From noreply at rubyforge.org  Mon Mar  2 04:40:48 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  2 Mar 2009 04:40:48 -0500 (EST)
Subject: [BioCatalogue-developers] [457] trunk: Used the non-minimised
 version of the tabber JS code so that enhancements can be made much more
 easily .
Message-ID: <20090302094049.59DEA18580FE@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Mon Mar  2 09:22:51 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 02 Mar 2009 14:22:51 +0000
Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
In-Reply-To: <0D9849CC-8FF6-431F-9966-BA78CFDE23EA@manchester.ac.uk>
References: <49A7E381.2060803@ebi.ac.uk>
	<0D9849CC-8FF6-431F-9966-BA78CFDE23EA@manchester.ac.uk>
Message-ID: <49ABEBBB.2050403@ebi.ac.uk>

Hi Steve,
Have you had a look at this mail?

cheers,
Eric

Steve Pettifer wrote:
> Will do; just in a meeting at the mo I'll reply properly shortly
>
> Steve
>
>
> On 27 Feb 2009, at 12:58, Eric Nzuobontane wrote:
>
>> Hi Steve,
>> Could you help with these questions about the embrace registry?
>>
>> Eric
>>
>>
>> *From: *Yasumasa Shigemoto <yshigemo at genes.nig.ac.jp
>> <mailto:yshigemo at genes.nig.ac.jp>>
>> *Date: *27 February 2009 12:43:28 GMT
>> *To: *Eric Nzuobontane <ericnzuo at ebi.ac.uk <mailto:ericnzuo at ebi.ac.uk>>
>> *Cc: *SUGAWARA Hideaki <hsugawar at genes.nig.ac.jp
>> <mailto:hsugawar at genes.nig.ac.jp>>, Yoshikazu kuwana
>> <ykuwana at genes.nig.ac.jp <mailto:ykuwana at genes.nig.ac.jp>>,
>> biocatalogue-developers at rubyforge.org
>> <mailto:biocatalogue-developers at rubyforge.org>
>> *Subject: **Re: question about biocatalogue*
>>
>>
>> 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
>> <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
>>>
>>>
>>
>>
>> <ericnzuo.vcf>
>

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From noreply at rubyforge.org  Mon Mar  2 13:00:53 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  2 Mar 2009 13:00:53 -0500 (EST)
Subject: [BioCatalogue-developers] [458] trunk/app/models/soaplab_server.rb:
 use soap4r gem instead of the standard ruby lib process soap and add name
 aliases to soaplab services
Message-ID: <20090302180053.D3A7215B801E@rubyforge.org>

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From noreply at rubyforge.org  Mon Mar  2 13:02:31 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  2 Mar 2009 13:02:31 -0500 (EST)
Subject: [BioCatalogue-developers] [459] trunk/config/environment.rb: load
 soap4r gem at start up, needed to create proxy to soap services
Message-ID: <20090302180231.D282F15B801E@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Tue Mar  3 08:13:11 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Tue, 03 Mar 2009 13:13:11 +0000
Subject: [BioCatalogue-developers] geocoding returning questionable results
Message-ID: <49AD2CE7.301@ebi.ac.uk>

hi,
I just submitted a service
http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678
 which I expected to be located in Germany but geocoding claims it is in 
the US!

Eric

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From ytanoh at cs.man.ac.uk  Tue Mar  3 09:41:43 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Tue, 3 Mar 2009 14:41:43 -0000
Subject: [BioCatalogue-developers] geocoding returning questionable
	results
In-Reply-To: <49AD2CE7.301@ebi.ac.uk>
Message-ID: <E1LeVoW-0000OK-6q@muffin>

Eric, 

This is a BioMoby service (therefore a dummy wsdl). The tool was made in
germany (http://www.biomedcentral.com/1471-2105/7/535) but the web service
was implemented by the BioMoby group. So the geocoding make sense. 

The service should therefore be tagged as BioMoby service. The list of
BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList 

Franck 

-----Original Message-----
From: biocatalogue-developers-bounces at rubyforge.org
[mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
Nzuobontane
Sent: 03 March 2009 13:13
To: biocatalogue-developers at rubyforge.org
Subject: [BioCatalogue-developers] geocoding returning questionable results

hi,
I just submitted a service
http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678
 which I expected to be located in Germany but geocoding claims it is in 
the US!

Eric



From ericnzuo at ebi.ac.uk  Tue Mar  3 09:51:48 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Tue, 03 Mar 2009 14:51:48 +0000
Subject: [BioCatalogue-developers] geocoding returning questionable
	results
In-Reply-To: <E1LeVoW-0000OK-6q@muffin>
References: <E1LeVoW-0000OK-6q@muffin>
Message-ID: <49AD4404.6030105@ebi.ac.uk>

Hi Franck,
I am not sure I understand. Geocoding has no knowledge of the the 
history of whatever it goecodes, as far as I understand. I think the 
enpoint has a german domain and would expect the goecode follow that... 
Except I completely missundestand what goeoding does.

Eric


Franck Tanoh wrote:
> Eric, 
>
> This is a BioMoby service (therefore a dummy wsdl). The tool was made in
> germany (http://www.biomedcentral.com/1471-2105/7/535) but the web service
> was implemented by the BioMoby group. So the geocoding make sense. 
>
> The service should therefore be tagged as BioMoby service. The list of
> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList 
>
> Franck 
>
> -----Original Message-----
> From: biocatalogue-developers-bounces at rubyforge.org
> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
> Nzuobontane
> Sent: 03 March 2009 13:13
> To: biocatalogue-developers at rubyforge.org
> Subject: [BioCatalogue-developers] geocoding returning questionable results
>
> hi,
> I just submitted a service
> http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678
>  which I expected to be located in Germany but geocoding claims it is in 
> the US!
>
> Eric
>
>   

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From noreply at rubyforge.org  Tue Mar  3 10:09:29 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  3 Mar 2009 10:09:29 -0500 (EST)
Subject: [BioCatalogue-developers] [460]
	trunk/app/views/layouts/_footer.html.erb: put full url for wiki
Message-ID: <20090303150929.3022818580ED@rubyforge.org>

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From jits at cs.man.ac.uk  Tue Mar  3 10:35:51 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 03 Mar 2009 15:35:51 +0000
Subject: [BioCatalogue-developers] geocoding returning
	questionable	results
In-Reply-To: <49AD4404.6030105@ebi.ac.uk>
References: <E1LeVoW-0000OK-6q@muffin> <49AD4404.6030105@ebi.ac.uk>
Message-ID: <49AD4E57.5030203@cs.man.ac.uk>

We're using a free online IP to location mapping service called hostip 
(http://www.hostip.info/) so unfortunately we rely on their database 
(which can be populated and updated by anyone through their website).

Also, we do DNS name to IP resolving at submission time, which is at the 
mercy of DNS servers and load balancers.

Jits


Eric Nzuobontane wrote:
> Hi Franck,
> I am not sure I understand. Geocoding has no knowledge of the the 
> history of whatever it goecodes, as far as I understand. I think the 
> enpoint has a german domain and would expect the goecode follow 
> that... Except I completely missundestand what goeoding does.
>
> Eric
>
>
> Franck Tanoh wrote:
>> Eric,
>> This is a BioMoby service (therefore a dummy wsdl). The tool was made in
>> germany (http://www.biomedcentral.com/1471-2105/7/535) but the web 
>> service
>> was implemented by the BioMoby group. So the geocoding make sense.
>> The service should therefore be tagged as BioMoby service. The list of
>> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList
>> Franck
>> -----Original Message-----
>> From: biocatalogue-developers-bounces at rubyforge.org
>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
>> Nzuobontane
>> Sent: 03 March 2009 13:13
>> To: biocatalogue-developers at rubyforge.org
>> Subject: [BioCatalogue-developers] geocoding returning questionable 
>> results
>>
>> hi,
>> I just submitted a service
>> http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678
>>  which I expected to be located in Germany but geocoding claims it is 
>> in the US!
>>
>> Eric
>>
>>   
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From noreply at rubyforge.org  Tue Mar  3 10:41:15 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  3 Mar 2009 10:41:15 -0500 (EST)
Subject: [BioCatalogue-developers] [461] trunk: Fixes and additions to allow
 us to remember which tab the user was on when submitting an annotation so
 that the appropriate tab is shown after .
Message-ID: <20090303154115.CFFD018580ED@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Tue Mar  3 11:01:03 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Tue, 03 Mar 2009 16:01:03 +0000
Subject: [BioCatalogue-developers] geocoding returning
	questionable	results
In-Reply-To: <49AD4E57.5030203@cs.man.ac.uk>
References: <E1LeVoW-0000OK-6q@muffin> <49AD4404.6030105@ebi.ac.uk>
	<49AD4E57.5030203@cs.man.ac.uk>
Message-ID: <49AD543F.4080605@ebi.ac.uk>

Hi Jits,
Sorry about the power failure & unliable connection...We are not there 
yet in africa :(  .  I understand that we depend on some external 
service. Just wanted us to be aware of this.

Peace...

Eric


Jiten Bhagat wrote:
> We're using a free online IP to location mapping service called hostip 
> (http://www.hostip.info/) so unfortunately we rely on their database 
> (which can be populated and updated by anyone through their website).
>
> Also, we do DNS name to IP resolving at submission time, which is at 
> the mercy of DNS servers and load balancers.
>
> Jits
>
>
> Eric Nzuobontane wrote:
>> Hi Franck,
>> I am not sure I understand. Geocoding has no knowledge of the the 
>> history of whatever it goecodes, as far as I understand. I think the 
>> enpoint has a german domain and would expect the goecode follow 
>> that... Except I completely missundestand what goeoding does.
>>
>> Eric
>>
>>
>> Franck Tanoh wrote:
>>> Eric,
>>> This is a BioMoby service (therefore a dummy wsdl). The tool was 
>>> made in
>>> germany (http://www.biomedcentral.com/1471-2105/7/535) but the web 
>>> service
>>> was implemented by the BioMoby group. So the geocoding make sense.
>>> The service should therefore be tagged as BioMoby service. The list of
>>> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList
>>> Franck
>>> -----Original Message-----
>>> From: biocatalogue-developers-bounces at rubyforge.org
>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of 
>>> Eric
>>> Nzuobontane
>>> Sent: 03 March 2009 13:13
>>> To: biocatalogue-developers at rubyforge.org
>>> Subject: [BioCatalogue-developers] geocoding returning questionable 
>>> results
>>>
>>> hi,
>>> I just submitted a service
>>> http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678
>>>  which I expected to be located in Germany but geocoding claims it 
>>> is in the US!
>>>
>>> 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  Tue Mar  3 11:07:22 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 03 Mar 2009 16:07:22 +0000
Subject: [BioCatalogue-developers] geocoding returning
	questionable	results
In-Reply-To: <49AD543F.4080605@ebi.ac.uk>
References: <E1LeVoW-0000OK-6q@muffin> <49AD4404.6030105@ebi.ac.uk>
	<49AD4E57.5030203@cs.man.ac.uk> <49AD543F.4080605@ebi.ac.uk>
Message-ID: <49AD55BA.5090807@cs.man.ac.uk>

Hi Eric,

Yeah, I know what you mean, and a good point raised :-)

Yeah, these power and internet failures are bloody annoying! Power not 
so much as there are generators at the hotel, but internet, well, i cant 
live without!!!! How sad...

See you guys soon.

Cheers,
Jits


Eric Nzuobontane wrote:
> Hi Jits,
> Sorry about the power failure & unliable connection...We are not there 
> yet in africa :(  .  I understand that we depend on some external 
> service. Just wanted us to be aware of this.
>
> Peace...
>
> Eric
>
>
> Jiten Bhagat wrote:
>> We're using a free online IP to location mapping service called 
>> hostip (http://www.hostip.info/) so unfortunately we rely on their 
>> database (which can be populated and updated by anyone through their 
>> website).
>>
>> Also, we do DNS name to IP resolving at submission time, which is at 
>> the mercy of DNS servers and load balancers.
>>
>> Jits
>>
>>
>> Eric Nzuobontane wrote:
>>> Hi Franck,
>>> I am not sure I understand. Geocoding has no knowledge of the the 
>>> history of whatever it goecodes, as far as I understand. I think the 
>>> enpoint has a german domain and would expect the goecode follow 
>>> that... Except I completely missundestand what goeoding does.
>>>
>>> Eric
>>>
>>>
>>> Franck Tanoh wrote:
>>>> Eric,
>>>> This is a BioMoby service (therefore a dummy wsdl). The tool was 
>>>> made in
>>>> germany (http://www.biomedcentral.com/1471-2105/7/535) but the web 
>>>> service
>>>> was implemented by the BioMoby group. So the geocoding make sense.
>>>> The service should therefore be tagged as BioMoby service. The list of
>>>> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList
>>>> Franck
>>>> -----Original Message-----
>>>> From: biocatalogue-developers-bounces at rubyforge.org
>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of 
>>>> Eric
>>>> Nzuobontane
>>>> Sent: 03 March 2009 13:13
>>>> To: biocatalogue-developers at rubyforge.org
>>>> Subject: [BioCatalogue-developers] geocoding returning questionable 
>>>> results
>>>>
>>>> hi,
>>>> I just submitted a service
>>>> http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678 
>>>>
>>>>  which I expected to be located in Germany but geocoding claims it 
>>>> is in the US!
>>>>
>>>> Eric
>>>>
>>>>   
>>>
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>   
>


From noreply at rubyforge.org  Tue Mar  3 11:19:57 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  3 Mar 2009 11:19:57 -0500 (EST)
Subject: [BioCatalogue-developers] [462] trunk/.project: Removed from repo
 as this is Eclipse workspace specific.
Message-ID: <20090303161957.69BE618580ED@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar  3 11:25:03 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  3 Mar 2009 11:25:03 -0500 (EST)
Subject: [BioCatalogue-developers] [463] trunk/app/models/soaplab_server.rb:
 added dumping raw soap xml for debug purposes
Message-ID: <20090303162503.B8EE118580ED@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Tue Mar  3 11:33:28 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Tue, 03 Mar 2009 16:33:28 +0000
Subject: [BioCatalogue-developers] one of the recent updates thows an
	exception!!!!
Message-ID: <49AD5BD8.5030802@ebi.ac.uk>


  NameError in Home#index

Showing /app/views/layouts/_head_tabber.html.erb/ where line *#36* raised:

|undefined local variable or method `get_and_reset_use_tab_cookie_param_value' for #<ActionView::Base:0x2aaab06be6a0>|

Extracted source (around line *#36*):

|33:     // Only use cookie if anchor has not been explicitly specified in the URL 
34: 		// AND the use_tabs_cookie variable is set to true.
35: 		
36: 		var useCookie = <%= get_and_reset_use_tab_cookie_param_value -%>;
37: 		
38: 		if ((window.location.hash == null || window.location.hash == "") && useCookie == true) {
39: 			var t = argsObj.tabber;
|

Trace of template inclusion: app/views/layouts/_head.html.erb, 
app/views/layouts/application_wide.html.erb

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

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From jits at cs.man.ac.uk  Tue Mar  3 11:43:42 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 03 Mar 2009 16:43:42 +0000
Subject: [BioCatalogue-developers] one of the recent updates thows an
 exception!!!!
In-Reply-To: <49AD5BD8.5030802@ebi.ac.uk>
References: <49AD5BD8.5030802@ebi.ac.uk>
Message-ID: <49AD5E3E.30500@cs.man.ac.uk>

As mentioned a few times before: please restart mongrel servers on every 
update :-) not all files will get reloaded in dev mode.

Jits


Eric Nzuobontane wrote:
>
>  NameError in Home#index
>
> Showing /app/views/layouts/_head_tabber.html.erb/ where line *#36* 
> raised:
>
> |undefined local variable or method 
> `get_and_reset_use_tab_cookie_param_value' for 
> #<ActionView::Base:0x2aaab06be6a0>|
>
> Extracted source (around line *#36*):
>
> |33:     // Only use cookie if anchor has not been explicitly 
> specified in the URL 34:         // AND the use_tabs_cookie variable 
> is set to true.
> 35:        
> 36:         var useCookie = <%= 
> get_and_reset_use_tab_cookie_param_value -%>;
> 37:        
> 38:         if ((window.location.hash == null || window.location.hash 
> == "") && useCookie == true) {
> 39:             var t = argsObj.tabber;
> |
>
> Trace of template inclusion: app/views/layouts/_head.html.erb, 
> app/views/layouts/application_wide.html.erb
>
> |RAILS_ROOT: 
> /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue|
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From jits at cs.man.ac.uk  Tue Mar  3 11:48:14 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 03 Mar 2009 16:48:14 +0000
Subject: [BioCatalogue-developers] one of the recent updates thows an
 exception!!!!
In-Reply-To: <49AD5E3E.30500@cs.man.ac.uk>
References: <49AD5BD8.5030802@ebi.ac.uk> <49AD5E3E.30500@cs.man.ac.uk>
Message-ID: <49AD5F4E.9010005@cs.man.ac.uk>

Also, was this on the beta or test site? If beta site then we should 
make sure we check with all devs if it is safe to do an update! 
Generally trunk should be left as stable as possible but we still need 
to test thoroughly on the test/staging server.

Jits


Jiten Bhagat wrote:
> As mentioned a few times before: please restart mongrel servers on 
> every update :-) not all files will get reloaded in dev mode.
>
> Jits
>
>
> Eric Nzuobontane wrote:
>>
>>  NameError in Home#index
>>
>> Showing /app/views/layouts/_head_tabber.html.erb/ where line *#36* 
>> raised:
>>
>> |undefined local variable or method 
>> `get_and_reset_use_tab_cookie_param_value' for 
>> #<ActionView::Base:0x2aaab06be6a0>|
>>
>> Extracted source (around line *#36*):
>>
>> |33:     // Only use cookie if anchor has not been explicitly 
>> specified in the URL 34:         // AND the use_tabs_cookie variable 
>> is set to true.
>> 35:        36:         var useCookie = <%= 
>> get_and_reset_use_tab_cookie_param_value -%>;
>> 37:        38:         if ((window.location.hash == null || 
>> window.location.hash == "") && useCookie == true) {
>> 39:             var t = argsObj.tabber;
>> |
>>
>> Trace of template inclusion: app/views/layouts/_head.html.erb, 
>> app/views/layouts/application_wide.html.erb
>>
>> |RAILS_ROOT: 
>> /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue|
>>
>> _______________________________________________
>> 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 Mar  3 11:49:48 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  3 Mar 2009 11:49:48 -0500 (EST)
Subject: [BioCatalogue-developers] [464] trunk: - Added .project to
	svn:ignore.
Message-ID: <20090303164948.61A7418580ED@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Tue Mar  3 11:51:41 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Tue, 03 Mar 2009 16:51:41 +0000
Subject: [BioCatalogue-developers] one of the recent updates thows an
 exception!!!!
In-Reply-To: <49AD5F4E.9010005@cs.man.ac.uk>
References: <49AD5BD8.5030802@ebi.ac.uk> <49AD5E3E.30500@cs.man.ac.uk>
	<49AD5F4E.9010005@cs.man.ac.uk>
Message-ID: <49AD601D.1040006@ebi.ac.uk>

the test site. I think as a general principle, we should not make adhoc 
update to the beta site.

Eric


Jiten Bhagat wrote:
> Also, was this on the beta or test site? If beta site then we should 
> make sure we check with all devs if it is safe to do an update! 
> Generally trunk should be left as stable as possible but we still need 
> to test thoroughly on the test/staging server.
>
> Jits
>
>
> Jiten Bhagat wrote:
>> As mentioned a few times before: please restart mongrel servers on 
>> every update :-) not all files will get reloaded in dev mode.
>>
>> Jits
>>
>>
>> Eric Nzuobontane wrote:
>>>
>>>  NameError in Home#index
>>>
>>> Showing /app/views/layouts/_head_tabber.html.erb/ where line *#36* 
>>> raised:
>>>
>>> |undefined local variable or method 
>>> `get_and_reset_use_tab_cookie_param_value' for 
>>> #<ActionView::Base:0x2aaab06be6a0>|
>>>
>>> Extracted source (around line *#36*):
>>>
>>> |33:     // Only use cookie if anchor has not been explicitly 
>>> specified in the URL 34:         // AND the use_tabs_cookie variable 
>>> is set to true.
>>> 35:        36:         var useCookie = <%= 
>>> get_and_reset_use_tab_cookie_param_value -%>;
>>> 37:        38:         if ((window.location.hash == null || 
>>> window.location.hash == "") && useCookie == true) {
>>> 39:             var t = argsObj.tabber;
>>> |
>>>
>>> Trace of template inclusion: app/views/layouts/_head.html.erb, 
>>> app/views/layouts/application_wide.html.erb
>>>
>>> |RAILS_ROOT: 
>>> /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue|
>>>
>>> _______________________________________________
>>> 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  Tue Mar  3 12:34:42 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 03 Mar 2009 17:34:42 +0000
Subject: [BioCatalogue-developers] [462] trunk/.project: Removed from
 repo as this is Eclipse workspace specific.
In-Reply-To: <20090303161957.69BE618580ED@rubyforge.org>
References: <20090303161957.69BE618580ED@rubyforge.org>
Message-ID: <49AD6A32.8000201@cs.man.ac.uk>

Guys,

If this causes an issue then you can recreate the .project or 
Eclipse/Aptana should recreate it.

Because its added to the svn:ignore list now, it won't get committed.

Jits


noreply at rubyforge.org wrote:
>
> Revision
>     462
> Author
>     jits
> Date
>     2009-03-03 11:19:57 -0500 (Tue, 03 Mar 2009)
>
>
>       Log Message
>
> Removed from repo as this is Eclipse workspace specific.
>
>
>       Removed Paths
>
>     * trunk/.project <#trunkproject>
>
>
>       Diff
>
>
>         Deleted: trunk/.project (461 => 462)
>
>
> --- trunk/.project	2009-03-03 15:41:15 UTC (rev 461)
> +++ trunk/.project	2009-03-03 16:19:57 UTC (rev 462)
> @@ -1,18 +0,0 @@
> -<?xml version="1.0" encoding="UTF-8"?>
> -<projectDescription>
> -	<name>biocatalogue_trunk</name>
> -	<comment></comment>
> -	<projects>
> -	</projects>
> -	<buildSpec>
> -		<buildCommand>
> -			<name>org.rubypeople.rdt.core.rubybuilder</name>
> -			<arguments>
> -			</arguments>
> -		</buildCommand>
> -	</buildSpec>
> -	<natures>
> -		<nature>org.rubypeople.rdt.core.rubynature</nature>
> -		<nature>org.radrails.rails.core.railsnature</nature>
> -	</natures>
> -</projectDescription>
> ------------------------------------------------------------------------
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From ericnzuo at ebi.ac.uk  Wed Mar  4 05:56:31 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 04 Mar 2009 10:56:31 +0000
Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
Message-ID: <49AE5E5F.1080009@ebi.ac.uk>


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Subject: Re: question about biocatalogue
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From ytanoh at cs.man.ac.uk  Wed Mar  4 06:30:26 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 4 Mar 2009 11:30:26 -0000
Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
In-Reply-To: <49AE5E5F.1080009@ebi.ac.uk>
Message-ID: <E1LepIw-00016U-MI@muffin>


Eric,

Have you just sent this email to the list? I've just received it but I
remember seeing a reply from Steve last week about that. 

Franck 


-----Original Message-----
From: biocatalogue-developers-bounces at rubyforge.org
[mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
Nzuobontane
Sent: 04 March 2009 10:57
To: biocatalogue-developers at rubyforge.org
Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]




From ericnzuo at ebi.ac.uk  Wed Mar  4 06:34:41 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 04 Mar 2009 11:34:41 +0000
Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
In-Reply-To: <E1LepIw-00016U-MI@muffin>
References: <E1LepIw-00016U-MI@muffin>
Message-ID: <49AE6751.4010200@ebi.ac.uk>

I forwarded it again to escalate... Yes, Steve acknowledged receipt of 
the mail but I did not see a proper reply yet.


Franck Tanoh wrote:
> Eric,
>
> Have you just sent this email to the list? I've just received it but I
> remember seeing a reply from Steve last week about that. 
>
> Franck 
>
>
> -----Original Message-----
> From: biocatalogue-developers-bounces at rubyforge.org
> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
> Nzuobontane
> Sent: 04 March 2009 10:57
> To: biocatalogue-developers at rubyforge.org
> Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
>
>
>   

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From ytanoh at cs.man.ac.uk  Wed Mar  4 06:39:09 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 4 Mar 2009 11:39:09 -0000
Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
In-Reply-To: <49AE6751.4010200@ebi.ac.uk>
Message-ID: <E1LepRN-000182-MT@muffin>

Who is the other developer on the Embrace project? I think you guys met him
when you came to Manchester. We'll certainly receive a quick response from
him as Steve is quite busy at the moment. 

