilities than
> the current embrace registry does.
> 
>>> 1. URL to REST collection
>>>    What does "What does "URL to REST collection"?mean ? Is the
>>> following page is suitable?
>>>
>>> http://xml.nig.ac.jp/wabi/Method?serviceName=GetEntry&mode=methodList&lang=en
>>>   
>>   
> The URL to REST collection simple means the endpoint to the rest
> services without the parameters
> ie http://xml.nig.ac.jp/wabi/
> Then please describe the service and you can add the url
> 
> http://xml.nig.ac.jp/wabi/Method?serviceName=GetEntry&mode=methodList&lang=en
> 
> as an example of how to invoke the service
> 
> 
>>> 2. Vocabularies
>>>    Do you intend to control the vocabularies of the Web service
>>> description ?
>>>   
>>   
> Not directly at this point. But we intend to leverage existing
> vocabularies like the myGrid ontology so that people can associate
> service descriptions with ontologies
> 
>>> 3. Rating
>>>    What algorithm is "Your rating" estimated based on ?
>>>   
>>   
> This is a simple 5-star rating system. So the user determines the rating
> rather than it being computed using an algorithm
> 
> I hope that helps. If there are any questions, please do not hesitate to
> contact us
> 
> 
> Regards,
> 
> BioCatalogue Team
> 
> 


From jits at cs.man.ac.uk  Fri Feb 27 09:34:26 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 27 Feb 2009 14:34:26 +0000
Subject: [BioCatalogue-developers] BioCatalogue API
Message-ID: <49A7F9F2.7000205@cs.man.ac.uk>

Hello Sam,

Very glad to see someone interested in BioCatalogue APIs :-)

I'm one of the developers on the project and maybe I can help with your questions....

As Franck has mentioned, we plan on having public, supported APIs after the April release, in Q2/Q3 of this year, but in the meantime we're very keen on having some alpha and test APIs beforehand (for example, we already have a basic RESTful Search API that is being used in a proof of concept application).

Your idea to drill down to the level of the algorithms in a service and provide a structured API over this is interesting. I see your need as being a deeper analysis of the metadata (and structures) about services. Something we keenly welcome, but there is a slight tension there since BioCatalogue is mainly aimed at a higher level than that - our priority is to provide human readable metadata that is curated by professionals, to aid people in the discovery and use of services. That is not to say that we won't go into machine readable and more structured metadata for analysis and other purposes, but this is further down the line in the project. 

At the moment, the algorithms and anything else about a service can be described using free text annotations. So far it's only things like 'descriptions', 'tags' and 'examples', but our annotation model is generic enough to cater for any attribute + value pair. We are working on a more exact metadata model to describe services, possibly even tying it into controlled vocabularies and ontologies (more on this post April). All these annotations are then exposed in a RESTful way so you could potentially build your diagrams from this?

If you have any specific, but generic types of annotations you would find useful then please do let us know.

If you haven't already, please sign up for the Friends list - http://listserv.manchester.ac.uk/cgi-bin/wa?SUBED1=biocatalogue-friends&A=1 where we'll update on the status of the beta site and any alpha APIs.

Let me know if I can help you in any other way.

Cheers,
Jits




-----Original Message-----
From: sammyschmidt at gmail.com [mailto:sammyschmidt at gmail.com] On Behalf Of
Sam Schmidt
Sent: 24 February 2009 22:18
To: Franck Tanoh
Subject: Re: BioCatalogue API

G'day Franck,

Thanks for your response. I would be interested in developing an alpha
API - http://www.deakin.edu.au/~sschm/GST2 - to produce a diagram such
as that (very rough!) based upon the catalogue.

It would be great to go down a further level and detail what
algorithms are implemented in various software, and generate diagrams
based upon algorithms used and such - but I am not sure if the
proposed catalogue details this information? -- I did this for about
30 different phylogenetic software packages, which produced
interesting results (such as MrBayes is the second most cited
phylogeny software package, but the only of which that is based on
Bayesian Inference) - so while it was not an exhaustive search, it is
interesting to see where there may be room for further research and
development in bio software.

Cheers,

Sam.