Franck

-----Original Message-----
From: Eric Nzuobontane [mailto:ericnzuo at ebi.ac.uk] 
Sent: 04 March 2009 11:35
To: Franck Tanoh
Cc: biocatalogue-developers at rubyforge.org
Subject: Re: [BioCatalogue-developers] [Fwd: Re: question about
biocatalogue]

I forwarded it again to escalate... Yes, Steve acknowledged receipt of 
the mail but I did not see a proper reply yet.


Franck Tanoh wrote:
> Eric,
>
> Have you just sent this email to the list? I've just received it but I
> remember seeing a reply from Steve last week about that. 
>
> Franck 
>
>
> -----Original Message-----
> From: biocatalogue-developers-bounces at rubyforge.org
> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
> Nzuobontane
> Sent: 04 March 2009 10:57
> To: biocatalogue-developers at rubyforge.org
> Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
>
>
>   



From ericnzuo at ebi.ac.uk  Wed Mar  4 06:48:00 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 04 Mar 2009 11:48:00 +0000
Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
In-Reply-To: <E1LepRN-000182-MT@muffin>
References: <E1LepRN-000182-MT@muffin>
Message-ID: <49AE6A70.7040508@ebi.ac.uk>

Joachim is his name, but I do not have his email.

Eric

Franck Tanoh wrote:
> Who is the other developer on the Embrace project? I think you guys met him
> when you came to Manchester. We'll certainly receive a quick response from
> him as Steve is quite busy at the moment. 
>
> Franck
>
> -----Original Message-----
> From: Eric Nzuobontane [mailto:ericnzuo at ebi.ac.uk] 
> Sent: 04 March 2009 11:35
> To: Franck Tanoh
> Cc: biocatalogue-developers at rubyforge.org
> Subject: Re: [BioCatalogue-developers] [Fwd: Re: question about
> biocatalogue]
>
> I forwarded it again to escalate... Yes, Steve acknowledged receipt of 
> the mail but I did not see a proper reply yet.
>
>
> Franck Tanoh wrote:
>   
>> Eric,
>>
>> Have you just sent this email to the list? I've just received it but I
>> remember seeing a reply from Steve last week about that. 
>>
>> Franck 
>>
>>
>> -----Original Message-----
>> From: biocatalogue-developers-bounces at rubyforge.org
>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
>> Nzuobontane
>> Sent: 04 March 2009 10:57
>> To: biocatalogue-developers at rubyforge.org
>> Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
>>
>>
>>   
>>     
>
>   

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From jits at cs.man.ac.uk  Wed Mar  4 08:38:29 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 04 Mar 2009 13:38:29 +0000
Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
In-Reply-To: <49AE6A70.7040508@ebi.ac.uk>
References: <E1LepRN-000182-MT@muffin> <49AE6A70.7040508@ebi.ac.uk>
Message-ID: <49AE8455.6040806@cs.man.ac.uk>

Eric,

joachim.baran at cs.manchester.ac.uk

You can tell them to put the documentation URL in the description for 
now, that way people can still get to it.

It's important that the endpoint is the actual endpoint to the service, 
not to any documentation or anything else.

In BioCatalogue we will have a specific field for documentation URL and 
also attempt to cache documentation info from URLs.

Jits


Eric Nzuobontane wrote:
> Joachim is his name, but I do not have his email.
>
> Eric
>
> Franck Tanoh wrote:
>> Who is the other developer on the Embrace project? I think you guys 
>> met him
>> when you came to Manchester. We'll certainly receive a quick response 
>> from
>> him as Steve is quite busy at the moment.
>> Franck
>>
>> -----Original Message-----
>> From: Eric Nzuobontane [mailto:ericnzuo at ebi.ac.uk] Sent: 04 March 
>> 2009 11:35
>> To: Franck Tanoh
>> Cc: biocatalogue-developers at rubyforge.org
>> Subject: Re: [BioCatalogue-developers] [Fwd: Re: question about
>> biocatalogue]
>>
>> I forwarded it again to escalate... Yes, Steve acknowledged receipt 
>> of the mail but I did not see a proper reply yet.
>>
>>
>> Franck Tanoh wrote:
>>  
>>> Eric,
>>>
>>> Have you just sent this email to the list? I've just received it but I
>>> remember seeing a reply from Steve last week about that.
>>> Franck
>>>
>>> -----Original Message-----
>>> From: biocatalogue-developers-bounces at rubyforge.org
>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of 
>>> Eric
>>> Nzuobontane
>>> Sent: 04 March 2009 10:57
>>> To: biocatalogue-developers at rubyforge.org
>>> Subject: [BioCatalogue-developers] [Fwd: Re: question about 
>>> biocatalogue]
>>>
>>>
>>>       
>>
>>   
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From jits at cs.man.ac.uk  Wed Mar  4 08:40:36 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 04 Mar 2009 13:40:36 +0000
Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
In-Reply-To: <49AE5E5F.1080009@ebi.ac.uk>
References: <49AE5E5F.1080009@ebi.ac.uk>
Message-ID: <49AE84D4.9010509@cs.man.ac.uk>

Instead of just forwarding the email, add some comment/text to explain
what action needs to be done and what questions/issues you're not sure
about :-)

Jits


Eric Nzuobontane wrote:
>
> ------------------------------------------------------------------------
>
> Subject:
> Re: question about biocatalogue
> From:
> Yasumasa Shigemoto <yshigemo at genes.nig.ac.jp>
> Date:
> Fri, 27 Feb 2009 21:43:28 +0900
> To:
> Eric Nzuobontane <ericnzuo at ebi.ac.uk>
>
> To:
> Eric Nzuobontane <ericnzuo at ebi.ac.uk>
> CC:
> SUGAWARA Hideaki <hsugawar at genes.nig.ac.jp>, Yoshikazu kuwana
> <ykuwana at genes.nig.ac.jp>, biocatalogue-developers at rubyforge.org
>
>
> 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
>>
>>
>>     
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>     


From ericnzuo at ebi.ac.uk  Wed Mar  4 08:54:23 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 04 Mar 2009 13:54:23 +0000
Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
In-Reply-To: <49AE84D4.9010509@cs.man.ac.uk>
References: <49AE5E5F.1080009@ebi.ac.uk> <49AE84D4.9010509@cs.man.ac.uk>
Message-ID: <49AE880F.80303@ebi.ac.uk>

Jiten Bhagat wrote:
> Instead of just forwarding the email, add some comment/text to explain
> what action needs to be done and what questions/issues you're not sure
> about :-)
>   
Well, you are presuming that I will be responding to the mail and that I
know what action needs to be taken. Hmmm
On this particular one, I wanted someone from the embrace registry to
respond to it and I asked Steve. Just thought the mail was clear...


> Jits
>
>
> Eric Nzuobontane wrote:
>   
>> ------------------------------------------------------------------------
>>
>> Subject:
>> Re: question about biocatalogue
>> From:
>> Yasumasa Shigemoto <yshigemo at genes.nig.ac.jp>
>> Date:
>> Fri, 27 Feb 2009 21:43:28 +0900
>> To:
>> Eric Nzuobontane <ericnzuo at ebi.ac.uk>
>>
>> To:
>> Eric Nzuobontane <ericnzuo at ebi.ac.uk>
>> CC:
>> SUGAWARA Hideaki <hsugawar at genes.nig.ac.jp>, Yoshikazu kuwana
>> <ykuwana at genes.nig.ac.jp>, biocatalogue-developers at rubyforge.org
>>
>>
>> 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
>>>
>>>
>>>     
>>> _______________________________________________
>>> 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  Wed Mar  4 09:02:01 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 04 Mar 2009 14:02:01 +0000
Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
In-Reply-To: <49AE880F.80303@ebi.ac.uk>
References: <49AE5E5F.1080009@ebi.ac.uk> <49AE84D4.9010509@cs.man.ac.uk>
	<49AE880F.80303@ebi.ac.uk>
Message-ID: <49AE89D9.6090707@cs.man.ac.uk>

Eric Nzuobontane wrote:
> Jiten Bhagat wrote:
>   
>> Instead of just forwarding the email, add some comment/text to explain
>> what action needs to be done and what questions/issues you're not sure
>> about :-)
>>   
>>     
> Well, you are presuming that I will be responding to the mail and that I
> know what action needs to be taken. Hmmm
> On this particular one, I wanted someone from the embrace registry to
> respond to it and I asked Steve. Just thought the mail was clear...
>   

I wasn't presuming anything - the mail was a conversation you were
having with the DDBJ people which you said you had to escalate because
you weren't sure what to respond back to them. It wasn't immediately
obvious what exactly needed to be addressed, but yes, when I read
through it I had an idea of what it might be. It's just that it would be
easier if you mentioned what you mentioned above in the first place :-)

It's a bit like that ISMB abstract thing - just need to ask Franck if
the action was done, but its much easier if Franck informs everyone when
it's done in the first place :-)

Usually, if I get an email which is a forward with no text from the
sender, I treat it as an FYI and move on.

Cheers,
Jits

>
>   
>> Jits
>>
>>
>> Eric Nzuobontane wrote:
>>   
>>     
>>> ------------------------------------------------------------------------
>>>
>>> Subject:
>>> Re: question about biocatalogue
>>> From:
>>> Yasumasa Shigemoto <yshigemo at genes.nig.ac.jp>
>>> Date:
>>> Fri, 27 Feb 2009 21:43:28 +0900
>>> To:
>>> Eric Nzuobontane <ericnzuo at ebi.ac.uk>
>>>
>>> To:
>>> Eric Nzuobontane <ericnzuo at ebi.ac.uk>
>>> CC:
>>> SUGAWARA Hideaki <hsugawar at genes.nig.ac.jp>, Yoshikazu kuwana
>>> <ykuwana at genes.nig.ac.jp>, biocatalogue-developers at rubyforge.org
>>>
>>>
>>> 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
>>>>
>>>>
>>>>     
>>>> _______________________________________________
>>>> BioCatalogue-developers mailing list
>>>> BioCatalogue-developers at rubyforge.org
>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>>     
>>>>       
>>>>         
>
>   


From jits at cs.man.ac.uk  Wed Mar  4 09:32:09 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 04 Mar 2009 14:32:09 +0000
Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
In-Reply-To: <49AE89D9.6090707@cs.man.ac.uk>
References: <49AE5E5F.1080009@ebi.ac.uk>
	<49AE84D4.9010509@cs.man.ac.uk>	<49AE880F.80303@ebi.ac.uk>
	<49AE89D9.6090707@cs.man.ac.uk>
Message-ID: <49AE90E9.7030501@cs.man.ac.uk>

Sorry, I really don't mean to sound confrontational... must be the air
here ;-)

See you guys soon!

Jits


Jiten Bhagat wrote:
> Eric Nzuobontane wrote:
>   
>> Jiten Bhagat wrote:
>>   
>>     
>>> Instead of just forwarding the email, add some comment/text to explain
>>> what action needs to be done and what questions/issues you're not sure
>>> about :-)
>>>   
>>>     
>>>       
>> Well, you are presuming that I will be responding to the mail and that I
>> know what action needs to be taken. Hmmm
>> On this particular one, I wanted someone from the embrace registry to
>> respond to it and I asked Steve. Just thought the mail was clear...
>>   
>>     
>
> I wasn't presuming anything - the mail was a conversation you were
> having with the DDBJ people which you said you had to escalate because
> you weren't sure what to respond back to them. It wasn't immediately
> obvious what exactly needed to be addressed, but yes, when I read
> through it I had an idea of what it might be. It's just that it would be
> easier if you mentioned what you mentioned above in the first place :-)
>
> It's a bit like that ISMB abstract thing - just need to ask Franck if
> the action was done, but its much easier if Franck informs everyone when
> it's done in the first place :-)
>
> Usually, if I get an email which is a forward with no text from the
> sender, I treat it as an FYI and move on.
>
> Cheers,
> Jits
>
>   
>>   
>>     
>>> Jits
>>>
>>>
>>> Eric Nzuobontane wrote:
>>>   
>>>     
>>>       
>>>> ------------------------------------------------------------------------
>>>>
>>>> Subject:
>>>> Re: question about biocatalogue
>>>> From:
>>>> Yasumasa Shigemoto <yshigemo at genes.nig.ac.jp>
>>>> Date:
>>>> Fri, 27 Feb 2009 21:43:28 +0900
>>>> To:
>>>> Eric Nzuobontane <ericnzuo at ebi.ac.uk>
>>>>
>>>> To:
>>>> Eric Nzuobontane <ericnzuo at ebi.ac.uk>
>>>> CC:
>>>> SUGAWARA Hideaki <hsugawar at genes.nig.ac.jp>, Yoshikazu kuwana
>>>> <ykuwana at genes.nig.ac.jp>, biocatalogue-developers at rubyforge.org
>>>>
>>>>
>>>> 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
>>>>>
>>>>>
>>>>>     
>>>>> _______________________________________________
>>>>> 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  Wed Mar  4 09:49:08 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 4 Mar 2009 14:49:08 -0000
Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]
In-Reply-To: <49AE90E9.7030501@cs.man.ac.uk>
Message-ID: <E1LesPE-0001wn-FQ@muffin>

Jits,
>Sorry, I really don't mean to sound confrontational... must be the air
>here ;-)
You sound that way but I'm sure it's not your intention...so no worries.

Enjoy your last full day in Malawi!

Franck 

-----Original Message-----
From: biocatalogue-developers-bounces at rubyforge.org
[mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Jiten
Bhagat
Sent: 04 March 2009 14:32
To: Eric Nzuobontane
Cc: biocatalogue-developers at rubyforge.org
Subject: Re: [BioCatalogue-developers] [Fwd: Re: question about
biocatalogue]

Sorry, I really don't mean to sound confrontational... must be the air
here ;-)

See you guys soon!

Jits


Jiten Bhagat wrote:
> Eric Nzuobontane wrote:
>   
>> Jiten Bhagat wrote:
>>   
>>     
>>> Instead of just forwarding the email, add some comment/text to explain
>>> what action needs to be done and what questions/issues you're not sure
>>> about :-)
>>>   
>>>     
>>>       
>> Well, you are presuming that I will be responding to the mail and that I
>> know what action needs to be taken. Hmmm
>> On this particular one, I wanted someone from the embrace registry to
>> respond to it and I asked Steve. Just thought the mail was clear...
>>   
>>     
>
> I wasn't presuming anything - the mail was a conversation you were
> having with the DDBJ people which you said you had to escalate because
> you weren't sure what to respond back to them. It wasn't immediately
> obvious what exactly needed to be addressed, but yes, when I read
> through it I had an idea of what it might be. It's just that it would be
> easier if you mentioned what you mentioned above in the first place :-)
>
> It's a bit like that ISMB abstract thing - just need to ask Franck if
> the action was done, but its much easier if Franck informs everyone when
> it's done in the first place :-)
>
> Usually, if I get an email which is a forward with no text from the
> sender, I treat it as an FYI and move on.
>
> Cheers,
> Jits
>
>   
>>   
>>     
>>> Jits
>>>
>>>
>>> Eric Nzuobontane wrote:
>>>   
>>>     
>>>       
>>>>
------------------------------------------------------------------------
>>>>
>>>> Subject:
>>>> Re: question about biocatalogue
>>>> From:
>>>> Yasumasa Shigemoto <yshigemo at genes.nig.ac.jp>
>>>> Date:
>>>> Fri, 27 Feb 2009 21:43:28 +0900
>>>> To:
>>>> Eric Nzuobontane <ericnzuo at ebi.ac.uk>
>>>>
>>>> To:
>>>> Eric Nzuobontane <ericnzuo at ebi.ac.uk>
>>>> CC:
>>>> SUGAWARA Hideaki <hsugawar at genes.nig.ac.jp>, Yoshikazu kuwana
>>>> <ykuwana at genes.nig.ac.jp>, biocatalogue-developers at rubyforge.org
>>>>
>>>>
>>>> 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=e
n
>>>>   
>>>>     
>>>>       
>>>>         
>>>>> 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&access
ion=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=e
n
>>>>>>>   
>>>>>>>         
>>>>>>>           
>>>>>>>             
>>>>>>>               
>>>>>>   
>>>>>>       
>>>>>>         
>>>>>>           
>>>>>>             
>>>>> 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=e
n
>>>>>
>>>>> 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
>>>>>
>>>>>
>>>>>     
>>>>> _______________________________________________
>>>>> 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  Wed Mar  4 10:02:11 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 4 Mar 2009 15:02:11 -0000
Subject: [BioCatalogue-developers] FW: [Fwd: Re: question about biocatalogue]
Message-ID: <E1Lesbr-0002Gj-DC@muffin>

Hi Joachin, 

I am Franck from the BioCatalogue project. 

The DDBJ team in Japan http://www.ddbj.nig.ac.jp/ wants to submit their REST
services to the Embrace registry but are struggling. 
Could you answer their query please? 

Thanks 

Franck 

-----Original Message-----
From: biocatalogue-developers-bounces at rubyforge.org
[mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
Nzuobontane
Sent: 04 March 2009 10:57
To: biocatalogue-developers at rubyforge.org
Subject: [BioCatalogue-developers] [Fwd: Re: question about biocatalogue]


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Subject: Re: question about biocatalogue
Date: Fri, 27 Feb 2009 12:43:28 -0000
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From noreply at rubyforge.org  Wed Mar  4 10:47:06 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Mar 2009 10:47:06 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2566] Investigate solr indexing in
	relation to application slowdown
Message-ID: <20090304154706.22EF71858104@rubyforge.org>

Task #2566 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Investigate solr indexing in relation to application slowdown
Complete: 0%
Status: Open

Description: It has been observed that when a service submission is made, solr reindexing is triggered and the respond from the submit is received only after the indexing is complete. This seems to enormously slow down the application. It will be of interest to possibly de-synchronize the indexing and the return of a submit response.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2566&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Wed Mar  4 11:07:47 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  4 Mar 2009 11:07:47 -0500 (EST)
Subject: [BioCatalogue-developers] [465]
 trunk/app/views/soap_services/_show_service_tabs.html.erb: Style changes
 for the operations tab.
Message-ID: <20090304160747.25FFA185810B@rubyforge.org>

An HTML attachment was scrubbed...
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From noreply at rubyforge.org  Thu Mar  5 10:18:25 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  5 Mar 2009 10:18:25 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2399] Refactor activate account
	action for users
Message-ID: <20090305151825.5FC1B18580EB@rubyforge.org>

Task #2399 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Refactor activate account action for users
Complete: 0%
Status: Open

Description: - use User.find_by_security_token(params[:security_token]), instead of User.find(:all)
- the .update_attribute method bypasses validation checks so can be dangerous to use. Maybe a user.activate! method is better, thereby moving that logic into the model

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2399&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Mar  5 10:19:04 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  5 Mar 2009 10:19:04 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2399] Refactor activate account
	action for users
Message-ID: <20090305151904.9810E18580EB@rubyforge.org>

Task #2399 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Refactor activate account action for users
Complete: 100%
Status: Open

Description: - use User.find_by_security_token(params[:security_token]), instead of User.find(:all)
- the .update_attribute method bypasses validation checks so can be dangerous to use. Maybe a user.activate! method is better, thereby moving that logic into the model

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2399&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Mar  5 10:23:02 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  5 Mar 2009 10:23:02 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2399] Refactor activate account
	action for users
Message-ID: <20090305152302.6C60B18580EB@rubyforge.org>

Task #2399 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Refactor activate account action for users
Complete: 100%
Status: Open

Description: - use User.find_by_security_token(params[:security_token]), instead of User.find(:all)
- the .update_attribute method bypasses validation checks so can be dangerous to use. Maybe a user.activate! method is better, thereby moving that logic into the model

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2399&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Mar  5 10:26:44 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  5 Mar 2009 10:26:44 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2412] Catch mail send exception
Message-ID: <20090305152645.0AA4518580EB@rubyforge.org>

Task #2412 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Catch mail send exception
Complete: 0%
Status: Open

Description: When sending the account activation email, if the mail sending fails then an exception is thrown and the user will get a generic error. 

We need to catch this exception and take appropriate action (such as logging the error so that the mail can be sent manually later). The user shouldn't need to know that the exception was ever raised.

Follow-Ups:

-------------------------------------------------------
Date: 2009-03-05 15:26
By: ebontane

Comment:
Thomas, I think this is done?

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2412&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Fri Mar  6 05:13:29 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  6 Mar 2009 05:13:29 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2568] unable to submit some
	services
Message-ID: <20090306101330.049B618580F5@rubyforge.org>

Task #2568 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: unable to submit some services 
Complete: 0%
Status: Open

Description: The registry treats these services as the same; so I can only register one of them. But in reality they are doing different things: 

 

http://www.cbs.dtu.dk/ws/MaxAlign/MaxAlign_1_1_ws0.wsdl      and  http://www.cbs.dtu.dk/ws/SignalP/SignalP_3_1_ws0.wsdl

 

http://www.cbs.dtu.dk/ws/RNAmmer/RNAmmer_1_2_ws0.wsdl   and  http://www.cbs.dtu.dk/ws/BLASTatlas/BLASTatlas_1_0_ws2.wsdl

 

http://www.cbs.dtu.dk/ws/NetGlycate/NetGlycate_1_0.wsdl and  http://www.cbs.dtu.dk/ws/SIDDbase/SIDDbase_1_0.wsdl

 

http://www.cbs.dtu.dk/ws/NetNGlyc/NetNGlyc_1_0a_ws0.wsdl and  http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_2a_ws0.wsdl

?..

The provider: http://www.cbs.dtu.dk/ws/



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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2568&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Fri Mar  6 07:13:37 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  6 Mar 2009 07:13:37 -0500 (EST)
Subject: [BioCatalogue-developers] [466] trunk/app/models: disable solr
 commits on model saves to speed up updates
Message-ID: <20090306121337.CFED318580FD@rubyforge.org>

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From noreply at rubyforge.org  Fri Mar  6 07:16:01 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  6 Mar 2009 07:16:01 -0500 (EST)
Subject: [BioCatalogue-developers] [467]
 trunk/vendor/plugins/acts_as_solr/solr/solr/conf/solrconfig.xml: allow solr
 to manage it own commits.
Message-ID: <20090306121601.C4EF21858100@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Fri Mar  6 09:03:27 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Fri, 06 Mar 2009 14:03:27 +0000
Subject: [BioCatalogue-developers] Updating the beta site
Message-ID: <49B12D2F.9030002@ebi.ac.uk>

Hi Guys,
I intend to update the beta site. But before I do that I will keep a 
copy code corrently running on the beta site and also create a tag for 
the current head version.

Eric

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From noreply at rubyforge.org  Fri Mar  6 09:35:53 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  6 Mar 2009 09:35:53 -0500 (EST)
Subject: [BioCatalogue-developers] [468] tags/biocatalogue-00-00-01/: create
	new tag 00-00-01
Message-ID: <20090306143553.2C6B118580FD@rubyforge.org>

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From noreply at rubyforge.org  Fri Mar  6 09:39:02 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  6 Mar 2009 09:39:02 -0500 (EST)
Subject: [BioCatalogue-developers] [469] tags/biocatalogue-00-00-01/trunk/:
	create new
Message-ID: <20090306143902.A97D118580E4@rubyforge.org>

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From noreply at rubyforge.org  Mon Mar  9 06:03:54 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  9 Mar 2009 06:03:54 -0400 (EDT)
Subject: [BioCatalogue-developers] [470]
 trunk/app/views/services/new.html.erb: remove soaplab from the ' coming
 soon' list
Message-ID: <20090309100354.B41861858109@rubyforge.org>

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From jits at cs.man.ac.uk  Mon Mar  9 12:42:28 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 09 Mar 2009 16:42:28 +0000
Subject: [BioCatalogue-developers] [466] trunk/app/models: disable solr
 commits on model saves to speed up updates
In-Reply-To: <20090306121337.CFED318580FD@rubyforge.org>
References: <20090306121337.CFED318580FD@rubyforge.org>
Message-ID: <49B546F4.2020001@cs.man.ac.uk>

Eric,

Is there a way of telling it not to auto_commit globally, instead of 
putting :auto_commit => false on each acts_as_solr instruction?

Cheers,
Jits


noreply at rubyforge.org wrote:
>
> Revision
>     466
> Author
>     ebontane
> Date
>     2009-03-06 07:13:37 -0500 (Fri, 06 Mar 2009)
>
>
>       Log Message
>
> disable solr commits on model saves to speed up updates
> acts_as_solr( :auto_commit => false)
>
>
>       Modified Paths
>
>     * trunk/app/models/annotation.rb <#trunkappmodelsannotationrb>
>     * trunk/app/models/service.rb <#trunkappmodelsservicerb>
>     * trunk/app/models/service_deployment.rb
>       <#trunkappmodelsservice_deploymentrb>
>     * trunk/app/models/service_provider.rb
>       <#trunkappmodelsservice_providerrb>
>     * trunk/app/models/service_version.rb
>       <#trunkappmodelsservice_versionrb>
>     * trunk/app/models/soap_input.rb <#trunkappmodelssoap_inputrb>
>     * trunk/app/models/soap_operation.rb <#trunkappmodelssoap_operationrb>
>     * trunk/app/models/soap_output.rb <#trunkappmodelssoap_outputrb>
>     * trunk/app/models/soap_service.rb <#trunkappmodelssoap_servicerb>
>     * trunk/app/models/soaplab_server.rb <#trunkappmodelssoaplab_serverrb>
>     * trunk/app/models/user.rb <#trunkappmodelsuserrb>
>
>
>       Diff
>
>
>         Modified: trunk/app/models/annotation.rb (465 => 466)
>
>
> --- trunk/app/models/annotation.rb	2009-03-04 16:07:46 UTC (rev 465)
> +++ trunk/app/models/annotation.rb	2009-03-06 12:13:37 UTC (rev 466)
> @@ -23,7 +23,7 @@
>    end
>    
>    if ENABLE_SEARCH
> -    acts_as_solr(:fields => [ :value ])
> +    acts_as_solr(:fields => [ :value ], :auto_commit => false )
>    end
>    
>    protected
>
>
>         Modified: trunk/app/models/service.rb (465 => 466)
>
>
> --- trunk/app/models/service.rb	2009-03-04 16:07:46 UTC (rev 465)
> +++ trunk/app/models/service.rb	2009-03-06 12:13:37 UTC (rev 466)
> @@ -37,7 +37,7 @@
>    validates_existence_of :submitter   # User must exist in the db beforehand.
>    
>    if ENABLE_SEARCH
> -    acts_as_solr(:fields => [ :name, :unique_code, :submitter_name ])
> +    acts_as_solr(:fields => [ :name, :unique_code, :submitter_name ], :auto_commit => false )
>    end
>    
>    if USE_EVENT_LOG
>
>
>         Modified: trunk/app/models/service_deployment.rb (465 => 466)
>
>
> --- trunk/app/models/service_deployment.rb	2009-03-04 16:07:46 UTC (rev 465)
> +++ trunk/app/models/service_deployment.rb	2009-03-06 12:13:37 UTC (rev 466)
> @@ -29,7 +29,7 @@
>    
>    if ENABLE_SEARCH
>      acts_as_solr(:fields => [ :endpoint, :city, :country ],
> -                 :include => [ :provider ])
> +                 :include => [ :provider ], :auto_commit => false )
>    end
>    
>    if USE_EVENT_LOG
>
>
>         Modified: trunk/app/models/service_provider.rb (465 => 466)
>
>
> --- trunk/app/models/service_provider.rb	2009-03-04 16:07:46 UTC (rev 465)
> +++ trunk/app/models/service_provider.rb	2009-03-06 12:13:37 UTC (rev 466)
> @@ -18,7 +18,7 @@
>    validates_presence_of :name
>    
>    if ENABLE_SEARCH
> -    acts_as_solr(:fields => [ :name ])
> +    acts_as_solr(:fields => [ :name ], :auto_commit => false )
>    end
>    
>    if USE_EVENT_LOG
>
>
>         Modified: trunk/app/models/service_version.rb (465 => 466)
>
>
> --- trunk/app/models/service_version.rb	2009-03-04 16:07:46 UTC (rev 465)
> +++ trunk/app/models/service_version.rb	2009-03-06 12:13:37 UTC (rev 466)
> @@ -24,7 +24,7 @@
>    validates_presence_of :version, :version_display_text
>    
>    if ENABLE_SEARCH
> -    acts_as_solr(:fields => [ :version_display_text ])
> +    acts_as_solr(:fields => [ :version_display_text ], :auto_commit => false )
>    end
>    
>    if USE_EVENT_LOG
>
>
>         Modified: trunk/app/models/soap_input.rb (465 => 466)
>
>
> --- trunk/app/models/soap_input.rb	2009-03-04 16:07:46 UTC (rev 465)
> +++ trunk/app/models/soap_input.rb	2009-03-06 12:13:37 UTC (rev 466)
> @@ -12,7 +12,7 @@
>    belongs_to :soap_operation
>    
>    if ENABLE_SEARCH
> -    acts_as_solr(:fields => [ :name, :description, :computational_type ])
> +    acts_as_solr(:fields => [ :name, :description, :computational_type ], :auto_commit => false )
>    end
>    
>    if USE_EVENT_LOG
>
>
>         Modified: trunk/app/models/soap_operation.rb (465 => 466)
>
>
> --- trunk/app/models/soap_operation.rb	2009-03-04 16:07:46 UTC (rev 465)
> +++ trunk/app/models/soap_operation.rb	2009-03-06 12:13:37 UTC (rev 466)
> @@ -15,7 +15,7 @@
>    has_many :soap_outputs, :dependent => :destroy
>    
>    if ENABLE_SEARCH
> -    acts_as_solr(:fields => [ :name, :description, :parent_port_type ])
> +    acts_as_solr(:fields => [ :name, :description, :parent_port_type ], :auto_commit => false )
>    end
>    
>    if USE_EVENT_LOG
>
>
>         Modified: trunk/app/models/soap_output.rb (465 => 466)
>
>
> --- trunk/app/models/soap_output.rb	2009-03-04 16:07:46 UTC (rev 465)
> +++ trunk/app/models/soap_output.rb	2009-03-06 12:13:37 UTC (rev 466)
> @@ -12,7 +12,7 @@
>    belongs_to :soap_operation
>    
>    if ENABLE_SEARCH
> -    acts_as_solr(:fields => [ :name, :description, :computational_type ])
> +    acts_as_solr(:fields => [ :name, :description, :computational_type ], :auto_commit => false )
>    end
>    
>    if USE_EVENT_LOG
>
>
>         Modified: trunk/app/models/soap_service.rb (465 => 466)
>
>
> --- trunk/app/models/soap_service.rb	2009-03-04 16:07:46 UTC (rev 465)
> +++ trunk/app/models/soap_service.rb	2009-03-06 12:13:37 UTC (rev 466)
> @@ -39,7 +39,8 @@
>                            :message => 'is not valid'
>     
>    if ENABLE_SEARCH
> -    acts_as_solr(:fields => [ :name, :description, :documentation_url, :wsdl_location, :service_type_name ])
> +    acts_as_solr(:fields => [ :name, :description, :documentation_url, :wsdl_location, :service_type_name ], 
> +                            :auto_commit => false )
>    end
>    
>    if USE_EVENT_LOG
>
>
>         Modified: trunk/app/models/soaplab_server.rb (465 => 466)
>
>
> --- trunk/app/models/soaplab_server.rb	2009-03-04 16:07:46 UTC (rev 465)
> +++ trunk/app/models/soaplab_server.rb	2009-03-06 12:13:37 UTC (rev 466)
> @@ -21,6 +21,10 @@
>    validates_uniqueness_of :location, :message => " for this server seems to exist in BioCatalogue"
>    validates_url_format_of :location,
>                            :allow_nil => false
> +  
> +  if ENABLE_SEARCH
> +    acts_as_solr(:fields => [ :location ], :auto_commit => false )
> +  end
>  
>    # save the soap services from this server in
>    # the database
>
>
>         Modified: trunk/app/models/user.rb (465 => 466)
>
>
> --- trunk/app/models/user.rb	2009-03-04 16:07:46 UTC (rev 465)
> +++ trunk/app/models/user.rb	2009-03-06 12:13:37 UTC (rev 466)
> @@ -19,7 +19,7 @@
>    end
>  
>    if ENABLE_SEARCH
> -    acts_as_solr(:fields => [ :display_name, :affiliation, :country ])
> +    acts_as_solr(:fields => [ :display_name, :affiliation, :country ], :auto_commit => false )
>    end
>  
>    validates_presence_of       :email
> ------------------------------------------------------------------------
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From noreply at rubyforge.org  Tue Mar 10 09:40:32 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 09:40:32 -0400 (EDT)
Subject: [BioCatalogue-developers] [471]
 branches/rest-support/vendor/plugins/annotations/lib/annotations/
 acts_as_annotatable.rb: Annotations plugin: count_annotation_by helper now
 can take in a nil source_type_in,
 which is the same as specifiying source_type_in = "all".
Message-ID: <20090310134032.8CFC91779926@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 10 11:00:38 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 11:00:38 -0400 (EDT)
Subject: [BioCatalogue-developers] [472]
 trunk/vendor/plugins/acts_as_solr/lib/acts_methods.rb: set auto_commit =>
 false in the plugin.
Message-ID: <20090310150038.E199718580F7@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 10 11:02:34 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 11:02:34 -0400 (EDT)
Subject: [BioCatalogue-developers] [473]
	branches/rest-support/vendor/plugins/annotations: Annotations
	plugin:
Message-ID: <20090310150234.13CEE18580F7@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 10 11:06:40 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 11:06:40 -0400 (EDT)
Subject: [BioCatalogue-developers] [474] branches/rest-support: [UNSTABLE]
 REST service submission ongoing work:
Message-ID: <20090310150640.AA69B1779926@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 10 11:07:48 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 11:07:48 -0400 (EDT)
Subject: [BioCatalogue-developers] [475] trunk/app/models: remove
 auto_commit switch in the act_as_solr macro calls as it is already set in
 the plugin to our required default (false)
Message-ID: <20090310150748.EF29B18580F7@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 10 11:27:18 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 11:27:18 -0400 (EDT)
Subject: [BioCatalogue-developers] [476] branches/rest-support/app/models:
 REST support: updates to some of the REST models.
Message-ID: <20090310152718.14C7C1779926@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 10 12:01:46 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 12:01:46 -0400 (EDT)
Subject: [BioCatalogue-developers] [477]
 branches/rest-support/lib/acts_as_service_versionified.rb: Fix - forgot to
 put the method stub correctly.
Message-ID: <20090310160146.A020A18580E2@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 10 12:07:51 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 12:07:51 -0400 (EDT)
Subject: [BioCatalogue-developers] [478]
 branches/rest-support/app/views/services/new.html.erb: - Updated buttons to
 have SOAP, SOAPLAB Server and REST all in one line.
Message-ID: <20090310160751.A9D2C18580E2@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 10 12:26:52 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 12:26:52 -0400 (EDT)
Subject: [BioCatalogue-developers] [479] trunk/app/models/service.rb: bug
	fix, from incomplete commit
Message-ID: <20090310162652.9FDAC18580E1@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 10 13:07:43 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 13:07:43 -0400 (EDT)
Subject: [BioCatalogue-developers] [480] trunk/public/images: add icons for
	adding annotations and tags
Message-ID: <20090310170743.C4D641779926@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 10 13:12:15 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 13:12:15 -0400 (EDT)
Subject: [BioCatalogue-developers] [481] trunk/app: work on the styles and
 icons for adding annotations and tags
Message-ID: <20090310171216.1636518580EB@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 10 13:23:45 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 13:23:45 -0400 (EDT)
Subject: [BioCatalogue-developers] [482] trunk/app/models/soap_service.rb:
	Important bugfix for geolocating!
Message-ID: <20090310172345.B690918580E3@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 10 13:24:46 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 13:24:46 -0400 (EDT)
Subject: [BioCatalogue-developers] [483]
 branches/rest-support/lib/acts_as_service_versionified.rb: Bugfix for
 geolocating.
Message-ID: <20090310172446.5BC3F18580E3@rubyforge.org>

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From jits at cs.man.ac.uk  Tue Mar 10 13:30:02 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 10 Mar 2009 17:30:02 +0000
Subject: [BioCatalogue-developers] geocoding
	returning	questionable	results
In-Reply-To: <49AD4E57.5030203@cs.man.ac.uk>
References: <E1LeVoW-0000OK-6q@muffin> <49AD4404.6030105@ebi.ac.uk>
	<49AD4E57.5030203@cs.man.ac.uk>
Message-ID: <49B6A39A.1000101@cs.man.ac.uk>

Guys,

Seems like this was indeed a bug!! We were finding out the location of 
the wsdl file not the actual endpoint.

I have committed a fix for this on trunk, so when the beta site is next 
updated it should work fine. The existing data will then need to be 
updated by first removing all the city and country data in the 
service_deployments table (backup first!) and then running the 
regeolocate.rb script.

Jits


Jiten Bhagat wrote:
> We're using a free online IP to location mapping service called hostip 
> (http://www.hostip.info/) so unfortunately we rely on their database 
> (which can be populated and updated by anyone through their website).
>
> Also, we do DNS name to IP resolving at submission time, which is at 
> the mercy of DNS servers and load balancers.
>
> Jits
>
>
> Eric Nzuobontane wrote:
>> Hi Franck,
>> I am not sure I understand. Geocoding has no knowledge of the the 
>> history of whatever it goecodes, as far as I understand. I think the 
>> enpoint has a german domain and would expect the goecode follow 
>> that... Except I completely missundestand what goeoding does.
>>
>> Eric
>>
>>
>> Franck Tanoh wrote:
>>> Eric,
>>> This is a BioMoby service (therefore a dummy wsdl). The tool was 
>>> made in
>>> germany (http://www.biomedcentral.com/1471-2105/7/535) but the web 
>>> service
>>> was implemented by the BioMoby group. So the geocoding make sense.
>>> The service should therefore be tagged as BioMoby service. The list of
>>> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList
>>> Franck
>>> -----Original Message-----
>>> From: biocatalogue-developers-bounces at rubyforge.org
>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of 
>>> Eric
>>> Nzuobontane
>>> Sent: 03 March 2009 13:13
>>> To: biocatalogue-developers at rubyforge.org
>>> Subject: [BioCatalogue-developers] geocoding returning questionable 
>>> results
>>>
>>> hi,
>>> I just submitted a service
>>> http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678
>>>  which I expected to be located in Germany but geocoding claims it 
>>> is in the US!
>>>
>>> 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  Tue Mar 10 13:42:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 13:42:09 -0400 (EDT)
Subject: [BioCatalogue-developers] [484] branches/rest-support: REST
 support: implemented the create action so now REST services can be
 submitted.
Message-ID: <20090310174209.DB67B18580E2@rubyforge.org>

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From jits at cs.man.ac.uk  Tue Mar 10 13:51:53 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 10 Mar 2009 17:51:53 +0000
Subject: [BioCatalogue-developers] Next update to beta site
Message-ID: <49B6A8B9.4050206@cs.man.ac.uk>

Please let me know when the next update to the beta site is done as I'd 
like to merge REST support work to trunk after that.

Thanks,
Jits

From noreply at rubyforge.org  Tue Mar 10 14:04:04 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 10 Mar 2009 14:04:04 -0400 (EDT)
Subject: [BioCatalogue-developers] [485]
 branches/rest-support/app/controllers/rest_services_controller.rb: Minor
 bugfix for the appending of annotations when the service already exists .
Message-ID: <20090310180404.1031F18580E3@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Wed Mar 11 05:29:35 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 11 Mar 2009 09:29:35 +0000
Subject: [BioCatalogue-developers] Next update to beta site
In-Reply-To: <49B6A8B9.4050206@cs.man.ac.uk>
References: <49B6A8B9.4050206@cs.man.ac.uk>
Message-ID: <49B7847F.8050200@ebi.ac.uk>

I think the current code on the beta site is functionally the same as 
the trunk/head. So there is really nothing to update from the trunk at 
the moment. I would say go ahead and do the merge.

Eric


Jiten Bhagat wrote:
> Please let me know when the next update to the beta site is done as 
> I'd like to merge REST support work to trunk after that.
>
> Thanks,
> Jits
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From ericnzuo at ebi.ac.uk  Wed Mar 11 05:32:04 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 11 Mar 2009 09:32:04 +0000
Subject: [BioCatalogue-developers] geocoding
	returning	questionable	results
In-Reply-To: <49B6A39A.1000101@cs.man.ac.uk>
References: <E1LeVoW-0000OK-6q@muffin> <49AD4404.6030105@ebi.ac.uk>
	<49AD4E57.5030203@cs.man.ac.uk> <49B6A39A.1000101@cs.man.ac.uk>
Message-ID: <49B78514.7010106@ebi.ac.uk>

while we are on that... geocoding service thinks Switzerland & Norway 
are in the EU

Jiten Bhagat wrote:
> Guys,
>
> Seems like this was indeed a bug!! We were finding out the location of 
> the wsdl file not the actual endpoint.
>
> I have committed a fix for this on trunk, so when the beta site is 
> next updated it should work fine. The existing data will then need to 
> be updated by first removing all the city and country data in the 
> service_deployments table (backup first!) and then running the 
> regeolocate.rb script.
>
> Jits
>
>
> Jiten Bhagat wrote:
>> We're using a free online IP to location mapping service called 
>> hostip (http://www.hostip.info/) so unfortunately we rely on their 
>> database (which can be populated and updated by anyone through their 
>> website).
>>
>> Also, we do DNS name to IP resolving at submission time, which is at 
>> the mercy of DNS servers and load balancers.
>>
>> Jits
>>
>>
>> Eric Nzuobontane wrote:
>>> Hi Franck,
>>> I am not sure I understand. Geocoding has no knowledge of the the 
>>> history of whatever it goecodes, as far as I understand. I think the 
>>> enpoint has a german domain and would expect the goecode follow 
>>> that... Except I completely missundestand what goeoding does.
>>>
>>> Eric
>>>
>>>
>>> Franck Tanoh wrote:
>>>> Eric,
>>>> This is a BioMoby service (therefore a dummy wsdl). The tool was 
>>>> made in
>>>> germany (http://www.biomedcentral.com/1471-2105/7/535) but the web 
>>>> service
>>>> was implemented by the BioMoby group. So the geocoding make sense.
>>>> The service should therefore be tagged as BioMoby service. The list of
>>>> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList
>>>> Franck
>>>> -----Original Message-----
>>>> From: biocatalogue-developers-bounces at rubyforge.org
>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of 
>>>> Eric
>>>> Nzuobontane
>>>> Sent: 03 March 2009 13:13
>>>> To: biocatalogue-developers at rubyforge.org
>>>> Subject: [BioCatalogue-developers] geocoding returning questionable 
>>>> results
>>>>
>>>> hi,
>>>> I just submitted a service
>>>> http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678 
>>>>
>>>>  which I expected to be located in Germany but geocoding claims it 
>>>> is in the US!
>>>>
>>>> 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  Wed Mar 11 05:46:22 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 11 Mar 2009 09:46:22 +0000
Subject: [BioCatalogue-developers] geocoding
	returning	questionable	results
In-Reply-To: <49B6A39A.1000101@cs.man.ac.uk>
References: <E1LeVoW-0000OK-6q@muffin> <49AD4404.6030105@ebi.ac.uk>
	<49AD4E57.5030203@cs.man.ac.uk> <49B6A39A.1000101@cs.man.ac.uk>
Message-ID: <49B7886E.3080903@ebi.ac.uk>

what if the regeolocate script did not check if the location has already 
been set or not for this situation?


Jiten Bhagat wrote:
> Guys,
>
> Seems like this was indeed a bug!! We were finding out the location of 
> the wsdl file not the actual endpoint.
>
> I have committed a fix for this on trunk, so when the beta site is 
> next updated it should work fine. The existing data will then need to 
> be updated by first removing all the city and country data in the 
> service_deployments table (backup first!) and then running the 
> regeolocate.rb script.
>
> Jits
>
>
> Jiten Bhagat wrote:
>> We're using a free online IP to location mapping service called 
>> hostip (http://www.hostip.info/) so unfortunately we rely on their 
>> database (which can be populated and updated by anyone through their 
>> website).
>>
>> Also, we do DNS name to IP resolving at submission time, which is at 
>> the mercy of DNS servers and load balancers.
>>
>> Jits
>>
>>
>> Eric Nzuobontane wrote:
>>> Hi Franck,
>>> I am not sure I understand. Geocoding has no knowledge of the the 
>>> history of whatever it goecodes, as far as I understand. I think the 
>>> enpoint has a german domain and would expect the goecode follow 
>>> that... Except I completely missundestand what goeoding does.
>>>
>>> Eric
>>>
>>>
>>> Franck Tanoh wrote:
>>>> Eric,
>>>> This is a BioMoby service (therefore a dummy wsdl). The tool was 
>>>> made in
>>>> germany (http://www.biomedcentral.com/1471-2105/7/535) but the web 
>>>> service
>>>> was implemented by the BioMoby group. So the geocoding make sense.
>>>> The service should therefore be tagged as BioMoby service. The list of
>>>> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList
>>>> Franck
>>>> -----Original Message-----
>>>> From: biocatalogue-developers-bounces at rubyforge.org
>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of 
>>>> Eric
>>>> Nzuobontane
>>>> Sent: 03 March 2009 13:13
>>>> To: biocatalogue-developers at rubyforge.org
>>>> Subject: [BioCatalogue-developers] geocoding returning questionable 
>>>> results
>>>>
>>>> hi,
>>>> I just submitted a service
>>>> http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678 
>>>>
>>>>  which I expected to be located in Germany but geocoding claims it 
>>>> is in the US!
>>>>
>>>> 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 jits at cs.man.ac.uk  Wed Mar 11 06:16:52 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 11 Mar 2009 10:16:52 +0000
Subject: [BioCatalogue-developers] Next update to beta site
In-Reply-To: <49B7847F.8050200@ebi.ac.uk>
References: <49B6A8B9.4050206@cs.man.ac.uk> <49B7847F.8050200@ebi.ac.uk>
Message-ID: <49B78F94.8000708@cs.man.ac.uk>

There is the bugfix for gelocating...

Jits


Eric Nzuobontane wrote:
> I think the current code on the beta site is functionally the same as 
> the trunk/head. So there is really nothing to update from the trunk at 
> the moment. I would say go ahead and do the merge.
>
> Eric
>
>
> Jiten Bhagat wrote:
>> Please let me know when the next update to the beta site is done as 
>> I'd like to merge REST support work to trunk after that.
>>
>> Thanks,
>> Jits
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>


From jits at cs.man.ac.uk  Wed Mar 11 06:18:11 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 11 Mar 2009 10:18:11 +0000
Subject: [BioCatalogue-developers] geocoding
	returning	questionable	results
In-Reply-To: <49B78514.7010106@ebi.ac.uk>
References: <E1LeVoW-0000OK-6q@muffin> <49AD4404.6030105@ebi.ac.uk>
	<49AD4E57.5030203@cs.man.ac.uk> <49B6A39A.1000101@cs.man.ac.uk>
	<49B78514.7010106@ebi.ac.uk>
Message-ID: <49B78FE3.2070300@cs.man.ac.uk>

Oh, and they aren't? I'm afraid I'm not European so pardon my ignorance ;-)

Jits


Eric Nzuobontane wrote:
> while we are on that... geocoding service thinks Switzerland & Norway 
> are in the EU
>
> Jiten Bhagat wrote:
>> Guys,
>>
>> Seems like this was indeed a bug!! We were finding out the location 
>> of the wsdl file not the actual endpoint.
>>
>> I have committed a fix for this on trunk, so when the beta site is 
>> next updated it should work fine. The existing data will then need to 
>> be updated by first removing all the city and country data in the 
>> service_deployments table (backup first!) and then running the 
>> regeolocate.rb script.
>>
>> Jits
>>
>>
>> Jiten Bhagat wrote:
>>> We're using a free online IP to location mapping service called 
>>> hostip (http://www.hostip.info/) so unfortunately we rely on their 
>>> database (which can be populated and updated by anyone through their 
>>> website).
>>>
>>> Also, we do DNS name to IP resolving at submission time, which is at 
>>> the mercy of DNS servers and load balancers.
>>>
>>> Jits
>>>
>>>
>>> Eric Nzuobontane wrote:
>>>> Hi Franck,
>>>> I am not sure I understand. Geocoding has no knowledge of the the 
>>>> history of whatever it goecodes, as far as I understand. I think 
>>>> the enpoint has a german domain and would expect the goecode follow 
>>>> that... Except I completely missundestand what goeoding does.
>>>>
>>>> Eric
>>>>
>>>>
>>>> Franck Tanoh wrote:
>>>>> Eric,
>>>>> This is a BioMoby service (therefore a dummy wsdl). The tool was 
>>>>> made in
>>>>> germany (http://www.biomedcentral.com/1471-2105/7/535) but the web 
>>>>> service
>>>>> was implemented by the BioMoby group. So the geocoding make sense.
>>>>> The service should therefore be tagged as BioMoby service. The 
>>>>> list of
>>>>> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList
>>>>> Franck
>>>>> -----Original Message-----
>>>>> From: biocatalogue-developers-bounces at rubyforge.org
>>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf 
>>>>> Of Eric
>>>>> Nzuobontane
>>>>> Sent: 03 March 2009 13:13
>>>>> To: biocatalogue-developers at rubyforge.org
>>>>> Subject: [BioCatalogue-developers] geocoding returning 
>>>>> questionable results
>>>>>
>>>>> hi,
>>>>> I just submitted a service
>>>>> http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678 
>>>>>
>>>>>  which I expected to be located in Germany but geocoding claims it 
>>>>> is in the US!
>>>>>
>>>>> 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 jits at cs.man.ac.uk  Wed Mar 11 06:20:02 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 11 Mar 2009 10:20:02 +0000
Subject: [BioCatalogue-developers] geocoding
	returning	questionable	results
In-Reply-To: <49B7886E.3080903@ebi.ac.uk>
References: <E1LeVoW-0000OK-6q@muffin> <49AD4404.6030105@ebi.ac.uk>
	<49AD4E57.5030203@cs.man.ac.uk> <49B6A39A.1000101@cs.man.ac.uk>
	<49B7886E.3080903@ebi.ac.uk>
Message-ID: <49B79052.7020106@cs.man.ac.uk>

You could disable the if loop that does the check if you'd like, but I'd 
like to keep the original script having the check so that it doesn't 
overwrite anything.

So for now you could copy the script and name it something else, and 
then remove the if check in there.

Cheers,
Jits


Eric Nzuobontane wrote:
> what if the regeolocate script did not check if the location has 
> already been set or not for this situation?
>
>
> Jiten Bhagat wrote:
>> Guys,
>>
>> Seems like this was indeed a bug!! We were finding out the location 
>> of the wsdl file not the actual endpoint.
>>
>> I have committed a fix for this on trunk, so when the beta site is 
>> next updated it should work fine. The existing data will then need to 
>> be updated by first removing all the city and country data in the 
>> service_deployments table (backup first!) and then running the 
>> regeolocate.rb script.
>>
>> Jits
>>
>>
>> Jiten Bhagat wrote:
>>> We're using a free online IP to location mapping service called 
>>> hostip (http://www.hostip.info/) so unfortunately we rely on their 
>>> database (which can be populated and updated by anyone through their 
>>> website).
>>>
>>> Also, we do DNS name to IP resolving at submission time, which is at 
>>> the mercy of DNS servers and load balancers.
>>>
>>> Jits
>>>
>>>
>>> Eric Nzuobontane wrote:
>>>> Hi Franck,
>>>> I am not sure I understand. Geocoding has no knowledge of the the 
>>>> history of whatever it goecodes, as far as I understand. I think 
>>>> the enpoint has a german domain and would expect the goecode follow 
>>>> that... Except I completely missundestand what goeoding does.
>>>>
>>>> Eric
>>>>
>>>>
>>>> Franck Tanoh wrote:
>>>>> Eric,
>>>>> This is a BioMoby service (therefore a dummy wsdl). The tool was 
>>>>> made in
>>>>> germany (http://www.biomedcentral.com/1471-2105/7/535) but the web 
>>>>> service
>>>>> was implemented by the BioMoby group. So the geocoding make sense.
>>>>> The service should therefore be tagged as BioMoby service. The 
>>>>> list of
>>>>> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList
>>>>> Franck
>>>>> -----Original Message-----
>>>>> From: biocatalogue-developers-bounces at rubyforge.org
>>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf 
>>>>> Of Eric
>>>>> Nzuobontane
>>>>> Sent: 03 March 2009 13:13
>>>>> To: biocatalogue-developers at rubyforge.org
>>>>> Subject: [BioCatalogue-developers] geocoding returning 
>>>>> questionable results
>>>>>
>>>>> hi,
>>>>> I just submitted a service
>>>>> http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678 
>>>>>
>>>>>  which I expected to be located in Germany but geocoding claims it 
>>>>> is in the US!
>>>>>
>>>>> 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 jits at cs.man.ac.uk  Wed Mar 11 06:33:20 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 11 Mar 2009 10:33:20 +0000
Subject: [BioCatalogue-developers] geocoding
	returning	questionable	results
In-Reply-To: <49B78FE3.2070300@cs.man.ac.uk>
References: <E1LeVoW-0000OK-6q@muffin> <49AD4404.6030105@ebi.ac.uk>
	<49AD4E57.5030203@cs.man.ac.uk> <49B6A39A.1000101@cs.man.ac.uk>
	<49B78514.7010106@ebi.ac.uk> <49B78FE3.2070300@cs.man.ac.uk>
Message-ID: <49B79370.6060103@cs.man.ac.uk>

Oh yeah, they aren't... that's very weird! OK, what do you reckon we do 
about this?

Jiten Bhagat wrote:
> Oh, and they aren't? I'm afraid I'm not European so pardon my 
> ignorance ;-)
>
> Jits
>
>
> Eric Nzuobontane wrote:
>> while we are on that... geocoding service thinks Switzerland & Norway 
>> are in the EU
>>
>> Jiten Bhagat wrote:
>>> Guys,
>>>
>>> Seems like this was indeed a bug!! We were finding out the location 
>>> of the wsdl file not the actual endpoint.
>>>
>>> I have committed a fix for this on trunk, so when the beta site is 
>>> next updated it should work fine. The existing data will then need 
>>> to be updated by first removing all the city and country data in the 
>>> service_deployments table (backup first!) and then running the 
>>> regeolocate.rb script.
>>>
>>> Jits
>>>
>>>
>>> Jiten Bhagat wrote:
>>>> We're using a free online IP to location mapping service called 
>>>> hostip (http://www.hostip.info/) so unfortunately we rely on their 
>>>> database (which can be populated and updated by anyone through 
>>>> their website).
>>>>
>>>> Also, we do DNS name to IP resolving at submission time, which is 
>>>> at the mercy of DNS servers and load balancers.
>>>>
>>>> Jits
>>>>
>>>>
>>>> Eric Nzuobontane wrote:
>>>>> Hi Franck,
>>>>> I am not sure I understand. Geocoding has no knowledge of the the 
>>>>> history of whatever it goecodes, as far as I understand. I think 
>>>>> the enpoint has a german domain and would expect the goecode 
>>>>> follow that... Except I completely missundestand what goeoding does.
>>>>>
>>>>> Eric
>>>>>
>>>>>
>>>>> Franck Tanoh wrote:
>>>>>> Eric,
>>>>>> This is a BioMoby service (therefore a dummy wsdl). The tool was 
>>>>>> made in
>>>>>> germany (http://www.biomedcentral.com/1471-2105/7/535) but the 
>>>>>> web service
>>>>>> was implemented by the BioMoby group. So the geocoding make sense.
>>>>>> The service should therefore be tagged as BioMoby service. The 
>>>>>> list of
>>>>>> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList
>>>>>> Franck
>>>>>> -----Original Message-----
>>>>>> From: biocatalogue-developers-bounces at rubyforge.org
>>>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf 
>>>>>> Of Eric
>>>>>> Nzuobontane
>>>>>> Sent: 03 March 2009 13:13
>>>>>> To: biocatalogue-developers at rubyforge.org
>>>>>> Subject: [BioCatalogue-developers] geocoding returning 
>>>>>> questionable results
>>>>>>
>>>>>> hi,
>>>>>> I just submitted a service
>>>>>> http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678 
>>>>>>
>>>>>>  which I expected to be located in Germany but geocoding claims 
>>>>>> it is in the US!
>>>>>>
>>>>>> 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  Wed Mar 11 06:44:50 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 11 Mar 2009 06:44:50 -0400 (EDT)
Subject: [BioCatalogue-developers] [486]
	trunk/app/helpers/application_helper.rb: add documentation
Message-ID: <20090311104451.1BD7A18580E4@rubyforge.org>

An HTML attachment was scrubbed...
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From noreply at rubyforge.org  Wed Mar 11 06:45:41 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 11 Mar 2009 06:45:41 -0400 (EDT)
Subject: [BioCatalogue-developers] [487] trunk/app/views/annotations: remove
	code duplication
Message-ID: <20090311104541.49D9918580E4@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Wed Mar 11 07:34:47 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 11 Mar 2009 11:34:47 +0000
Subject: [BioCatalogue-developers] geocoding
	returning	questionable	results
In-Reply-To: <49B79370.6060103@cs.man.ac.uk>
References: <E1LeVoW-0000OK-6q@muffin> <49AD4404.6030105@ebi.ac.uk>
	<49AD4E57.5030203@cs.man.ac.uk> <49B6A39A.1000101@cs.man.ac.uk>
	<49B78514.7010106@ebi.ac.uk> <49B78FE3.2070300@cs.man.ac.uk>
	<49B79370.6060103@cs.man.ac.uk>
Message-ID: <49B7A1D7.5090700@ebi.ac.uk>

You would see why they do not want to join. They are small countries 
that are rich. Small so they cannot have much influence in the face of 
UK, Germany, France ... and rich mean they get to contribute more to 
prop up the poorer nations. And for Switzerland in particular, it means 
they lose the banking secrecy protection which is a big source of their 
wealth. And guess what, they have more or less the same privileges and 
EU citizens within the EU.... hmmm

On what we do about it, submit a bug report to google or whoever is 
offering the service. Otherwise, I do not know.

Eric


Jiten Bhagat wrote:
> Oh yeah, they aren't... that's very weird! OK, what do you reckon we 
> do about this?
>
> Jiten Bhagat wrote:
>> Oh, and they aren't? I'm afraid I'm not European so pardon my 
>> ignorance ;-)
>>
>> Jits
>>
>>
>> Eric Nzuobontane wrote:
>>> while we are on that... geocoding service thinks Switzerland & 
>>> Norway are in the EU
>>>
>>> Jiten Bhagat wrote:
>>>> Guys,
>>>>
>>>> Seems like this was indeed a bug!! We were finding out the location 
>>>> of the wsdl file not the actual endpoint.
>>>>
>>>> I have committed a fix for this on trunk, so when the beta site is 
>>>> next updated it should work fine. The existing data will then need 
>>>> to be updated by first removing all the city and country data in 
>>>> the service_deployments table (backup first!) and then running the 
>>>> regeolocate.rb script.
>>>>
>>>> Jits
>>>>
>>>>
>>>> Jiten Bhagat wrote:
>>>>> We're using a free online IP to location mapping service called 
>>>>> hostip (http://www.hostip.info/) so unfortunately we rely on their 
>>>>> database (which can be populated and updated by anyone through 
>>>>> their website).
>>>>>
>>>>> Also, we do DNS name to IP resolving at submission time, which is 
>>>>> at the mercy of DNS servers and load balancers.
>>>>>
>>>>> Jits
>>>>>
>>>>>
>>>>> Eric Nzuobontane wrote:
>>>>>> Hi Franck,
>>>>>> I am not sure I understand. Geocoding has no knowledge of the the 
>>>>>> history of whatever it goecodes, as far as I understand. I think 
>>>>>> the enpoint has a german domain and would expect the goecode 
>>>>>> follow that... Except I completely missundestand what goeoding does.
>>>>>>
>>>>>> Eric
>>>>>>
>>>>>>
>>>>>> Franck Tanoh wrote:
>>>>>>> Eric,
>>>>>>> This is a BioMoby service (therefore a dummy wsdl). The tool was 
>>>>>>> made in
>>>>>>> germany (http://www.biomedcentral.com/1471-2105/7/535) but the 
>>>>>>> web service
>>>>>>> was implemented by the BioMoby group. So the geocoding make sense.
>>>>>>> The service should therefore be tagged as BioMoby service. The 
>>>>>>> list of
>>>>>>> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList
>>>>>>> Franck
>>>>>>> -----Original Message-----
>>>>>>> From: biocatalogue-developers-bounces at rubyforge.org
>>>>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf 
>>>>>>> Of Eric
>>>>>>> Nzuobontane
>>>>>>> Sent: 03 March 2009 13:13
>>>>>>> To: biocatalogue-developers at rubyforge.org
>>>>>>> Subject: [BioCatalogue-developers] geocoding returning 
>>>>>>> questionable results
>>>>>>>
>>>>>>> hi,
>>>>>>> I just submitted a service
>>>>>>> http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678 
>>>>>>>
>>>>>>>  which I expected to be located in Germany but geocoding claims 
>>>>>>> it is in the US!
>>>>>>>
>>>>>>> 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  Wed Mar 11 07:40:55 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 11 Mar 2009 11:40:55 +0000
Subject: [BioCatalogue-developers] geocoding
	returning	questionable	results
In-Reply-To: <49B7A1D7.5090700@ebi.ac.uk>
References: <E1LeVoW-0000OK-6q@muffin> <49AD4404.6030105@ebi.ac.uk>
	<49AD4E57.5030203@cs.man.ac.uk> <49B6A39A.1000101@cs.man.ac.uk>
	<49B78514.7010106@ebi.ac.uk> <49B78FE3.2070300@cs.man.ac.uk>
	<49B79370.6060103@cs.man.ac.uk> <49B7A1D7.5090700@ebi.ac.uk>
Message-ID: <49B7A347.4050108@cs.man.ac.uk>

Eric Nzuobontane wrote:
> You would see why they do not want to join. They are small countries 
> that are rich. Small so they cannot have much influence in the face of 
> UK, Germany, France ... and rich mean they get to contribute more to 
> prop up the poorer nations. And for Switzerland in particular, it 
> means they lose the banking secrecy protection which is a big source 
> of their wealth. And guess what, they have more or less the same 
> privileges and EU citizens within the EU.... hmmm

So true! Though I heard recently that they are having to drop some of 
the secrecy protection? (Or atleast were discussing it, in the face of 
the current banking problems).

>
> On what we do about it, submit a bug report to google or whoever is 
> offering the service. Otherwise, I do not know.

Okay. The service we're using is: hostip (http://www.hostip.info/).

If we can find out which IP addresses are being geolocated to EU then we 
can edit the info about them on hostip directly. I assume right now they 
just return location as "Europe" or "European Union".

Speaking of which, let's check the DB first as it could be that we are 
doing some wrong mapping of location to flags. When you get a moment, 
could you check the city and country fields for their exact content (in 
the service_deployments table), so we can know what exactly is being 
returned by hostip.

Cheers,
Jits


>
> Eric
>
>
> Jiten Bhagat wrote:
>> Oh yeah, they aren't... that's very weird! OK, what do you reckon we 
>> do about this?
>>
>> Jiten Bhagat wrote:
>>> Oh, and they aren't? I'm afraid I'm not European so pardon my 
>>> ignorance ;-)
>>>
>>> Jits
>>>
>>>
>>> Eric Nzuobontane wrote:
>>>> while we are on that... geocoding service thinks Switzerland & 
>>>> Norway are in the EU
>>>>
>>>> Jiten Bhagat wrote:
>>>>> Guys,
>>>>>
>>>>> Seems like this was indeed a bug!! We were finding out the 
>>>>> location of the wsdl file not the actual endpoint.
>>>>>
>>>>> I have committed a fix for this on trunk, so when the beta site is 
>>>>> next updated it should work fine. The existing data will then need 
>>>>> to be updated by first removing all the city and country data in 
>>>>> the service_deployments table (backup first!) and then running the 
>>>>> regeolocate.rb script.
>>>>>
>>>>> Jits
>>>>>
>>>>>
>>>>> Jiten Bhagat wrote:
>>>>>> We're using a free online IP to location mapping service called 
>>>>>> hostip (http://www.hostip.info/) so unfortunately we rely on 
>>>>>> their database (which can be populated and updated by anyone 
>>>>>> through their website).
>>>>>>
>>>>>> Also, we do DNS name to IP resolving at submission time, which is 
>>>>>> at the mercy of DNS servers and load balancers.
>>>>>>
>>>>>> Jits
>>>>>>
>>>>>>
>>>>>> Eric Nzuobontane wrote:
>>>>>>> Hi Franck,
>>>>>>> I am not sure I understand. Geocoding has no knowledge of the 
>>>>>>> the history of whatever it goecodes, as far as I understand. I 
>>>>>>> think the enpoint has a german domain and would expect the 
>>>>>>> goecode follow that... Except I completely missundestand what 
>>>>>>> goeoding does.
>>>>>>>
>>>>>>> Eric
>>>>>>>
>>>>>>>
>>>>>>> Franck Tanoh wrote:
>>>>>>>> Eric,
>>>>>>>> This is a BioMoby service (therefore a dummy wsdl). The tool 
>>>>>>>> was made in
>>>>>>>> germany (http://www.biomedcentral.com/1471-2105/7/535) but the 
>>>>>>>> web service
>>>>>>>> was implemented by the BioMoby group. So the geocoding make sense.
>>>>>>>> The service should therefore be tagged as BioMoby service. The 
>>>>>>>> list of
>>>>>>>> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList
>>>>>>>> Franck
>>>>>>>> -----Original Message-----
>>>>>>>> From: biocatalogue-developers-bounces at rubyforge.org
>>>>>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On 
>>>>>>>> Behalf Of Eric
>>>>>>>> Nzuobontane
>>>>>>>> Sent: 03 March 2009 13:13
>>>>>>>> To: biocatalogue-developers at rubyforge.org
>>>>>>>> Subject: [BioCatalogue-developers] geocoding returning 
>>>>>>>> questionable results
>>>>>>>>
>>>>>>>> hi,
>>>>>>>> I just submitted a service
>>>>>>>> http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678 
>>>>>>>>
>>>>>>>>  which I expected to be located in Germany but geocoding claims 
>>>>>>>> it is in the US!
>>>>>>>>
>>>>>>>> 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  Wed Mar 11 08:58:16 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 11 Mar 2009 08:58:16 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2570] Add the addthis.com
	bookmarking widget
Message-ID: <20090311125816.F063318580EB@rubyforge.org>

Task #2570 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Add the addthis.com bookmarking widget
Complete: 0%
Status: Open

Description: Like on myexperiment

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2570&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Wed Mar 11 09:01:37 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 11 Mar 2009 09:01:37 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2571] Add google analytics
Message-ID: <20090311130137.9B17918580ED@rubyforge.org>

Task #2571 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Add google analytics
Complete: 0%
Status: Open

Description: Need to add google analytics to the website

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2571&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Wed Mar 11 09:02:08 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 11 Mar 2009 09:02:08 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2571] Add google analytics
Message-ID: <20090311130208.7097C18580ED@rubyforge.org>

Task #2571 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Add google analytics
Complete: 0%
Status: Open

Description: Need to add google analytics to the website

Follow-Ups:

-------------------------------------------------------
Date: 2009-03-11 13:02
By: jits

Comment:
Have the EBI registered for a Google Analytics account as Rodrigo mentioned?

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2571&group_id=6901&group_project_id=12540

From ytanoh at cs.man.ac.uk  Wed Mar 11 09:09:31 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 11 Mar 2009 13:09:31 -0000
Subject: [BioCatalogue-developers] service operation annotation
In-Reply-To: <49B7A1D7.5090700@ebi.ac.uk>
Message-ID: <E1LhOBh-0000yH-Dy@muffin>

Hi Jits, 

When I edit an operation description and save it, I'm redirected to the
service page. you fixed the bit where users create a brand new description
and save it... thx for that; but the 'edit' and 'delete' still redirecting
to the service page.
Cheers, 

Franck  

-----Original Message-----
From: biocatalogue-developers-bounces at rubyforge.org
[mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
Nzuobontane
Sent: 11 March 2009 11:35
To: Jiten Bhagat
Cc: biocatalogue-developers at rubyforge.org
Subject: Re: [BioCatalogue-developers] geocodingreturning questionable
results

You would see why they do not want to join. They are small countries 
that are rich. Small so they cannot have much influence in the face of 
UK, Germany, France ... and rich mean they get to contribute more to 
prop up the poorer nations. And for Switzerland in particular, it means 
they lose the banking secrecy protection which is a big source of their 
wealth. And guess what, they have more or less the same privileges and 
EU citizens within the EU.... hmmm

On what we do about it, submit a bug report to google or whoever is 
offering the service. Otherwise, I do not know.

Eric


Jiten Bhagat wrote:
> Oh yeah, they aren't... that's very weird! OK, what do you reckon we 
> do about this?
>
> Jiten Bhagat wrote:
>> Oh, and they aren't? I'm afraid I'm not European so pardon my 
>> ignorance ;-)
>>
>> Jits
>>
>>
>> Eric Nzuobontane wrote:
>>> while we are on that... geocoding service thinks Switzerland & 
>>> Norway are in the EU
>>>
>>> Jiten Bhagat wrote:
>>>> Guys,
>>>>
>>>> Seems like this was indeed a bug!! We were finding out the location 
>>>> of the wsdl file not the actual endpoint.
>>>>
>>>> I have committed a fix for this on trunk, so when the beta site is 
>>>> next updated it should work fine. The existing data will then need 
>>>> to be updated by first removing all the city and country data in 
>>>> the service_deployments table (backup first!) and then running the 
>>>> regeolocate.rb script.
>>>>
>>>> Jits
>>>>
>>>>
>>>> Jiten Bhagat wrote:
>>>>> We're using a free online IP to location mapping service called 
>>>>> hostip (http://www.hostip.info/) so unfortunately we rely on their 
>>>>> database (which can be populated and updated by anyone through 
>>>>> their website).
>>>>>
>>>>> Also, we do DNS name to IP resolving at submission time, which is 
>>>>> at the mercy of DNS servers and load balancers.
>>>>>
>>>>> Jits
>>>>>
>>>>>
>>>>> Eric Nzuobontane wrote:
>>>>>> Hi Franck,
>>>>>> I am not sure I understand. Geocoding has no knowledge of the the 
>>>>>> history of whatever it goecodes, as far as I understand. I think 
>>>>>> the enpoint has a german domain and would expect the goecode 
>>>>>> follow that... Except I completely missundestand what goeoding does.
>>>>>>
>>>>>> Eric
>>>>>>
>>>>>>
>>>>>> Franck Tanoh wrote:
>>>>>>> Eric,
>>>>>>> This is a BioMoby service (therefore a dummy wsdl). The tool was 
>>>>>>> made in
>>>>>>> germany (http://www.biomedcentral.com/1471-2105/7/535) but the 
>>>>>>> web service
>>>>>>> was implemented by the BioMoby group. So the geocoding make sense.
>>>>>>> The service should therefore be tagged as BioMoby service. The 
>>>>>>> list of
>>>>>>> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList
>>>>>>> Franck
>>>>>>> -----Original Message-----
>>>>>>> From: biocatalogue-developers-bounces at rubyforge.org
>>>>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf 
>>>>>>> Of Eric
>>>>>>> Nzuobontane
>>>>>>> Sent: 03 March 2009 13:13
>>>>>>> To: biocatalogue-developers at rubyforge.org
>>>>>>> Subject: [BioCatalogue-developers] geocoding returning 
>>>>>>> questionable results
>>>>>>>
>>>>>>> hi,
>>>>>>> I just submitted a service
>>>>>>>
http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678 
>>>>>>>
>>>>>>>  which I expected to be located in Germany but geocoding claims 
>>>>>>> it is in the US!
>>>>>>>
>>>>>>> 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 jits at cs.man.ac.uk  Wed Mar 11 09:10:41 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 11 Mar 2009 13:10:41 +0000
Subject: [BioCatalogue-developers] service operation annotation
In-Reply-To: <E1LhOBh-0000yH-Dy@muffin>
References: <E1LhOBh-0000yH-Dy@muffin>
Message-ID: <49B7B851.6070208@cs.man.ac.uk>

Ah yes, could you add a rubyforge task for this please, at highest 
priority and assigned to me.

Thanks,
Jits


Franck Tanoh wrote:
> Hi Jits, 
>
> When I edit an operation description and save it, I'm redirected to the
> service page. you fixed the bit where users create a brand new description
> and save it... thx for that; but the 'edit' and 'delete' still redirecting
> to the service page.
> Cheers, 
>
> Franck  
>
> -----Original Message-----
> From: biocatalogue-developers-bounces at rubyforge.org
> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric
> Nzuobontane
> Sent: 11 March 2009 11:35
> To: Jiten Bhagat
> Cc: biocatalogue-developers at rubyforge.org
> Subject: Re: [BioCatalogue-developers] geocodingreturning questionable
> results
>
> You would see why they do not want to join. They are small countries 
> that are rich. Small so they cannot have much influence in the face of 
> UK, Germany, France ... and rich mean they get to contribute more to 
> prop up the poorer nations. And for Switzerland in particular, it means 
> they lose the banking secrecy protection which is a big source of their 
> wealth. And guess what, they have more or less the same privileges and 
> EU citizens within the EU.... hmmm
>
> On what we do about it, submit a bug report to google or whoever is 
> offering the service. Otherwise, I do not know.
>
> Eric
>
>
> Jiten Bhagat wrote:
>   
>> Oh yeah, they aren't... that's very weird! OK, what do you reckon we 
>> do about this?
>>
>> Jiten Bhagat wrote:
>>     
>>> Oh, and they aren't? I'm afraid I'm not European so pardon my 
>>> ignorance ;-)
>>>
>>> Jits
>>>
>>>
>>> Eric Nzuobontane wrote:
>>>       
>>>> while we are on that... geocoding service thinks Switzerland & 
>>>> Norway are in the EU
>>>>
>>>> Jiten Bhagat wrote:
>>>>         
>>>>> Guys,
>>>>>
>>>>> Seems like this was indeed a bug!! We were finding out the location 
>>>>> of the wsdl file not the actual endpoint.
>>>>>
>>>>> I have committed a fix for this on trunk, so when the beta site is 
>>>>> next updated it should work fine. The existing data will then need 
>>>>> to be updated by first removing all the city and country data in 
>>>>> the service_deployments table (backup first!) and then running the 
>>>>> regeolocate.rb script.
>>>>>
>>>>> Jits
>>>>>
>>>>>
>>>>> Jiten Bhagat wrote:
>>>>>           
>>>>>> We're using a free online IP to location mapping service called 
>>>>>> hostip (http://www.hostip.info/) so unfortunately we rely on their 
>>>>>> database (which can be populated and updated by anyone through 
>>>>>> their website).
>>>>>>
>>>>>> Also, we do DNS name to IP resolving at submission time, which is 
>>>>>> at the mercy of DNS servers and load balancers.
>>>>>>
>>>>>> Jits
>>>>>>
>>>>>>
>>>>>> Eric Nzuobontane wrote:
>>>>>>             
>>>>>>> Hi Franck,
>>>>>>> I am not sure I understand. Geocoding has no knowledge of the the 
>>>>>>> history of whatever it goecodes, as far as I understand. I think 
>>>>>>> the enpoint has a german domain and would expect the goecode 
>>>>>>> follow that... Except I completely missundestand what goeoding does.
>>>>>>>
>>>>>>> Eric
>>>>>>>
>>>>>>>
>>>>>>> Franck Tanoh wrote:
>>>>>>>               
>>>>>>>> Eric,
>>>>>>>> This is a BioMoby service (therefore a dummy wsdl). The tool was 
>>>>>>>> made in
>>>>>>>> germany (http://www.biomedcentral.com/1471-2105/7/535) but the 
>>>>>>>> web service
>>>>>>>> was implemented by the BioMoby group. So the geocoding make sense.
>>>>>>>> The service should therefore be tagged as BioMoby service. The 
>>>>>>>> list of
>>>>>>>> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList
>>>>>>>> Franck
>>>>>>>> -----Original Message-----
>>>>>>>> From: biocatalogue-developers-bounces at rubyforge.org
>>>>>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf 
>>>>>>>> Of Eric
>>>>>>>> Nzuobontane
>>>>>>>> Sent: 03 March 2009 13:13
>>>>>>>> To: biocatalogue-developers at rubyforge.org
>>>>>>>> Subject: [BioCatalogue-developers] geocoding returning 
>>>>>>>> questionable results
>>>>>>>>
>>>>>>>> hi,
>>>>>>>> I just submitted a service
>>>>>>>>
>>>>>>>>                 
> http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678 
>   
>>>>>>>>  which I expected to be located in Germany but geocoding claims 
>>>>>>>> it is in the US!
>>>>>>>>
>>>>>>>> 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  Wed Mar 11 09:57:58 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 11 Mar 2009 09:57:58 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2572] service operation description
Message-ID: <20090311135758.57ABF18580F8@rubyforge.org>

Task #2572 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: service operation description
Complete: 0%
Status: Open

Description: When I edit or delete an operation description and save it, I'm redirected to the service page. 

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2572&group_id=6901&group_project_id=12540

From jits at cs.man.ac.uk  Wed Mar 11 10:57:39 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 11 Mar 2009 14:57:39 +0000
Subject: [BioCatalogue-developers] Disqus integration
Message-ID: <49B7D163.80504@cs.man.ac.uk>

Hi guys,

Just some info and an early warning about the Disqus integration work. 
I've put some info here: 
http://www.ebi.ac.uk/ebiwiki/biocatalogue/doku.php?id=development:pilot_dev_notes#disqus_integration

The main point being that when it comes to releasing this on the beta 
site, it is absolutely crucial to set the "account" correctly in the 
local settings file (ie: app/config/initializers/biocat_local.rb). 
Likewise for local test development. As follows:
- For beta/main site: account should be "biocatalogue"
- For local dev/testing: account should ne "biocatalogue-test"

I haven't yet fully implemented this, so if things change I will let you 
know and also keep the wiki page updated.

Cheers,
JIts

From noreply at rubyforge.org  Wed Mar 11 11:19:16 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 11 Mar 2009 11:19:16 -0400 (EDT)
Subject: [BioCatalogue-developers] [488] branches/social: Initial
	integration of the Disqus system.
Message-ID: <20090311151917.2E2A61779921@rubyforge.org>

An HTML attachment was scrubbed...
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From noreply at rubyforge.org  Wed Mar 11 12:32:26 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 11 Mar 2009 12:32:26 -0400 (EDT)
Subject: [BioCatalogue-developers] [489] branches/social: Customisations for
	Disqus integration.
Message-ID: <20090311163226.E93C718580ED@rubyforge.org>

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From jits at cs.man.ac.uk  Thu Mar 12 05:55:09 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Thu, 12 Mar 2009 09:55:09 +0000
Subject: [BioCatalogue-developers] A question on integrating Disqus
In-Reply-To: <919995550903111130j3137d602lbcfff48006397c4f@mail.gmail.com>
References: <49B7D5F9.8050602@cs.man.ac.uk>
	<919995550903111130j3137d602lbcfff48006397c4f@mail.gmail.com>
Message-ID: <49B8DBFD.9090500@cs.man.ac.uk>

Okay, thanks Giannii.

Jiten


Giannii Calvert wrote:
> Jiten,
>
> When you're ready to switch over give us a 24 hours notice and we'll 
> change the permalinks to reflect the new site url.
>
> Giannii
> DISQUS
> Community Manager
> giannii at disqus.com <mailto:giannii at disqus.com>
> http://twitter.com/giannii
>
> On Wed, Mar 11, 2009 at 8:17 AM, Jiten Bhagat <jits at cs.man.ac.uk 
> <mailto:jits at cs.man.ac.uk>> wrote:
>
>     Hello,
>
>     Firstly, let me say, I love the concept of Disqus and I think you
>     guys are doing great :-)
>
>     I have a question I was hoping you could help with. Apologies if
>     this question has already been answered on your help pages or forum.
>
>     I work on the BioCatalogue project (http://www.biocatalogue.org)
>     and we are looking to use your service for commenting/discussing
>     on the BioCatalogue. For now we have a private beta site
>     (http://beta.biocatalogue.org) which will use Disqus. However, we
>     plan on moving to a public beta site fairly soon which will be at
>     the URL http://www.biocatalogue.org/. My concern is that we will
>     lose all comments made on http://beta.biocatalogue.org when we do
>     so. Will it be possible, in the future, to change the hostname of
>     all the things that have comment threads on them?
>
>     Thanks,
>     Jits
>
>
>
>
> -- 
>


From noreply at rubyforge.org  Thu Mar 12 07:11:47 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 07:11:47 -0400 (EDT)
Subject: [BioCatalogue-developers] [490]
 branches/rest-support/app/views/rest_services/_service_listing_info.
 html.erb: Added a view partial that will be required when merging back into
 trunk.
Message-ID: <20090312111147.4571618580FA@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 12 07:21:42 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 07:21:42 -0400 (EDT)
Subject: [BioCatalogue-developers] [491] trunk/app/controllers: Fix for task
 2572 - editing and deleting annotations would not remember the correct tab
 after the action .
Message-ID: <20090312112142.8FEDA18580FA@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 12 07:49:18 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 07:49:18 -0400 (EDT)
Subject: [BioCatalogue-developers] [492] trunk: [UNSTABLE] Merged the
 rest-support branch into trunk ( from revision 428), fixed all conflicts,
 and ensured functionality is in place and working.
Message-ID: <20090312114918.F086318580FB@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 12 07:55:30 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 07:55:30 -0400 (EDT)
Subject: [BioCatalogue-developers] [493]
 trunk/vendor/plugins/annotations/lib/annotations/acts_as_annotatable. rb:
 Updated documentation for create_annotations method.
Message-ID: <20090312115530.2554118580F9@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 12 08:02:31 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 08:02:31 -0400 (EDT)
Subject: [BioCatalogue-developers] [494]
 trunk/vendor/plugins/annotations/lib/annotations/acts_as_annotatable. rb:
 Added a code example to the create_annotations method to help people using
 it .
Message-ID: <20090312120232.6AB5B18580FB@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 12 08:04:17 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 08:04:17 -0400 (EDT)
Subject: [BioCatalogue-developers] [495] branches/rest-support/: Removed
 rest-support branch as it has now been merged into trunk and development on
 it should CEASE and DESIST!
Message-ID: <20090312120417.63A6318580E4@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 12 08:04:55 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 08:04:55 -0400 (EDT)
Subject: [BioCatalogue-developers] [496] branches/annotations/: Removed
 annotations branch as it has already been merged into trunk and development
 on it should CEASE and DESIST!
Message-ID: <20090312120455.CEE4518580E2@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 12 09:17:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 09:17:09 -0400 (EDT)
Subject: [BioCatalogue-developers] [497] trunk/app/models/soaplab_server.rb:
 fix soaplab in accordance with soap service refactoring
Message-ID: <20090312131710.02E931779921@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 12 09:20:16 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 09:20:16 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2572] service operation description
Message-ID: <20090312132016.34FB918580F9@rubyforge.org>

Task #2572 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: service operation description
Complete: 100%
Status: Closed

Description: When I edit or delete an operation description and save it, I'm redirected to the service page. 

Follow-Ups:

-------------------------------------------------------
Date: 2009-03-12 13:20
By: jits

Comment:
fixed

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2572&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Mar 12 09:20:55 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 09:20:55 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2564] Add index/contents table on
	operations tab for easy navigation
Message-ID: <20090312132055.5462E18580ED@rubyforge.org>

Task #2564 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Add index/contents table on operations tab for easy navigation
Complete: 100%
Status: Closed

Description: ... with full anchor links

Follow-Ups:

-------------------------------------------------------
Date: 2009-03-12 13:20
By: jits

Comment:
Done

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

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

From noreply at rubyforge.org  Thu Mar 12 10:13:44 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 10:13:44 -0400 (EDT)
Subject: [BioCatalogue-developers] [498] trunk/app/views: Style improvements,
	mainly increasing font sizes.
Message-ID: <20090312141344.41B2018580EB@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 12 12:12:41 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 12:12:41 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2573] Improve perf by combining
	and compressing assets (JS/CSS)
Message-ID: <20090312161241.A985D18580F9@rubyforge.org>

Task #2573 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Improve perf by combining and compressing assets (JS/CSS)
Complete: 0%
Status: Open

Description: E.g: using the asset_packager plugin (see: http://railsillustrated.com/more-speed-improvements-with-asset_packager.html)

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2573&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Mar 12 17:11:55 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 17:11:55 -0400 (EDT)
Subject: [BioCatalogue-developers] [499] trunk/vendor/plugins/annotations:
 Annotations plugin: modified the create_annotations method to return the
 set of Annotation objects that were successfully created .
Message-ID: <20090312211155.DF84B1858105@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 12 17:41:45 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 17:41:45 -0400 (EDT)
Subject: [BioCatalogue-developers] [500]
 trunk/vendor/plugins/annotations/lib: Fix for the create_annotations method,
 with a change that now allows annotations to have a blank value ( because
 the presence of an annotation object with a specific key might be enough ,
 without ua value).
Message-ID: <20090312214145.878EF1858102@rubyforge.org>

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From jits at cs.man.ac.uk  Thu Mar 12 19:24:30 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Thu, 12 Mar 2009 23:24:30 +0000
Subject: [BioCatalogue-developers] Article on background processing - might
	be useful
Message-ID: <49B999AE.3070206@cs.man.ac.uk>

http://napkin.highgroove.com/articles/2008/05/21/running-background-jobs-in-ruby-on-rails-revisited 


From noreply at rubyforge.org  Thu Mar 12 20:22:37 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 20:22:37 -0400 (EDT)
Subject: [BioCatalogue-developers] [501]
 branches/social/vendor/plugins/annotations: Annotations plugin: in
 preparation for the Ratings work,
 introduced a new config option - limits_per_source - that allows
 configuration of the plugin so that certain annotations can only be made a
 certain number of times per source per annotatable .
Message-ID: <20090313002237.E1F441779921@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 12 20:26:45 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 20:26:45 -0400 (EDT)
Subject: [BioCatalogue-developers] [502]
 branches/social/config/initializers/biocat_main.rb: Added configuration
 options to allow only 1 rating and allow existing records to be updated
 (using the feature introduced in the last commit).
Message-ID: <20090313002645.6784518580F0@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 12 20:28:41 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 12 Mar 2009 20:28:41 -0400 (EDT)
Subject: [BioCatalogue-developers] [503] branches/social: - Updated the
 styles of the yellow boxes in the inner sidebar on the show service page .
Message-ID: <20090313002841.303E71779921@rubyforge.org>

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From noreply at rubyforge.org  Fri Mar 13 13:10:05 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 13 Mar 2009 13:10:05 -0400 (EDT)
Subject: [BioCatalogue-developers] [504] branches/social: Latest work on
	ratings.
Message-ID: <20090313171005.916C118580F6@rubyforge.org>

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From jits at cs.man.ac.uk  Sat Mar 14 06:03:24 2009
From: jits at cs.man.ac.uk (jits at cs.man.ac.uk)
Date: Sat, 14 Mar 2009 10:03:24 -0000 (UTC)
Subject: [BioCatalogue-developers] geocoding
 returning	questionable	results
In-Reply-To: <49B7A1D7.5090700@ebi.ac.uk>
References: <E1LeVoW-0000OK-6q@muffin> <49AD4404.6030105@ebi.ac.uk>
	<49AD4E57.5030203@cs.man.ac.uk> <49B6A39A.1000101@cs.man.ac.uk>
	<49B78514.7010106@ebi.ac.uk> <49B78FE3.2070300@cs.man.ac.uk>
	<49B79370.6060103@cs.man.ac.uk> <49B7A1D7.5090700@ebi.ac.uk>
Message-ID: <fbafff6675594c98df34562c0ea37392.squirrel@webmail.cs.man.ac.uk>

> You would see why they do not want to join. They are small countries
> that are rich. Small so they cannot have much influence in the face of
> UK, Germany, France ... and rich mean they get to contribute more to
> prop up the poorer nations. And for Switzerland in particular, it means
> they lose the banking secrecy protection which is a big source of their
> wealth. And guess what, they have more or less the same privileges and
> EU citizens within the EU.... hmmm

http://news.bbc.co.uk/1/hi/business/7941717.stm

Jits

>
> On what we do about it, submit a bug report to google or whoever is
> offering the service. Otherwise, I do not know.
>
> Eric
>
>
> Jiten Bhagat wrote:
>> Oh yeah, they aren't... that's very weird! OK, what do you reckon we
>> do about this?
>>
>> Jiten Bhagat wrote:
>>> Oh, and they aren't? I'm afraid I'm not European so pardon my
>>> ignorance ;-)
>>>
>>> Jits
>>>
>>>
>>> Eric Nzuobontane wrote:
>>>> while we are on that... geocoding service thinks Switzerland &
>>>> Norway are in the EU
>>>>
>>>> Jiten Bhagat wrote:
>>>>> Guys,
>>>>>
>>>>> Seems like this was indeed a bug!! We were finding out the location
>>>>> of the wsdl file not the actual endpoint.
>>>>>
>>>>> I have committed a fix for this on trunk, so when the beta site is
>>>>> next updated it should work fine. The existing data will then need
>>>>> to be updated by first removing all the city and country data in
>>>>> the service_deployments table (backup first!) and then running the
>>>>> regeolocate.rb script.
>>>>>
>>>>> Jits
>>>>>
>>>>>
>>>>> Jiten Bhagat wrote:
>>>>>> We're using a free online IP to location mapping service called
>>>>>> hostip (http://www.hostip.info/) so unfortunately we rely on their
>>>>>> database (which can be populated and updated by anyone through
>>>>>> their website).
>>>>>>
>>>>>> Also, we do DNS name to IP resolving at submission time, which is
>>>>>> at the mercy of DNS servers and load balancers.
>>>>>>
>>>>>> Jits
>>>>>>
>>>>>>
>>>>>> Eric Nzuobontane wrote:
>>>>>>> Hi Franck,
>>>>>>> I am not sure I understand. Geocoding has no knowledge of the the
>>>>>>> history of whatever it goecodes, as far as I understand. I think
>>>>>>> the enpoint has a german domain and would expect the goecode
>>>>>>> follow that... Except I completely missundestand what goeoding
>>>>>>> does.
>>>>>>>
>>>>>>> Eric
>>>>>>>
>>>>>>>
>>>>>>> Franck Tanoh wrote:
>>>>>>>> Eric,
>>>>>>>> This is a BioMoby service (therefore a dummy wsdl). The tool was
>>>>>>>> made in
>>>>>>>> germany (http://www.biomedcentral.com/1471-2105/7/535) but the
>>>>>>>> web service
>>>>>>>> was implemented by the BioMoby group. So the geocoding make sense.
>>>>>>>> The service should therefore be tagged as BioMoby service. The
>>>>>>>> list of
>>>>>>>> BioMoby dummy wsdl: http://biomoby.org/cgi-bin/serviceList
>>>>>>>> Franck
>>>>>>>> -----Original Message-----
>>>>>>>> From: biocatalogue-developers-bounces at rubyforge.org
>>>>>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf
>>>>>>>> Of Eric
>>>>>>>> Nzuobontane
>>>>>>>> Sent: 03 March 2009 13:13
>>>>>>>> To: biocatalogue-developers at rubyforge.org
>>>>>>>> Subject: [BioCatalogue-developers] geocoding returning
>>>>>>>> questionable results
>>>>>>>>
>>>>>>>> hi,
>>>>>>>> I just submitted a service
>>>>>>>> http://beta.biocatalogue.org/services/142-getbincodebysgnservice_616678
>>>>>>>>
>>>>>>>>  which I expected to be located in Germany but geocoding claims
>>>>>>>> it is in the US!
>>>>>>>>
>>>>>>>> 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  Sat Mar 14 14:31:16 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 14 Mar 2009 14:31:16 -0400 (EDT)
Subject: [BioCatalogue-developers] [505]
 branches/social/app/controllers/services_controller.rb: Small refactoring
Message-ID: <20090314183117.2483418580EA@rubyforge.org>

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From noreply at rubyforge.org  Sat Mar 14 14:52:26 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 14 Mar 2009 14:52:26 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2574] Implement search retrieval
	for REST services
Message-ID: <20090314185226.D0F3018580EA@rubyforge.org>

Task #2574 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Implement search retrieval for REST services
Complete: 0%
Status: Open

Description: This requires modifying the methods in the Util library to add logic for REST models.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2574&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Sat Mar 14 15:47:40 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 14 Mar 2009 15:47:40 -0400 (EDT)
Subject: [BioCatalogue-developers] [506]
 branches/social/vendor/plugins/annotations/test/config_test.rb: Annotations
 plugin: added a couple of asserts.
Message-ID: <20090314194740.7F4DC1779921@rubyforge.org>

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From noreply at rubyforge.org  Sat Mar 14 16:16:14 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 14 Mar 2009 16:16:14 -0400 (EDT)
Subject: [BioCatalogue-developers] [507] branches/social: Ratings can now be
	created!
Message-ID: <20090314201614.586CB18580EE@rubyforge.org>

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From noreply at rubyforge.org  Sat Mar 14 17:06:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 14 Mar 2009 17:06:09 -0400 (EDT)
Subject: [BioCatalogue-developers] [508] branches/social: Implemented
	deletion of user ratings.
Message-ID: <20090314210609.DC88E18580E3@rubyforge.org>

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From noreply at rubyforge.org  Sat Mar 14 17:33:14 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 14 Mar 2009 17:33:14 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2575] Ratings in service listings
Message-ID: <20090314213314.7A66B18580E9@rubyforge.org>

Task #2575 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Ratings in service listings
Complete: 0%
Status: Open

Description: Show the overall rating and possibly the ratings breakdowns in the service listings.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2575&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Sat Mar 14 22:03:40 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 14 Mar 2009 22:03:40 -0400 (EDT)
Subject: [BioCatalogue-developers] [509] branches/social: Style/layout
	improvements:
Message-ID: <20090315020341.00AFF18580EE@rubyforge.org>

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From noreply at rubyforge.org  Sun Mar 15 07:57:29 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 15 Mar 2009 07:57:29 -0400 (EDT)
Subject: [BioCatalogue-developers] [510]
	branches/social/config/initializers/biocat_main.rb: Fixed typo
Message-ID: <20090315115729.9EF8718580FD@rubyforge.org>

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From noreply at rubyforge.org  Sun Mar 15 08:13:28 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 15 Mar 2009 08:13:28 -0400 (EDT)
Subject: [BioCatalogue-developers] [511]
 branches/social/config/initializers/biocat_main.rb: Update to description
 of rating category "Documentation".
Message-ID: <20090315121329.0F58518580FA@rubyforge.org>

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From noreply at rubyforge.org  Mon Mar 16 06:18:19 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 16 Mar 2009 06:18:19 -0400 (EDT)
Subject: [BioCatalogue-developers] [512] branches/social/app/views/layouts:
 Added style overrides for IE6 for the ratings hover.
Message-ID: <20090316101819.530A018580F0@rubyforge.org>

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From noreply at rubyforge.org  Mon Mar 16 06:28:26 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 16 Mar 2009 06:28:26 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2576] Annotations plugin: add
	constrained values config setting
Message-ID: <20090316102826.79DBF18580F5@rubyforge.org>

Task #2576 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Annotations plugin: add constrained values config setting
Complete: 0%
Status: Open

Description: So that certain annotations will only be created if the value falls within a constrained set of values (eg: for ratings, values can only be [1,2,3,4,5])

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From noreply at rubyforge.org  Mon Mar 16 06:47:40 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 16 Mar 2009 06:47:40 -0400 (EDT)
Subject: [BioCatalogue-developers] [513] branches/social: Added overall
 ratings count and individual rating categories count.
Message-ID: <20090316104740.3F3C618580F9@rubyforge.org>

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From jits at cs.man.ac.uk  Mon Mar 16 06:53:56 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 16 Mar 2009 10:53:56 +0000
Subject: [BioCatalogue-developers] Social branch
Message-ID: <49BE2FC4.8060708@cs.man.ac.uk>

Hi guys,

If there are no objections, I will merge the "social" branch into trunk 
straight after lunch. The main things in this will be the Disqus 
integration (which will require updates to your local biocat_local.rb 
settings file as well as to the one on the beta site [different disqus 
accounts!]) and the new multi-ratings piece (which should require 
anything more than an svn update and restarting of mongrels.

Cheers,
Jits

From tlaurent at ebi.ac.uk  Mon Mar 16 07:01:10 2009
From: tlaurent at ebi.ac.uk (Thomas Laurent)
Date: Mon, 16 Mar 2009 11:01:10 +0000
Subject: [BioCatalogue-developers] Social branch
In-Reply-To: <49BE2FC4.8060708@cs.man.ac.uk>
References: <49BE2FC4.8060708@cs.man.ac.uk>
Message-ID: <49BE3176.30703@ebi.ac.uk>

That's fine for me.

Thomas

Jiten Bhagat wrote:
> Hi guys,
> 
> If there are no objections, I will merge the "social" branch into trunk 
> straight after lunch. The main things in this will be the Disqus 
> integration (which will require updates to your local biocat_local.rb 
> settings file as well as to the one on the beta site [different disqus 
> accounts!]) and the new multi-ratings piece (which should require 
> anything more than an svn update and restarting of mongrels.
> 
> Cheers,
> Jits

From noreply at rubyforge.org  Mon Mar 16 07:15:52 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 16 Mar 2009 07:15:52 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2577] Integrate the TinyMCE rich
	text editor
Message-ID: <20090316111552.C77EE1858101@rubyforge.org>

Task #2577 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Integrate the TinyMCE rich text editor
Complete: 0%
Status: Open

Description: ... so things like description and so on can have rich text

-------------------------------------------------------
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http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2577&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Mar 16 07:25:13 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 16 Mar 2009 07:25:13 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2578] Allow multiple name aliases
	to be provided
Message-ID: <20090316112514.2A43318580FF@rubyforge.org>

Task #2578 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Allow multiple name aliases to be provided
Complete: 0%
Status: Open

Description: So maybe comma seperated in the one field during submission...

-------------------------------------------------------
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From noreply at rubyforge.org  Mon Mar 16 07:36:33 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 16 Mar 2009 07:36:33 -0400 (EDT)
Subject: [BioCatalogue-developers] [514] trunk/app/views: Refactored the
 annotations fields that will be used on the service submission page into a
 partial so that it can be extended and reused easily .
Message-ID: <20090316113633.D9F0018580FF@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Mon Mar 16 07:42:56 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 16 Mar 2009 11:42:56 +0000
Subject: [BioCatalogue-developers] Social branch
In-Reply-To: <49BE3176.30703@ebi.ac.uk>
References: <49BE2FC4.8060708@cs.man.ac.uk> <49BE3176.30703@ebi.ac.uk>
Message-ID: <49BE3B40.70006@ebi.ac.uk>

fine by me as well

Eric


Thomas Laurent wrote:
> That's fine for me.
>
> Thomas
>
> Jiten Bhagat wrote:
>> Hi guys,
>>
>> If there are no objections, I will merge the "social" branch into 
>> trunk straight after lunch. The main things in this will be the 
>> Disqus integration (which will require updates to your local 
>> biocat_local.rb settings file as well as to the one on the beta site 
>> [different disqus accounts!]) and the new multi-ratings piece (which 
>> should require anything more than an svn update and restarting of 
>> mongrels.
>>
>> Cheers,
>> Jits

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From noreply at rubyforge.org  Mon Mar 16 09:44:15 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 16 Mar 2009 09:44:15 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2579] possibility to update tags
Message-ID: <20090316134415.CAE9C18580E3@rubyforge.org>

Task #2579 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: possibility to update tags 
Complete: 0%
Status: Open

Description: currently it is impossible to update tags. I've make a couple of spelling mistakes but there's no way to edit them. 

-------------------------------------------------------
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From noreply at rubyforge.org  Mon Mar 16 10:07:45 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 16 Mar 2009 10:07:45 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2580] my favorite services
Message-ID: <20090316140745.DE75A18580E4@rubyforge.org>

Task #2580 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: my favorite services
Complete: 0%
Status: Open

Description: i want to group a number of services as my favorite services. 

-------------------------------------------------------
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From noreply at rubyforge.org  Mon Mar 16 10:37:04 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 16 Mar 2009 10:37:04 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2581] Annontations plugin: prevent
	duplicate values
Message-ID: <20090316143704.31C7F18580EE@rubyforge.org>

Task #2581 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Annontations plugin: prevent duplicate values
Complete: 0%
Status: Open

Description: Basically, right now it is possible to add the same value for the same attribute (and even by the same user)... this is not ideal and by default it should probably not allow duplicate annotations (ie: same value on same attribute). Also add a config setting to override this for specific attributes (eg: we might want to allow multiple tags to be added, to indicate popularity).

-------------------------------------------------------
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From noreply at rubyforge.org  Mon Mar 16 10:48:00 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 16 Mar 2009 10:48:00 -0400 (EDT)
Subject: [BioCatalogue-developers] [515] trunk/vendor/plugins/annotations:
 Annotations plugin: blank annotations (ie: annotations with no value) are
 not allowed now as this was causing too many problems.
Message-ID: <20090316144801.3EFFF19784BE@rubyforge.org>

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From noreply at rubyforge.org  Mon Mar 16 13:05:42 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 16 Mar 2009 13:05:42 -0400 (EDT)
Subject: [BioCatalogue-developers] [516] trunk: Implemented tag annotations
 field in the service submission fields partial .
Message-ID: <20090316170542.9C1C7185810A@rubyforge.org>

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From noreply at rubyforge.org  Mon Mar 16 13:40:56 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 16 Mar 2009 13:40:56 -0400 (EDT)
Subject: [BioCatalogue-developers] [517] trunk: Merged the 'social' branch,
 from revision 443, to trunk, fixed all conflicts,
 fixed issues and tested (somewhat).
Message-ID: <20090316174056.6979E185810A@rubyforge.org>

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From noreply at rubyforge.org  Mon Mar 16 13:45:00 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 16 Mar 2009 13:45:00 -0400 (EDT)
Subject: [BioCatalogue-developers] [518] branches/social/: Removed the
 'social' branch as this has now been fully merged into trunk.
Message-ID: <20090316174500.7C38B1978561@rubyforge.org>

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From noreply at rubyforge.org  Mon Mar 16 13:45:35 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 16 Mar 2009 13:45:35 -0400 (EDT)
Subject: [BioCatalogue-developers] [519] branches/annotations-form/: Removed
 'annotations-form' branch because it is grossly out of date and no
 development has been done on it yet .
Message-ID: <20090316174535.9EF4C197856B@rubyforge.org>

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From jits at cs.man.ac.uk  Mon Mar 16 13:47:16 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 16 Mar 2009 17:47:16 +0000
Subject: [BioCatalogue-developers] [517] trunk: Merged the 'social'
 branch, from revision 443, to trunk, fixed all conflicts,
 fixed issues and tested (somewhat).
In-Reply-To: <20090316174056.6979E185810A@rubyforge.org>
References: <20090316174056.6979E185810A@rubyforge.org>
Message-ID: <49BE90A4.9010102@cs.man.ac.uk>

Hi guys,

When you update to this revision (or later), make sure you follow the 
instructions from here: 
http://www.ebi.ac.uk/ebiwiki/biocatalogue/doku.php?id=development:pilot_dev_notes#disqus_integration. 
This is for both your local development/test set ups as well as for the 
beta site.

Cheers,
Jits


noreply at rubyforge.org wrote:
>
> Revision
>     517
> Author
>     jits
> Date
>     2009-03-16 13:40:55 -0400 (Mon, 16 Mar 2009)
>
>
>       Log Message
>
> Merged the 'social' branch, from revision 443, to trunk, fixed all conflicts, fixed issues and tested (somewhat).
>
> This means trunk now has the multi-ratings and the disqus commenting.
>
>
>       Modified Paths
>
>     * trunk/app/controllers/services_controller.rb
>       <#trunkappcontrollersservices_controllerrb>
>     * trunk/app/helpers/application_helper.rb
>       <#trunkapphelpersapplication_helperrb>
>     * trunk/app/models/annotation.rb <#trunkappmodelsannotationrb>
>     * trunk/app/views/annotations/_tags_box.html.erb
>       <#trunkappviewsannotations_tags_boxhtmlerb>
>     * trunk/app/views/layouts/_head.html.erb
>       <#trunkappviewslayouts_headhtmlerb>
>     * trunk/app/views/layouts/_head_tabber.html.erb
>       <#trunkappviewslayouts_head_tabberhtmlerb>
>     * trunk/app/views/services/show.html.erb
>       <#trunkappviewsservicesshowhtmlerb>
>     * trunk/config/environment.rb <#trunkconfigenvironmentrb>
>     * trunk/config/initializers/biocat_local.rb.pre
>       <#trunkconfiginitializersbiocat_localrbpre>
>     * trunk/config/initializers/biocat_main.rb
>       <#trunkconfiginitializersbiocat_mainrb>
>     * trunk/config/routes.rb <#trunkconfigroutesrb>
>     * trunk/lib/util.rb <#trunklibutilrb>
>     * trunk/public/stylesheets/styles.css
>       <#trunkpublicstylesheetsstylescss>
>     * trunk/vendor/plugins/annotations/lib/annotations/acts_as_annotatable.rb
>       <#trunkvendorpluginsannotationslibannotationsacts_as_annotatablerb>
>     * trunk/vendor/plugins/annotations/lib/annotations/config.rb
>       <#trunkvendorpluginsannotationslibannotationsconfigrb>
>     * trunk/vendor/plugins/annotations/lib/app/models/annotation.rb
>       <#trunkvendorpluginsannotationslibappmodelsannotationrb>
>     * trunk/vendor/plugins/annotations/test/acts_as_annotatable_test.rb
>       <#trunkvendorpluginsannotationstestacts_as_annotatable_testrb>
>     * trunk/vendor/plugins/annotations/test/config_test.rb
>       <#trunkvendorpluginsannotationstestconfig_testrb>
>
>
>       Added Paths
>
>     * trunk/app/controllers/ratings_controller.rb
>       <#trunkappcontrollersratings_controllerrb>
>     * trunk/app/views/annotations/_ratings_box.html.erb
>       <#trunkappviewsannotations_ratings_boxhtmlerb>
>     * trunk/app/views/layouts/_head_browser_overrides.html.erb
>       <#trunkappviewslayouts_head_browser_overrideshtmlerb>
>     * trunk/lib/array.rb <#trunklibarrayrb>
>     * trunk/public/images/box-bg1.png <#trunkpublicimagesboxbg1png>
>     * trunk/public/images/delete.png <#trunkpublicimagesdeletepng>
>     * trunk/public/images/delete_faded.png
>       <#trunkpublicimagesdelete_fadedpng>
>     * trunk/public/images/star.gif <#trunkpublicimagesstargif>
>     * trunk/public/images/star_small.gif <#trunkpublicimagesstar_smallgif>
>     * trunk/public/stylesheets/ratings.css
>       <#trunkpublicstylesheetsratingscss>
>     * trunk/test/functional/ratings_controller_test.rb
>       <#trunktestfunctionalratings_controller_testrb>
>     * trunk/vendor/gems/
>
>
>       Diff
>
>
>         Copied: trunk/app/controllers/ratings_controller.rb (from rev
>         516, branches/social/app/controllers/ratings_controller.rb) (0
>         => 517)
>
>
> --- trunk/app/controllers/ratings_controller.rb	                        (rev 0)
> +++ trunk/app/controllers/ratings_controller.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -0,0 +1,51 @@
> +# BioCatalogue: app/controllers/ratings_controller.rb
> +#
> +# Copyright (c) 2009, University of Manchester, The European Bioinformatics 
> +# Institute (EMBL-EBI) and the University of Southampton.
> +# See license.txt for details
> +
> +class RatingsController < ApplicationController
> +  before_filter :login_required
> +  
> +  # POST /ratings
> +  def create
> +    annotatable = Annotation.find_annotatable(params[:annotatable_type], params[:annotatable_id])
> +    
> +    category = params[:category]
> +    rating = params[:rating].to_i
> +    
> +    if !annotatable.nil? and !category.blank? and [1,2,3,4,5].include?(rating)
> +      annotatable.annotations << Annotation.new(:attribute_name => category, 
> +                                                :value => rating, 
> +                                                :source_type => current_user.class.name, 
> +                                                :source_id => current_user.id)
> +    end
> +    
> +    respond_to do |format|
> +      format.html { render :partial => "annotations/ratings_box", 
> +                         :locals => { :annotatable => annotatable,
> +                                      :categories_config => BioCatalogue::Util.get_ratings_categories_config_for_model(annotatable.class)} }
> +    end
> +  end
> +  
> +  # DELETE /ratings
> +  def destroy
> +    annotatable = Annotation.find_annotatable(params[:annotatable_type], params[:annotatable_id])
> +    
> +    category = params[:category]
> +    
> +    if !annotatable.nil? and !category.blank?
> +      existing = annotatable.annotations.find(:all, 
> +                                              :conditions => { :attribute_id => AnnotationAttribute.find_by_name(category), 
> +                                                               :source_type => current_user.class.name,
> +                                                               :source_id => current_user.id })
> +      annotatable.annotations.delete(existing)
> +    end
> +    
> +    respond_to do |format|
> +      format.html { render :partial => "annotations/ratings_box", 
> +                         :locals => { :annotatable => annotatable,
> +                                      :categories_config => BioCatalogue::Util.get_ratings_categories_config_for_model(annotatable.class)} }
> +    end
> +  end
> +end
>
>
>         Modified: trunk/app/controllers/services_controller.rb (516 =>
>         517)
>
>
> --- trunk/app/controllers/services_controller.rb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/app/controllers/services_controller.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -1,6 +1,6 @@
>  # BioCatalogue: app/controllers/services_controller.rb
>  #
> -# Copyright (c) 2008, University of Manchester, The European Bioinformatics 
> +# Copyright (c) 2009, University of Manchester, The European Bioinformatics 
>  # Institute (EMBL-EBI) and the University of Southampton.
>  # See license.txt for details.
>  
> @@ -8,6 +8,8 @@
>    
>    before_filter :disable_action, :only => [ :edit, :update, :destroy ]
>    
> +  before_filter :find_service, :only => [ :show, :edit, :update, :destroy ]
> +  
>    # Set the sidebar layout for certain actions.
>    # Note: the set_sidebar_layout method resides in the ApplicationController.
>    #before_filter :set_sidebar_layout, :only => [ :show ]
> @@ -31,8 +33,6 @@
>    # GET /services/1
>    # GET /services/1.xml
>    def show
> -    @service = Service.find(params[:id])
> -    
>      @latest_version = @service.latest_version
>      @latest_version_instance = @latest_version.service_versionified
>      
> @@ -58,7 +58,6 @@
>  
>    # GET /services/1/edit
>    def edit
> -    @service = Service.find(params[:id])
>    end
>  
>    # POST /services
> @@ -75,8 +74,6 @@
>    # PUT /services/1
>    # PUT /services/1.xml
>    def update
> -    @service = Service.find(params[:id])
> -
>      respond_to do |format|
>        if @service.update_attributes(params[:service])
>          flash[:notice] = 'Service was successfully updated.'
> @@ -92,7 +89,6 @@
>    # DELETE /services/1
>    # DELETE /services/1.xml
>    def destroy
> -    @service = Service.find(params[:id])
>      @service.destroy
>  
>      respond_to do |format|
> @@ -101,4 +97,10 @@
>      end
>    end
>   
> +  protected
> + 
> +  def find_service
> +    @service = Service.find(params[:id])
> +  end
> + 
>  end
>
>
>         Modified: trunk/app/helpers/application_helper.rb (516 => 517)
>
>
> --- trunk/app/helpers/application_helper.rb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/app/helpers/application_helper.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -1,6 +1,6 @@
>  # BioCatalogue: app/helpers/application_helper.rb
>  #
> -# Copyright (c) 2008, University of Manchester, The European Bioinformatics
> +# Copyright (c) 2008, University of Manchester, The European Bioinformatics 
>  # Institute (EMBL-EBI) and the University of Southampton.
>  # See license.txt for details.
>  
> @@ -117,7 +117,12 @@
>                       :title => tooltip_title_attrib(info_text, delay),
>                       :style => "vertical-align:middle;")
>    end
> -
> +  
> +  
> +  # =======================
> +  # Helpers for Annotations
> +  # -----------------------
> +  
>    # This method is used to generate an icon and/or link that will popup up an in page dialog box for the user to add an annotation (or mutliple annotations at once).
>    #
>    # It takes in the annotatable object that needs to be annotated and some options (all optional):
> @@ -126,7 +131,7 @@
>    #  :tooltip_text - text that will be displayed in a tooltip over the icon/text.
>    #    default: 'Add annotation'
>    #  :style - any CSS inline styles that need to be applied to the icon/text.
> -  #    default: text-decoration: none; (to avoid the icon beeing underlined when used in combination with text)
> +  #    default: text-decoration: none; (to avoid the icon being underlined when used in combination with text)
>    #  :class - any CSS class that need to be applied to the icon/text.
>    #    default: nil
>    #  :link_text - text to be displayed as part of the link.
> @@ -290,6 +295,110 @@
>  
>      return desc
>    end
> +  
> +  # =======================
> +  
> +  # ===============
> +  # Ratings helpers
> +  # ---------------
> +  
> +  # Gets the average rating for a specific item (has to be an annotatable item),
> +  # in the category specified.
> +  # The 'category' is should be the annotation attribute name for that category.
> +  def get_average_rating(annotatable, category)
> +    avg = 0.0
> +    
> +    anns = annotatable.annotations_with_attribute(category)
> +    
> +    unless anns.empty?
> +      # Note: this assumes that the values of the annotations are within constraints (ie: [1,2,3,4,5])
> +      avg = number_with_precision(anns.map{|x| x.value.to_i}.mean, :precision => 1)
> +    end
> +    
> +    return avg.to_f
> +  end
> +  
> +  # Gets the overall average ratings for a specific item (has to be an annotatable item).
> +  # This is the average of all the average ratings of all the categories of ratings for that annotatable model type.
> +  def get_overall_average_rating(annotatable)
> +    avg = 0.0
> +    
> +    ratings = [ ]
> +    
> +    BioCatalogue::Util.get_ratings_categories_config_for_model(annotatable.class).keys.each do |category|
> +      cat_avg = get_average_rating(annotatable, category)
> +      ratings << cat_avg if cat_avg > 0
> +    end
> +    
> +    avg = number_with_precision(ratings.mean, :precision => 1)
> +    
> +    return avg.to_f
> +  end
> +  
> +  def get_users_rating(annotatable, user, category)
> +    rating = 0
> +    
> +    rating_annotation = annotatable.annotations_with_attribute_and_by_source(category, user).first
> +    unless rating_annotation.nil?
> +      # Note: this assumes that the values of the annotations are within constraints (ie: [1,2,3,4,5])
> +      rating = rating_annotation.value.to_i
> +    end
> +    
> +    return rating
> +  end
> +  
> +  def get_count_of_ratings(annotatable, category)
> +    # Note: this assumes that the values of the annotations are within constraints (ie: [1,2,3,4,5])
> +    annotatable.annotations_with_attribute(category).length
> +  end
> +  
> +  def get_overall_count_of_ratings(annotatable)
> +    total_count = 0
> +    
> +    BioCatalogue::Util.get_ratings_categories_config_for_model(annotatable.class).keys.each do |category|
> +      total_count += get_count_of_ratings(annotatable, category)
> +    end
> +    
> +    return total_count
> +  end
> +  
> +  def rating_to_percentage(rating)
> +    return ((rating/5.to_f)*100).round
> +  end
> +  
> +  def render_star_rating_create_link(annotatable, category, rating_level, div_id)
> +    return link_to_remote(rating_level.to_s,
> +                          :url => "#{create_rating_url}?annotatable_type=#{annotatable.class.name}&annotatable_id=#{annotatable.id}&category=#{category}&rating=#{rating_level}",
> +                          :method => :post,
> +                          :update => { :success => div_id, :failure => '' },
> +                          :loading => "Element.show('ratings_spinner')",
> +                          :complete => "Element.hide('ratings_spinner')", 
> +                          :success => "new Effect.Highlight('#{div_id}', { duration: 0.5 });",
> +                          :failure => "Element.hide('ratings_spinner'); alert('Sorry, an error has occurred.');",
> +                          :html => { :class  => "#{rating_level_to_word(rating_level)}-stars", :title => "#{rating_level} star out of 5" } )
> +  end
> +  
> +  def rating_level_to_word(rating_level)
> +    word = ""
> +    
> +    case rating_level
> +      when 1
> +        word = "one"
> +      when 2
> +        word = "two"
> +      when 3
> +        word = "three"
> +      when 4
> +        word = "four"
> +      when 5
> +        word = "five"
> +    end
> +    
> +    return word
> +  end
> +  
> +  # ===============
> +  
>  
>    # ========================================
>    # Code to help with remembering which tab
>
>
>         Modified: trunk/app/models/annotation.rb (516 => 517)
>
>
> --- trunk/app/models/annotation.rb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/app/models/annotation.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -29,6 +29,6 @@
>    protected
>    
>    def sanitise_value
> -    self.value = white_list(self.value)
> +    self.value = white_list(self.value) if self.value.is_a?(String)
>    end
>  end
> \ No newline at end of file
>
>
>         Copied: trunk/app/views/annotations/_ratings_box.html.erb
>         (from rev 516,
>         branches/social/app/views/annotations/_ratings_box.html.erb)
>         (0 => 517)
>
>
> --- trunk/app/views/annotations/_ratings_box.html.erb	                        (rev 0)
> +++ trunk/app/views/annotations/_ratings_box.html.erb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -0,0 +1,101 @@
> +<%
> +
> +# BioCatalogue: app/views/annotations/_ratings_box.html.erb
> +#
> +# Copyright (c) 2008, University of Manchester, The European Bioinformatics 
> +# Institute (EMBL-EBI) and the University of Southampton.
> +# See license.txt for details
> +
> +%>
> +
> +<%# Set defaults for optional parameters to this partial... %>
> +<% div_id_after_ajax_rate = "ratings" unless local_assigns.has_key?(:div_id_after_ajax_rate) %>
> +
> +<div class="box_section">
> +	<p class="heading">
> +		User Ratings
> +		<span class="faded">(<%= get_overall_count_of_ratings(annotatable) -%>)</span>
> +	</p>
> +	
> +	<div class="center">
> +		<% overall_rating = get_overall_average_rating(annotatable) %>
> +		<p class="center" style="font-weight: bold; margin: 0; margin-bottom: 1em;">
> +			<span style="vertical-align: middle;">Overall:</span>
> +			<span class="inline-rating" style="margin-left: 0.5em;">
> +				<ul class="star-rating">
> +					<li class="current-rating" style="width:<%= rating_to_percentage(overall_rating) -%>%;">Currently <%= overall_rating -%>/5 Stars.</li>
> +				</ul>
> +			</span>
> +			
> +			<%= image_tag "spinner.gif", :id => "ratings_spinner", :style => "display: none; vertical-align: middle;" -%>
> +		</p>
> +		
> +		<center>
> +			<table class="ratings_table">
> +				<tr>
> +					<th>&nbsp;</th>
> +					<th>Average</th>
> +					<th>Your Rating</th>
> +				</tr>
> +				<% categories_config.each do |category, cat_data| %>
> +					<% cat_label = cat_data[0]; cat_help_text = cat_data[1]; %>
> +					<tr>
> +						<td style="font-weight: bold; text-align: right;">
> +							<%= h(cat_label) -%>
> +							<span style="margin-left: 0.2em;">
> +								<%= info_icon_with_tooltip(h(cat_help_text)) -%>
> +							</span>
> +						</td>
> +						<td>
> +							<% current_rating = get_average_rating(annotatable, category) %>
> +							<span class="inline-rating">
> +								<ul class="star-rating small-star">
> +									<li class="current-rating" style="width:<%= rating_to_percentage(current_rating) -%>%;">Currently <%= current_rating -%>/5 Stars.</li>
> +								</ul>
> +							</span>
> +							<span class="faded_plus_plus" style="margin-left: 0.2em;">(<%= get_count_of_ratings(annotatable, category) -%>)</span>
> +						</td>
> +						<td class="your_rating">
> +							<% if logged_in? %>
> +								<% users_rating = get_users_rating(annotatable, current_user, category) %>
> +								<span class="inline-rating">
> +									<ul class="star-rating small-star">
> +										<li class="current-rating" style="width:<%= rating_to_percentage(users_rating) -%>%;">Currently <%= users_rating -%>/5 Stars.</li>
> +										<li><%= render_star_rating_create_link(annotatable, category, 1, div_id_after_ajax_rate) -%></li>
> +										<li><%= render_star_rating_create_link(annotatable, category, 2, div_id_after_ajax_rate) -%></li>
> +										<li><%= render_star_rating_create_link(annotatable, category, 3, div_id_after_ajax_rate) -%></li>
> +										<li><%= render_star_rating_create_link(annotatable, category, 4, div_id_after_ajax_rate) -%></li>
> +										<li><%= render_star_rating_create_link(annotatable, category, 5, div_id_after_ajax_rate) -%></li>
> +									</ul>
> +								</span>
> +								
> +								<span class="delete_rating_faded<%= ' delete_rating' if users_rating > 0 -%>">
> +									<% if users_rating > 0 %>
> +										<%= link_to_remote("&nbsp",
> +						                          :url => "#{destroy_rating_url}?annotatable_type=#{annotatable.class.name}&annotatable_id=#{annotatable.id}&category=#{category}",
> +						                          :method => :delete,
> +						                          :update => { :success => div_id_after_ajax_rate, :failure => '' },
> +						                          :loading => "Element.show('ratings_spinner')",
> +						                          :complete => "Element.hide('ratings_spinner')", 
> +						                          :success => "new Effect.Highlight('#{div_id_after_ajax_rate}', { duration: 0.5 });",
> +						                          :failure => "Element.hide('ratings_spinner'); alert('Sorry, an error has occurred.');",
> +						                          :html => { :title => "Delete your rating for this category" },
> +																			:confirm => "Are you sure you want to delete your rating?" ) -%>
> +									<% end %>
> +								</span>
> +							<% else %>
> +								<center><span class="faded">--</span></center>
> +							<% end %>
> +						</td>
> +					</tr>
> +				<% end %>
> +			</table>
> +		</center>
> +		
> +		<% unless logged_in? %>
> +			<div class="footer">
> +				<small><%= link_to "Log in", login_path -%> to rate</small>
> +			</div>
> +		<% end %>
> + 	</div>
> +</div>
> \ No newline at end of file
>
>
>         Modified: trunk/app/views/annotations/_tags_box.html.erb (516
>         => 517)
>
>
> --- trunk/app/views/annotations/_tags_box.html.erb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/app/views/annotations/_tags_box.html.erb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -9,33 +9,34 @@
>  %>
>  
>  <% tag_annotations = annotatable.annotations_with_attribute("tag") %>
> -	<div class="box_info_standout" style="padding: 0.8em 1em; line-height: 1.5;">
> -		<p class="center" style="margin-top: 0; font-weight: bold;">
> -			Tags
> -			<span style="color: #999999;">(<%= tag_annotations.length -%>)</span>
> -		</p>
> -		
> -		<div class="center">
> -			<% unless tag_annotations.empty? %>
> -				<% tags = BioCatalogue::Tags.annotations_to_tags_structure(tag_annotations) %>
> -				<%= generate_tag_cloud(tags, :max_font_size => 20) %>
> +
> +<div class="box_section">
> +	<p class="heading">
> +		Tags
> +		<span class="faded">(<%= tag_annotations.length -%>)</span>
> +	</p>
> +	
> +	<div class="center">
> +		<% unless tag_annotations.empty? %>
> +			<% tags = BioCatalogue::Tags.annotations_to_tags_structure(tag_annotations) %>
> +			<%= generate_tag_cloud(tags, :max_font_size => 20) %>
> +		<% else %>
> +			<span class="none_text">none</span>
> +		<% end %>
> +	</div>
> +	
> +	<div class="footer">
> +		<% if logged_in? %>
> +			<%= annotation_add_by_popup_link annotatable,
> +												 :attribute_name => "Tag",
> +				                             	 :tooltip_text => '',
> +				                             	 :link_text => 'Add tags',
> +				                             	 :icon_filename => 'add_tag.gif', 
> +												 :icon_hover_filename => 'add_tag_hover.gif',
> +				                             	 :show_not_logged_in_text => false,
> +				                             	 :multiple => true -%>
>  			<% else %>
> -				<span class="none_text">none</span>
> +				<small><%= link_to "Log in", login_path -%> to add tags</small>
>  			<% end %>
> -		</div>
> -		
> -		<div class="center" style="margin-top: 1em; border-top: 1px dotted #666666; padding-top: 1em;">
> -			<% if logged_in? %>
> -				<%= annotation_add_by_popup_link annotatable,
> -																			 	 :attribute_name => "Tag",
> -				:tooltip_text => '',
> -				:link_text => 'Add tags',
> -				:icon_filename => 'add_tag.gif', 
> -				:icon_hover_filename => 'add_tag_hover.gif',
> -				:show_not_logged_in_text => false,
> -				:multiple => true -%>
> -		 <% else %>
> -		 	<%= link_to "Log in", login_path -%> to add tags
> -		 <% end %>
> -	 </div>
> -	</div>
> +  </div>
> +</div>
> \ No newline at end of file
>
>
>         Modified: trunk/app/views/layouts/_head.html.erb (516 => 517)
>
>
> --- trunk/app/views/layouts/_head.html.erb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/app/views/layouts/_head.html.erb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -19,6 +19,7 @@
>  	<%= stylesheet_link_tag 'reset-min' %>
>  	<%= stylesheet_link_tag 'styles' %>
>  	<%= stylesheet_link_tag 'redbox' %>
> +	<%= stylesheet_link_tag 'ratings' %>
>  	
>  	<%= javascript_include_tag :defaults %>
>  	
> @@ -31,4 +32,5 @@
>  	<%= render :partial => "layouts/feed_link_tags" %>
>  	<link rel="search" type="application/opensearchdescription+xml" title="BioCatalogue Search" href="/opensearch.xml" />
>  
> +	<%= render :partial => "layouts/head_browser_overrides" -%>
>  </head>	
> \ No newline at end of file
>
>
>         Copied:
>         trunk/app/views/layouts/_head_browser_overrides.html.erb (from
>         rev 516,
>         branches/social/app/views/layouts/_head_browser_overrides.html.erb)
>         (0 => 517)
>
>
> --- trunk/app/views/layouts/_head_browser_overrides.html.erb	                        (rev 0)
> +++ trunk/app/views/layouts/_head_browser_overrides.html.erb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -0,0 +1,17 @@
> +<%
> +
> +# BioCatalogue: app/views/layouts/_head_browser_ovverides.html.erb
> +#
> +# Copyright (c) 2009, University of Manchester, The European Bioinformatics 
> +# Institute (EMBL-EBI) and the University of Southampton.
> +# See license.txt for details
> +
> +%>
> +
> +<!--[if lt IE 7]>  
> +	<style type="text/css" media="screen">  
> +		.ratings_table .your_rating .delete_rating {
> +			background: url('/images/delete.png') no-repeat center;
> +		}
> +	</style>  
> +<![endif]--> 
> \ No newline at end of file
>
>
>         Modified: trunk/app/views/layouts/_head_tabber.html.erb (516
>         => 517)
>
>
> --- trunk/app/views/layouts/_head_tabber.html.erb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/app/views/layouts/_head_tabber.html.erb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -15,12 +15,6 @@
>  %>
>  <script type="text/javascript">
>  
> -/* Optional: Temporarily hide the "tabber" class so it does not "flash"
> -   on the page as plain HTML. After tabber runs, the class is changed
> -   to "tabberlive" and it will appear. */
> -
> -document.write('<style type="text/css">.tabber{display:none;}<\/style>');
> -
>  /*==================================================
>    Set the tabber options (must do this before including tabber.js)
>    ==================================================*/
>
>
>         Modified: trunk/app/views/services/show.html.erb (516 => 517)
>
>
> --- trunk/app/views/services/show.html.erb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/app/views/services/show.html.erb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -24,7 +24,7 @@
>      <h3>Overview</h3>
>  		
>  		<!-- Left column -->
> -		<div style="float: left; width: 70%;">
> +		<div style="float: left; width: 67%;">
>  			<p>
>  				<b>Aliases:</b>
>  				<br/>
> @@ -102,14 +102,21 @@
>  		</div>
>  		
>  		<!-- Right column -->
> -		<div style="float: right; width: 27%;">
> -			<div class="box_info_standout" style="margin-bottom: 1em; font-weight: bold; text-align: center; font-size: 1.2em;">
> +		<div style="float: right; width: 30%;">
> +			<div class="box_section" style="font-size: 115%; font-weight: bold; padding: 0.5em 1em;">
>  				<%= pluralize(total_number_of_annotations_for_service(@service, "User"), "user annotation") + " in total" -%>
>  			</div>
>  				
>  			<%= render :partial => "annotations/tags_box",
>  								 :locals => { :annotatable => @service } -%>
>  			
> +			<div id="ratings">
> +				<%= render :partial => "annotations/ratings_box",
> +								 	 :locals => { :annotatable => @latest_version_instance,
> +																:categories_config => BioCatalogue::Util.get_ratings_categories_config_for_model(@latest_version_instance.class) } -%>
> +			</div>					 
> +			
> +			
>  		</div>
>  		
>  		<span class="clear"></span>	
> @@ -119,3 +126,11 @@
>  					 	 :locals => { :service_version_instance =>  @latest_version_instance } %>
>  
>  </div>
> +
> +<div style="margin-top: 2em; border-top: 2px solid #CCF; padding-top: 1em;">
> +	<h2>Comments</h2>
> +	
> +	<%= disqus_comment_counts -%>
> +	
> +	<%= disqus_thread -%>
> +</div>
>
>
>         Modified: trunk/config/environment.rb (516 => 517)
>
>
> --- trunk/config/environment.rb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/config/environment.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -28,7 +28,9 @@
>    # config.gem "bj"
>    # config.gem "hpricot", :version => '0.6', :source => "http://code.whytheluckystiff.net"
>    # config.gem "aws-s3", :lib => "aws/s3"
> +  config.gem 'disqus', :version => '1.0.1'
>  
> +
>    # Only load the plugins named here, in the order given. By default, all plugins 
>    # in vendor/plugins are loaded in alphabetical order.
>    # :all can be used as a placeholder for all plugins not explicitly named
>
>
>         Modified: trunk/config/initializers/biocat_local.rb.pre (516
>         => 517)
>
>
> --- trunk/config/initializers/biocat_local.rb.pre	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/config/initializers/biocat_local.rb.pre	2009-03-16 17:40:55 UTC (rev 517)
> @@ -26,3 +26,11 @@
>  #are ignored and connection will be made to a server directly. 
>  HTTP_PROXY = true
>  
> +# ====================================================
> +# Configure local settings for the Disqus integration
> +# ----------------------------------------------------
> +
> +Disqus::defaults[:account] = "biocatalogue-test"
> +Disqus::defaults[:developer] = true # allows for threads to work on localhost during dev. Should be set to false on production sites!
> +
> +# ====================================================
>
>
>         Modified: trunk/config/initializers/biocat_main.rb (516 => 517)
>
>
> --- trunk/config/initializers/biocat_main.rb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/config/initializers/biocat_main.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -4,6 +4,9 @@
>  # Institute (EMBL-EBI) and the University of Southampton.
>  # See license.txt for details
>  
> +# Require the extensions to the Array class
> +require 'array' 
> +
>  # Mappings for service types supported, to corresponding model class names.
>  SERVICE_TYPES = {
>    "SOAP Web Service"  => "SoapService",
> @@ -36,14 +39,46 @@
>    @@per_page = 10
>  end
>  
> -# ==========
> -# Configure the Annotations plugin...
> -# ----------
>  
> +# ================================
> +# Configure the Annotations plugin
> +# --------------------------------
> +
>  # Remember that all attribute names specified MUST be in lowercase
>  
>  Annotations::Config.attribute_names_for_values_to_be_downcased.concat([ "tag" ])
>  
>  Annotations::Config.strip_text_rules.update({ "tag" => [ '"' ] })
>  
> -# ==========
> +Annotations::Config.limits_per_source = { "rating.speed" => [ 1, true ],
> +                                          "rating.reliability" => [ 1, true ],
> +                                          "rating.ease-of-use" => [ 1, true ] }
> +
> +# ================================
> +
> +
> +# ====================================================
> +# Configure global settings for the Disqus integration
> +# ----------------------------------------------------
> +
> +Disqus::defaults[:avatar_size] = 48
> +Disqus::defaults[:color] = "green"
> +Disqus::defaults[:default_tab] = "recent"
> +Disqus::defaults[:num_items] = 15
> +
> +# ====================================================
> +
> +
> +# ================================
> +# Ratings categories configuration
> +# --------------------------------
> +
> +# These take the form:
> +# { rating_annotation_attribute_name => [ visible_name, help_text ] }
> +
> +SERVICE_RATINGS_CATEGORIES = { "rating.speed" => [ "Speed", "Rate how fast this service has been for you" ],
> +                               "rating.reliability" => [ "Reliability", "Rate how reliable this service has been for you" ],
> +                               "rating.ease-of-use" => [ "Ease of Use", "Rate how easy this service has been to use for you" ],
> +                               "rating.documentation" => [ "Documentation",  "Rate the level and usefulness of documentation you feel this service has" ] }
> +
> +# ================================
> \ No newline at end of file
>
>
>         Modified: trunk/config/routes.rb (516 => 517)
>
>
> --- trunk/config/routes.rb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/config/routes.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -16,6 +16,10 @@
>    map.tags_auto_complete '/tags/auto_complete', :controller => 'tags', :action => 'auto_complete', :conditions => { :method => :get }
>    map.tag_show '/tags/:tag', :controller => 'tags', :action => 'show', :conditions => { :method => :get }
>  
> +  # Ratings
> +  map.create_rating '/ratings', :controller => 'ratings', :action => 'create', :conditions => { :method => :post }
> +  map.destroy_rating '/ratings', :controller => 'ratings', :action => 'destroy', :conditions => { :method => :delete }
> +  
>    # Search
>    map.search '/search', :controller => 'search', :action => 'show'
>    map.connect '/search.:format', :controller => 'search', :action => 'show'
>
>
>         Copied: trunk/lib/array.rb (from rev 516,
>         branches/social/lib/array.rb) (0 => 517)
>
>
> --- trunk/lib/array.rb	                        (rev 0)
> +++ trunk/lib/array.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -0,0 +1,18 @@
> +# BioCatalogue: app/lib/array.rb
> +
> +# From: http://snippets.dzone.com/posts/show/2161
> +
> +class Array
> +  def extract(sym)
> +    map { |e| e.send(sym) }
> +  end
> +  
> +  # Already in Rails:
> +  # def sum
> +  #   inject(0) { |sum,x| sum+x }
> +  # end
> +  
> +  def mean
> +    (size > 0) ? sum.to_f / size : 0
> +  end
> +end
> \ No newline at end of file
>
>
>         Modified: trunk/lib/util.rb (516 => 517)
>
>
> --- trunk/lib/util.rb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/lib/util.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -209,5 +209,19 @@
>        
>        return annotations_data
>      end
> +    
> +    # Helper method to get the ratings categories configuration hash for a specific model type.
> +    # This acts as a lookup table for ratings configuration to models and allows us to maintain different
> +    # ratings configurations for different models.
> +    def self.get_ratings_categories_config_for_model(model)
> +      ratings_config = { }
> +      
> +      case model.name
> +        when "Service", "SoapService", "RestService"  
> +          ratings_config = SERVICE_RATINGS_CATEGORIES
> +      end
> +      
> +      return ratings_config
> +    end
>    end
>  end
> \ No newline at end of file
>
>
>         Copied: trunk/public/images/box-bg1.png (from rev 516,
>         branches/social/public/images/box-bg1.png)
>
>
> (Binary files differ)
>
>
>         Copied: trunk/public/images/delete.png (from rev 516,
>         branches/social/public/images/delete.png)
>
>
> (Binary files differ)
>
>
>         Copied: trunk/public/images/delete_faded.png (from rev 516,
>         branches/social/public/images/delete_faded.png)
>
>
> (Binary files differ)
>
>
>         Copied: trunk/public/images/star.gif (from rev 516,
>         branches/social/public/images/star.gif)
>
>
> (Binary files differ)
>
>
>         Copied: trunk/public/images/star_small.gif (from rev 516,
>         branches/social/public/images/star_small.gif)
>
>
> (Binary files differ)
>
>
>         Copied: trunk/public/stylesheets/ratings.css (from rev 516,
>         branches/social/public/stylesheets/ratings.css) (0 => 517)
>
>
> --- trunk/public/stylesheets/ratings.css	                        (rev 0)
> +++ trunk/public/stylesheets/ratings.css	2009-03-16 17:40:55 UTC (rev 517)
> @@ -0,0 +1,95 @@
> + at charset "utf-8";
> +/**
> + * BioCatalogue: app/public/stylesheets/ratings.css
> + *
> + * Copyright (c) 2009, University of Manchester, The European Bioinformatics 
> + * Institute (EMBL-EBI) and the University of Southampton.
> + * See license.txt for details
> + */
> +
> +/* Mostly based on: http://www.komodomedia.com/blog/2007/01/css-star-rating-redux */
> +
> +.star-rating,
> +.star-rating a:hover,
> +.star-rating a:active,
> +.star-rating a:focus,
> +.star-rating .current-rating{
> +	background: url(/images/star.gif) left -1000px repeat-x;
> +}
> +.star-rating{
> +	position:relative;
> +	width:150px;
> +	height:30px;
> +	overflow:hidden;
> +	list-style:none;
> +	margin:0;
> +	padding:0;
> +	background-position: left top;
> +}
> +.star-rating li{
> +	display: inline;
> +}
> +.star-rating a, 
> +.star-rating .current-rating{
> +	position:absolute;
> +	top:0;
> +	left:0;
> +	text-indent:-1000em;
> +	height:30px;
> +	line-height:30px;
> +	outline:none;
> +	overflow:hidden;
> +	border: none;
> +}
> +.star-rating a:hover,
> +.star-rating a:active,
> +.star-rating a:focus{
> +	background-position: left bottom;
> +}
> +.star-rating a.one-stars{
> +	width:20%;
> +	z-index:6;
> +}
> +.star-rating a.two-stars{
> +	width:40%;
> +	z-index:5;
> +}
> +.star-rating a.three-stars{
> +	width:60%;
> +	z-index:4;
> +}
> +.star-rating a.four-stars{
> +	width:80%;
> +	z-index:3;
> +}
> +.star-rating a.five-stars{
> +	width:100%;
> +	z-index:2;
> +}
> +.star-rating .current-rating{
> +	z-index:1;
> +	background-position: left center;
> +}	
> +
> +/* for an inline rater */
> +.inline-rating{
> +	display:-moz-inline-block;
> +	display:-moz-inline-box;
> +	display:inline-block;
> +	vertical-align: middle;
> +}
> +
> +/* smaller star */
> +.small-star{
> +	width:50px;
> +	height:10px;
> +}
> +.small-star,
> +.small-star a:hover,
> +.small-star a:active,
> +.small-star a:focus,
> +.small-star .current-rating{
> +	background-image: url(/images/star_small.gif);
> +	line-height: 10px;
> +	height: 10px;
> +}
>
>
>         Modified: trunk/public/stylesheets/styles.css (516 => 517)
>
>
> --- trunk/public/stylesheets/styles.css	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/public/stylesheets/styles.css	2009-03-16 17:40:55 UTC (rev 517)
> @@ -1,8 +1,8 @@
>  @charset "utf-8";
>  /**
> - * BioCatalogue: app/public/stylesheets/styles_2.css
> + * BioCatalogue: app/public/stylesheets/styles.css
>   *
> - * Copyright (c) 2008, University of Manchester, The European Bioinformatics 
> + * Copyright (c) 2009, University of Manchester, The European Bioinformatics 
>   * Institute (EMBL-EBI) and the University of Southampton.
>   * See license.txt for details
>   */
> @@ -207,6 +207,7 @@
>  
>  hr {
>    margin: 0.5em 0;
> +	*margin: 0;
>    padding: 0;
>    border: none;
>    height: 1px;
> @@ -251,6 +252,18 @@
>  	line-height: 2.0;
>  }
>  
> +.faded {
> +	color: #999;
> +}
> +
> +.faded_plus {
> +	color: #AAA;
> +}
> +
> +.faded_plus_plus {
> +	color: #BBB;
> +}
> +
>  .green_box {
>  	border: 1px dotted #999999;
>  	background-color: #e9f7cc;
> @@ -1439,5 +1452,93 @@
>  .tag_cloud .tag {
>  	margin: 0 0.3em;
>  }
> -/* END tag cloud styles
> - */
> \ No newline at end of file
> +
> +/* END tag cloud styles */
> +
> +/* BEGIN Section Boxes (usually for inner sidebars) */
> +
> +.box_section {
> +	background-image: url('/images/box-bg1.png');
> +	background-position: top;
> +	background-repeat: repeat-x;
> +	background-color: #FFC;
> +	padding: 0.3em 0.3em;
> +	border: 1px dotted #DDD;
> +	text-align: center;
> +	margin-bottom: 1em;
> +	padding: 0.8em 1em; 
> +	line-height: 1.5;
> +}
> +
> +.box_section .heading {
> +	font-size: 110%;
> +	font-weight: bold;
> +	line-height: 1.0;
> +	margin-top: 0.2em;
> +}
> +
> +.box_section .footer {
> +	text-align: center;
> +	margin-top: 1em; 
> +	border-top: 1px dotted #CCC; 
> +	padding-top: 0.7em;
> +}
> +
> +/* END Section Boxes (usually for inner sidebars) */
> +
> + 
> +/* BEGIN ratings table styles */
> +
> +.ratings_table {
> +	border: 1px solid #cccccc;
> +	margin-bottom: 0.5em;
> +	background-color: #FFC;
> +}
> +
> +.ratings_table th {
> +	font-weight: bold;
> +	white-space: nowrap;
> +	vertical-align: middle;
> +	color: #333333;
> +	height: 2em;
> +	background: url(../images/box_title_bkgd_green_14.gif) repeat-x;
> +	background-position: bottom;
> +	padding-left: 6px;
> +	padding-right: 6px;
> +	border-right: 1px solid #cccccc;
> +	text-align: center;
> +}
> +
> +.ratings_table td {
> +	white-space: nowrap;
> +	padding: 4px 6px 4px 6px;
> +	border-left: 1px solid #cccccc;
> +	border-right: 1px solid #cccccc;
> +	vertical-align: middle;
> +	text-align: center;
> +}
> +
> +.ratings_table tr:hover {
> +	background-color: #F7F7F7;
> +}
> +
> +.ratings_table .your_rating .delete_rating_faded {
> +	width: 10px;
> +	height: 10px;
> +	margin-left: 0.5em;
> +	vertical-align: middle;
> +	display:-moz-inline-block;
> +	display:-moz-inline-box;
> +	display: inline-block;
> +	background: url('/images/delete_faded.png') no-repeat center;
> +}
> +
> +.ratings_table .your_rating .delete_rating a {
> +	text-decoration: none;	
> +}
> +
> +.ratings_table .your_rating:hover .delete_rating {
> +	background: url('/images/delete.png') no-repeat center;
> +}
> +
> +/* END ratings table styles */
> \ No newline at end of file
>
>
>         Copied: trunk/test/functional/ratings_controller_test.rb (from
>         rev 516,
>         branches/social/test/functional/ratings_controller_test.rb) (0
>         => 517)
>
>
> --- trunk/test/functional/ratings_controller_test.rb	                        (rev 0)
> +++ trunk/test/functional/ratings_controller_test.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -0,0 +1,45 @@
> +require 'test_helper'
> +
> +class RatingsControllerTest < ActionController::TestCase
> +  test "should get index" do
> +    get :index
> +    assert_response :success
> +    assert_not_nil assigns(:ratings)
> +  end
> +
> +  test "should get new" do
> +    get :new
> +    assert_response :success
> +  end
> +
> +  test "should create rating" do
> +    assert_difference('Rating.count') do
> +      post :create, :rating => { }
> +    end
> +
> +    assert_redirected_to rating_path(assigns(:rating))
> +  end
> +
> +  test "should show rating" do
> +    get :show, :id => ratings(:one).id
> +    assert_response :success
> +  end
> +
> +  test "should get edit" do
> +    get :edit, :id => ratings(:one).id
> +    assert_response :success
> +  end
> +
> +  test "should update rating" do
> +    put :update, :id => ratings(:one).id, :rating => { }
> +    assert_redirected_to rating_path(assigns(:rating))
> +  end
> +
> +  test "should destroy rating" do
> +    assert_difference('Rating.count', -1) do
> +      delete :destroy, :id => ratings(:one).id
> +    end
> +
> +    assert_redirected_to ratings_path
> +  end
> +end
>
>
>         Modified:
>         trunk/vendor/plugins/annotations/lib/annotations/acts_as_annotatable.rb
>         (516 => 517)
>
>
> --- trunk/vendor/plugins/annotations/lib/annotations/acts_as_annotatable.rb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/vendor/plugins/annotations/lib/annotations/acts_as_annotatable.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -22,7 +22,8 @@
>        # Class methods added to the model that has been made acts_as_annotatable (the mixing annotatable type).
>        module SingletonMethods
>          # Helper finder to get all objects of the mixin annotatable type that have the specified attribute name and value.
> -        # Note: both the attribute name and the value will be treated case insensitively.
> +        # NOTE (1): both the attribute name and the value will be treated case insensitively.
> +        # NOTE (2): the objects returned are Read Only.
>          def with_annotations_with_attribute_name_and_value(attribute_name, value)
>            return [ ] if attribute_name.blank? or value.nil?
>            
> @@ -74,19 +75,45 @@
>                            :limit => limit)
>          end
>          
> -        # Finder to get annotations with a specific attribute
> +        # Finder to get annotations with a specific attribute.
> +        # The input parameter is the attribute name 
> +        # (either a String or a Symbol representing the attribute's name).
> +        # NOTE: the objects returned are Read Only.
>          def annotations_with_attribute(attrib)
>            return [] if attrib.blank?
>            
> +          attrib = attrib.strip.downcase if attrib.is_a? String
> +          
>            Annotation.find(:all,
>                            :joins => "JOIN annotation_attributes ON annotations.attribute_id = annotation_attributes.id",
>                            :conditions => [ "annotations.annotatable_type = ? AND annotations.annotatable_id = ? AND annotation_attributes.name = ?", 
>                                             ActiveRecord::Base.send(:class_name_of_active_record_descendant, self.class).to_s, 
>                                             id,
> -                                           attrib.strip.downcase ],
> +                                           attrib ],
>                            :order => "created_at DESC")
>          end
>          
> +        # Finder to get annotations with a specific attribute by a specific source.
> +        # The first input parameter is the attribute name 
> +        # (either a String or a Symbol representing the attribute's name).
> +        # The second input is the source.
> +        # NOTE: the objects returned are Read Only.
> +        def annotations_with_attribute_and_by_source(attrib, source)
> +          return [] if attrib.blank? or source.nil?
> +          
> +          attrib = attrib.strip.downcase if attrib.is_a? String
> +          
> +          Annotation.find(:all,
> +                          :joins => "JOIN annotation_attributes ON annotations.attribute_id = annotation_attributes.id",
> +                          :conditions => [ "annotations.annotatable_type = ? AND annotations.annotatable_id = ? AND annotations.source_type = ? AND annotations.source_id = ? AND annotation_attributes.name = ?", 
> +                                           ActiveRecord::Base.send(:class_name_of_active_record_descendant, self.class).to_s, 
> +                                           id,
> +                                           source.class.name,
> +                                           source.id,
> +                                           attrib ],
> +                          :order => "created_at DESC")
> +        end
> +        
>          def annotatable_name
>            %w{ name title }.each do |w|
>              return eval("self.#{w}") if self.respond_to?(w)
>
>
>         Modified:
>         trunk/vendor/plugins/annotations/lib/annotations/config.rb
>         (516 => 517)
>
>
> --- trunk/vendor/plugins/annotations/lib/annotations/config.rb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/vendor/plugins/annotations/lib/annotations/config.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -13,20 +13,32 @@
>      # This defines a hash of attributes, and the characters/strings that need to be stripped (removed) out of values of the attributes specified.
>      # Regular expressions can also be used instead of characters/strings.
>      # ie: { attribute => [ array of characters to strip out ] }    (note: doesn't have to be an array, can be a single string)
> +    #
>      # e.g: { "tag" => [ '"', ','] } or { "tag" => '"' }
>      # 
> -    # NOTE: The attribute names specified MUST all be in lowercase.    
> +    # NOTE: The attribute name(s) specified MUST all be in lowercase.  
>      @@strip_text_rules = { }
>      
>      # This allows you to specify a different model name for users in the system (if different from the default: "User").
>      @@user_model_name = "User"
>      
> +    # This allows you to limit the number of annotations (of specified attribute names) per source per annotatable.
> +    # Key/value pairs in hash should follow the spec:
> +    # { :attribute_name => [ max_number_allowed, should_replace_existing? ] }
> +    #
> +    # e.g: { "rating" => [ 1, true ] } will only ever allow 1 "rating" annotation per annotatable by each source.
> +    #
> +    # NOTE (1): The attribute name(s) specified MUST all be in lowercase.
> +    # NOTE (2): The should_replace_existing? option is only used if the max_number_allowed is set to 1.
> +    @@limits_per_source = { }
> +    
>      # This makes the variables above available externally.
>      # Shamelessly borrowed from GeoKit.
>      [ :attribute_names_for_values_to_be_downcased,
>        :attribute_names_for_values_to_be_upcased,
>        :strip_text_rules,
> -      :user_model_name ].each do |sym|
> +      :user_model_name,
> +      :limits_per_source ].each do |sym|
>        class_eval <<-EOS, __FILE__, __LINE__
>          def self.#{sym}
>            if defined?(#{sym.to_s.upcase})
>
>
>         Modified:
>         trunk/vendor/plugins/annotations/lib/app/models/annotation.rb
>         (516 => 517)
>
>
> --- trunk/vendor/plugins/annotations/lib/app/models/annotation.rb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/vendor/plugins/annotations/lib/app/models/annotation.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -7,6 +7,8 @@
>    
>    before_save :process_value_adjustments
>    
> +  before_save :check_limits
> +  
>    belongs_to :annotatable, 
>               :polymorphic => true
>    
> @@ -58,7 +60,8 @@
>    # ========================
>    
>    # Returns all the annotatable objects that have a specified attribute name and value.
> -  # Note: both the attribute name and the value will be treated case insensitively.
> +  # NOTE (1): both the attribute name and the value will be treated case insensitively.
> +  # NOTE (2): the objects returned are Read Only.
>    def self.find_annotatables_with_attribute_name_and_value(attribute_name, value)
>      return [ ] if attribute_name.blank? or value.nil?
>      
> @@ -155,13 +158,14 @@
>    end
>    
>    def process_value_adjustments
> +    attr_name = self.attribute_name.downcase
>      # Make lowercase or uppercase if required
> -    self.value.downcase! if Annotations::Config::attribute_names_for_values_to_be_downcased.include?(self.attribute_name.downcase)
> -    self.value.upcase! if Annotations::Config::attribute_names_for_values_to_be_upcased.include?(self.attribute_name.downcase)
> +    self.value.downcase! if Annotations::Config::attribute_names_for_values_to_be_downcased.include?(attr_name)
> +    self.value.upcase! if Annotations::Config::attribute_names_for_values_to_be_upcased.include?(attr_name)
>      
>      # Apply strip text rules
>      Annotations::Config::strip_text_rules.each do |attr, strip_rules|
> -      if self.attribute_name.downcase == attr.downcase
> +      if attr_name == attr.downcase
>          if strip_rules.is_a? Array
>            strip_rules.each do |s|
>              self.value = self.value.gsub(s, '')
> @@ -172,4 +176,57 @@
>        end
>      end
>    end
> +  
> +  # This method uses the limits_per_source config setting
> +  # to check whether a limit has been reached and takes appropriate action if it has.
> +  # If a limit has been reach and the limit is 1 and the replace existing otion is true, 
> +  # it will overwrite the value of the existing annotation and then stop the save procedure. 
> +  # Otherwise it will just stop the save procedure.
> +  def check_limits
> +    attr_name = self.attribute_name.downcase
> +    if Annotations::Config::limits_per_source.has_key?(attr_name)
> +      options = Annotations::Config::limits_per_source[attr_name]
> +      max = options[0]
> +      can_replace = options[1]
> +      
> +      unless (found_annotatable = Annotation.find_annotatable(self.annotatable_type, self.annotatable_id)).nil?
> +        anns = found_annotatable.annotations_with_attribute_and_by_source(attr_name, self.source)
> +        
> +        # If this annotation is being updated (not created), remove it from the anns collection.
> +        # This prevents an infinite loop when an existing annotation is being updated as further below.
> +        unless self.new_record?
> +          anns.each do |a|
> +            anns.delete(a) if a.id == self.id
> +          end
> +        end
> +      
> +        if anns.length >= max
> +          # Only update an existing annotation if the limit is 1, AND 
> +          # only one existing was found (it's possible that this config was introduced afterwards 
> +          # in a situation where the limit has already been surpassed previously, so we need this check), AND
> +          # the config option says that we can replace it. 
> +          if max == 1 && anns.length == 1 && can_replace
> +            ann = anns[0]
> +            
> +            # Because the object is read only, load it up again.
> +            ann2 = Annotation.find(ann.id)
> +            
> +            ann2.value = self.value
> +            ann2.save
> +            self.errors.add_to_base("The limit has been reached for annotations with this attribute and by this source. The existing annotation has been updated.")
> +          else
> +            self.errors.add_to_base("The limit has been reached for annotations with this attribute and by this source. No further action has been taken.")
> +          end
> +          
> +          return false
> +        else
> +          return true
> +        end
> +      else
> +        return true
> +      end
> +    else
> +      return true
> +    end
> +  end
>  end
> \ No newline at end of file
>
>
>         Modified:
>         trunk/vendor/plugins/annotations/test/acts_as_annotatable_test.rb
>         (516 => 517)
>
>
> --- trunk/vendor/plugins/annotations/test/acts_as_annotatable_test.rb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/vendor/plugins/annotations/test/acts_as_annotatable_test.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -48,6 +48,13 @@
>      assert_equal 1, chapters(:br_c202).annotations_with_attribute("Title").length
>    end
>    
> +  def test_annotations_with_attribute_and_by_source_instance_method
> +    assert_equal 1, books(:h).annotations_with_attribute_and_by_source("tag", users(:jane)).length
> +    assert_equal 0, books(:r).annotations_with_attribute_and_by_source("doesnt_exist", users(:jane)).length
> +    assert_equal 1, chapters(:bh_c10).annotations_with_attribute_and_by_source("endingType", groups(:sci_fi_geeks)).length
> +    assert_equal 1, chapters(:br_c202).annotations_with_attribute_and_by_source("Title", users(:john)).length
> +  end
> +  
>    def test_annotatable_name_instance_method
>      assert_equal "Learning Ruby in 2 Seconds", books(:r).annotatable_name
>      assert_equal "Hashing It Up", chapters(:br_c2).annotatable_name
>
>
>         Modified: trunk/vendor/plugins/annotations/test/config_test.rb
>         (516 => 517)
>
>
> --- trunk/vendor/plugins/annotations/test/config_test.rb	2009-03-16 17:05:42 UTC (rev 516)
> +++ trunk/vendor/plugins/annotations/test/config_test.rb	2009-03-16 17:40:55 UTC (rev 517)
> @@ -5,12 +5,14 @@
>      Annotations::Config.attribute_names_for_values_to_be_downcased = [ "downcased_thing" ]
>      Annotations::Config.attribute_names_for_values_to_be_upcased = [ "upcased_thing" ]
>      Annotations::Config.strip_text_rules = { "tag" => [ '"', ',' ], "comma_stripped" => ',', "regex_strip" => /\d/ }
> +    Annotations::Config.limits_per_source = { "rating" => [ 1, true ] }
>    end
>    
>    def teardown
>      Annotations::Config.attribute_names_for_values_to_be_downcased = [ ]
>      Annotations::Config.attribute_names_for_values_to_be_upcased = [ "upcased_thing" ]
>      Annotations::Config.strip_text_rules = { }
> +    Annotations::Config.limits_per_source = { }
>    end
>    
>    def test_values_downcased_or_upcased
> @@ -104,4 +106,33 @@
>      assert_valid ann4
>      assert_equal 'v,al"ue', ann4.value
>    end
> +  
> +  def test_limits_per_source
> +    source = users(:john)
> +    
> +    bk = Book.create
> +    
> +    ann1 = bk.annotations << Annotation.new(:attribute_name => "rating", 
> +                                    :value => 4, 
> +                                    :source_type => source.class.name, 
> +                                    :source_id => source.id)
> +    
> +    assert_not_nil ann1
> +    assert_equal 1, bk.annotations.length
> +    
> +    ann2 = bk.annotations << Annotation.new(:attribute_name => "rating", 
> +                                    :value => 1, 
> +                                    :source_type => source.class.name, 
> +                                    :source_id => source.id)
> +    
> +    assert_not_nil ann2
> +    
> +    # Need to reload annotations collection
> +    bk.annotations(true)
> +    
> +    assert_equal 1, bk.annotations.length
> +    
> +    # Check that two versions of the annotation now exist
> +    assert_equal 2, bk.annotations[0].versions.length
> +  end
>  end
> \ No newline at end of file
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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  Tue Mar 17 09:49:52 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 17 Mar 2009 09:49:52 -0400 (EDT)
Subject: [BioCatalogue-developers] [520] trunk/lib/util.rb: Task 2574: REST
 services are now shown in search results.
Message-ID: <20090317134952.9D06A18580F7@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 17 09:55:35 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 17 Mar 2009 09:55:35 -0400 (EDT)
Subject: [BioCatalogue-developers] [521]
	trunk/app/views/search/show.xml.builder: Fix for Search API.
Message-ID: <20090317135535.7836B18580F7@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 17 10:01:24 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 17 Mar 2009 10:01:24 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2574] Implement search retrieval
	for REST services
Message-ID: <20090317140124.4615018580F7@rubyforge.org>

Task #2574 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Implement search retrieval for REST services
Complete: 100%
Status: Closed

Description: This requires modifying the methods in the Util library to add logic for REST models.

Follow-Ups:

-------------------------------------------------------
Date: 2009-03-17 14:01
By: jits

Comment:
Done

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2574&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Wed Mar 18 08:09:43 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 18 Mar 2009 08:09:43 -0400 (EDT)
Subject: [BioCatalogue-developers] [522] trunk: record status of pinging the
	hosts of service endpoints
Message-ID: <20090318120943.7A85D18580E3@rubyforge.org>

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From noreply at rubyforge.org  Wed Mar 18 10:41:28 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 18 Mar 2009 10:41:28 -0400 (EDT)
Subject: [BioCatalogue-developers] [523]
 trunk/record_service_deployment_status.rb: removed inconsistent comments in
 script
Message-ID: <20090318144128.B301918580EE@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 19 07:28:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 19 Mar 2009 07:28:09 -0400 (EDT)
Subject: [BioCatalogue-developers] [524] trunk/public/images: new icons for
	user profile pages
Message-ID: <20090319112809.456DB18580ED@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 19 07:29:23 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 19 Mar 2009 07:29:23 -0400 (EDT)
Subject: [BioCatalogue-developers] [525] trunk/config/routes.rb: define the
	route for change_password action
Message-ID: <20090319112923.A246818580ED@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 19 07:30:15 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 19 Mar 2009 07:30:15 -0400 (EDT)
Subject: [BioCatalogue-developers] [526]
	trunk/app/controllers/users_controller.rb: add
	change_password action
Message-ID: <20090319113015.7E80918580F0@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 19 07:32:30 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 19 Mar 2009 07:32:30 -0400 (EDT)
Subject: [BioCatalogue-developers] [527]
 trunk/app/views/users/change_password.html.erb: add view for
 change_password action
Message-ID: <20090319113230.34EDA18580ED@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 19 07:34:32 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 19 Mar 2009 07:34:32 -0400 (EDT)
Subject: [BioCatalogue-developers] [528]
 trunk/public/stylesheets/styles.css: added some new links styles and
 modified some error related styles
Message-ID: <20090319113432.BBDEF18580ED@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 19 07:35:25 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 19 Mar 2009 07:35:25 -0400 (EDT)
Subject: [BioCatalogue-developers] [529] trunk/app/views/users: slight UI
	changes
Message-ID: <20090319113525.6EA2A18580ED@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 19 07:36:03 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 19 Mar 2009 07:36:03 -0400 (EDT)
Subject: [BioCatalogue-developers] [530]
 trunk/app/views/home/index.html.erb: makes nb of users and services bold
Message-ID: <20090319113603.9D6B518580F0@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 19 09:57:10 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 19 Mar 2009 09:57:10 -0400 (EDT)
Subject: [BioCatalogue-developers] [531] trunk: - Fixed a bug in the tags
 business logic library to properly set limit on tags .
Message-ID: <20090319135711.0463318580ED@rubyforge.org>

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From noreply at rubyforge.org  Fri Mar 20 13:21:49 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 20 Mar 2009 13:21:49 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2582] Store extra log info during
	searches
Message-ID: <20090320172149.672941858102@rubyforge.org>

Task #2582 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Store extra log info during searches
Complete: 0%
Status: Open

Description: Add search results count and any other info to ActivityLog after search...

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2582&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Mar 26 08:09:15 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Mar 2009 08:09:15 -0400 (EDT)
Subject: [BioCatalogue-developers] [532] trunk: set ping status to unknown
	for newly registered services.
Message-ID: <20090326120915.7C51415B8028@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 26 08:17:02 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Mar 2009 08:17:02 -0400 (EDT)
Subject: [BioCatalogue-developers] [533] trunk/tmp/tuneup/: Removed folder
 in / tmp that was mistakenly committed to repo.
Message-ID: <20090326121702.F122715B8026@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 26 08:19:05 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Mar 2009 08:19:05 -0400 (EDT)
Subject: [BioCatalogue-developers] [534] trunk/tmp/: Added /tmp/tuneup to
 svn:ignore so it' s not committed to repo again.
Message-ID: <20090326121905.B20E515B801F@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 26 08:22:37 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Mar 2009 08:22:37 -0400 (EDT)
Subject: [BioCatalogue-developers] [535]
	trunk/app/views/services/show.html.erb: Fixed typo
Message-ID: <20090326122237.A704315B801F@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 26 08:42:11 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Mar 2009 08:42:11 -0400 (EDT)
Subject: [BioCatalogue-developers] [536] trunk: Tweaks and small
	refactorings for tag clouds.
Message-ID: <20090326124212.34D9F197858F@rubyforge.org>

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From noreply at rubyforge.org  Thu Mar 26 08:42:23 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Mar 2009 08:42:23 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2480] Allow tags during service
	submission
Message-ID: <20090326124223.ABFFF15B801F@rubyforge.org>

Task #2480 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Allow tags during service submission
Complete: 100%
Status: Closed

Description: This needs to use the special way of creating multiple annotations from one value.

Follow-Ups:

-------------------------------------------------------
Date: 2009-03-26 12:42
By: jits

Comment:
Done

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2480&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Mar 26 08:45:07 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Mar 2009 08:45:07 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2594] Tag frequency count fix for
	tags_box partial
Message-ID: <20090326124507.289FC15B801F@rubyforge.org>

Task #2594 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Tag frequency count fix for tags_box partial
Complete: 0%
Status: Open

Description: The partial annotations/_tags_box will currently only get a count of 1 per tag so all tags will be of the same size.

In myexperiment, the size of the tag, even on individual tag clouds, always represents the frequency of that tag word on the whole site. Maybe this should be the same for the partial.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2594&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Mar 26 09:29:01 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Mar 2009 09:29:01 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2595] Sourcing tags from ontology
Message-ID: <20090326132901.12AD115B801F@rubyforge.org>

Task #2595 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Sourcing tags from ontology 
Complete: 0%
Status: Open

Description: Sourcing tags from the myGrid ontology. This is the first step toward semantic annotation of web services.  

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2595&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Mar 26 10:53:14 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Mar 2009 10:53:14 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2596] 20 q: 1-number & type of
	service for a given provider
Message-ID: <20090326145315.0DBBB185810D@rubyforge.org>

Task #2596 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: 20 q: 1-number & type of service for a given provider
Complete: 0%
Status: Open

Description: How many services has provider X? ?currently implemented but need to make sure it clear enough for users? How many of those are REST? How many of those are SOAP? ?different type of services should be clear on the site and users should know the number of each type after a search. 

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2596&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Mar 26 10:56:22 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Mar 2009 10:56:22 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2597] 20 q: 2-number of submitter
	a given provider
Message-ID: <20090326145622.58A261858111@rubyforge.org>

Task #2597 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: 20 q: 2-number of submitter a given provider
Complete: 0%
Status: Open

Description: How many submitters does provider X have??number of submitter from a provider must be clear

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2597&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Mar 26 10:58:03 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Mar 2009 10:58:03 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2598] 20 q: 3- reliability profile
	of a service
Message-ID: <20090326145803.0FD2615B801F@rubyforge.org>

Task #2598 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: 20 q: 3- reliability profile of a service
Complete: 0%
Status: Open

Description: What is the reliability profile of service X? Can I see the usage history of service X? who is the provider? is it free? Each service should have a profile (reliability, history of use, free, licenses etc) 

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2598&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Mar 26 11:00:15 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Mar 2009 11:00:15 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2599] 20 q: 4- recently registered
	or updated services
Message-ID: <20090326150015.5E967185810D@rubyforge.org>

Task #2599 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: 20 q: 4- recently  registered or updated services
Complete: 0%
Status: Open

Description: Which are the most recently updated services? Which are the most recently registered services? Most search services? ?possibility to filter services based on these factors.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2599&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Mar 26 11:58:12 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Mar 2009 11:58:12 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2600] Add on-mouse-over message to
	service status icons
Message-ID: <20090326155812.F385E197859F@rubyforge.org>

Task #2600 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Add on-mouse-over message to service status icons
Complete: 0%
Status: Open

Description: get info to display over that icon by setting the HTML "title" attribute to the returned contents of the "tooltip_title_attrib(..)" method in the application helper.

(This uses a tooltip JS library to create the popup tooltip).

E.g:

<%= image_tag("success_icon.png", :title => tooltip_title_attrib("This service is alive! [Last checked: xxxxx]")) -%>

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2600&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Mar 26 12:23:20 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 26 Mar 2009 12:23:20 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2601] Remove resolr.rb script
Message-ID: <20090326162320.7FB3A15B8022@rubyforge.org>

Task #2601 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Remove resolr.rb script
Complete: 0%
Status: Open

Description: The resolr.rb script is outdated and not the recommended method anymore - the recommended method to reindex is using the rake task. See: http://www.ebi.ac.uk/ebiwiki/biocatalogue/doku.php?id=development:pilot_dev_notes#search_server_solr for more info.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2601&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Fri Mar 27 09:38:22 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 27 Mar 2009 09:38:22 -0400 (EDT)
Subject: [BioCatalogue-developers] [537]
 trunk/app/views/annotations/_tags_flat.html.erb: Improvements for tags in
 service listings.
Message-ID: <20090327133822.F099318580E9@rubyforge.org>

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From noreply at rubyforge.org  Fri Mar 27 10:24:07 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 27 Mar 2009 10:24:07 -0400 (EDT)
Subject: [BioCatalogue-developers] [538] trunk: Initial work on facets -
 service types and service providers breakdowns now show on service index
 page .
Message-ID: <20090327142407.320E715B801E@rubyforge.org>

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From noreply at rubyforge.org  Mon Mar 30 09:27:33 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 30 Mar 2009 09:27:33 -0400 (EDT)
Subject: [BioCatalogue-developers] [539] trunk: Annotations plugin:
Message-ID: <20090330132734.0E74B1858185@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 31 07:02:21 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 31 Mar 2009 07:02:21 -0400 (EDT)
Subject: [BioCatalogue-developers] [540] trunk/app: added mouse message to
	service status icon
Message-ID: <20090331110221.B78511858120@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 31 07:03:04 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 31 Mar 2009 07:03:04 -0400 (EDT)
Subject: [BioCatalogue-developers] [541]
	trunk/vendor/plugins/onlooker/lib/onlooker.rb:
Message-ID: <20090331110304.A6AD1185810C@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 31 12:13:15 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 31 Mar 2009 12:13:15 -0400 (EDT)
Subject: [BioCatalogue-developers] [542] trunk/app: added last update time
 to mouse-over info of service status
Message-ID: <20090331161315.390E218580F0@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 31 12:16:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 31 Mar 2009 12:16:09 -0400 (EDT)
Subject: [BioCatalogue-developers] [543] trunk/wget_deployment_endpoints.rb:
 use open-uri to get the status of service endpoints.
Message-ID: <20090331161609.428F718580F8@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 31 13:31:48 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 31 Mar 2009 13:31:48 -0400 (EDT)
Subject: [BioCatalogue-developers] [544] trunk/lib/tags.rb: Bugfix for
 incorrect calculations of tag font sizes.
Message-ID: <20090331173148.1AD0E1978584@rubyforge.org>

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From noreply at rubyforge.org  Tue Mar 31 20:06:18 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 31 Mar 2009 20:06:18 -0400 (EDT)
Subject: [BioCatalogue-developers] [545] trunk/feta_import.rb: Committing
 the work in progress for the Feta import script, in case of local data loss.
Message-ID: <20090401000618.D3E8618580FF@rubyforge.org>

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