From ericnzuo at ebi.ac.uk  Thu Oct  1 11:49:26 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 01 Oct 2009 16:49:26 +0100
Subject: [BioCatalogue-developers] XML::Compile::SOAP library problem
Message-ID: <4AC4CF86.8040102@ebi.ac.uk>

Hi Steve,
Many perl scripts from the embrace registry fail to run against the most 
recent version of XML::Compile::WSDL11 library. These include all the 
soaplab ones.
Looking at the CPAN site,

http://search.cpan.org/~markov/XML-Compile-SOAP-2.08/
 
there are 10 versions available for this library. I am not exactly sure 
which of those versions are needed for the scripts to run.

The little shell script below found on the web could help. If you could 
run it on the test box like below, it would give us the version number.

regards,

Eric



/the/little/script.sh XML::Compile::WSDL11

--------
#!/bin/sh

mod=$1

if test "x$mod" = "x"; then
    echo "Usage: $0 <module>"
    exit
fi

if test "x$PERL" = "x"; then
    PERL=perl
fi

$PERL -M$mod -e "print \"$mod: \$$mod::VERSION\n\""
--------

From twitter-follow-biocatalogue-developers=rubyforge.org at postmaster.twitter.com  Fri Oct  2 05:50:15 2009
From: twitter-follow-biocatalogue-developers=rubyforge.org at postmaster.twitter.com (Twitter)
Date: Fri, 2 Oct 2009 09:50:15 +0000
Subject: [BioCatalogue-developers] franck Tanoh is now following you on
	Twitter!
Message-ID: <4ac5ccd7e0ec5_27301584e1f8b7ec6418b@mx003.twitter.com.tmail>

Hi, BioCatalogue Test (biocat_test).

franck Tanoh (ftanoh) is now following your tweets on Twitter.

Check out franck Tanoh's profile here:
  http://twitter.com/ftanoh

You may follow franck Tanoh as well by clicking on the "follow" button.
franck Tanoh may not appear in your follower list. franck Tanoh may have
decided to stop following you, or the account may have been suspended
for a Terms of Service violation.

Best,
Twitter

--
Turn off these emails at: http://twitter.com/account/notifications
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From ericnzuo at ebi.ac.uk  Mon Oct  5 08:02:54 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 05 Oct 2009 13:02:54 +0100
Subject: [BioCatalogue-developers] wikipedia for BioCatalogue
In-Reply-To: <d0ee827d0910050256h54b73503y78044b894904878c@mail.gmail.com>
References: <d0ee827d0910050256h54b73503y78044b894904878c@mail.gmail.com>
Message-ID: <4AC9E06E.8040805@ebi.ac.uk>

Hi Franck, it is a good step and believe the wikipedia entry will bring 
quite a few people to the catalogue. Since this is very public, we 
should carefully monitor what goes on there so that it does not become a 
dis-service to the catalogue. The REST API is not released yet, so I 
believe we should not be writing about it just yet.

Eric


Franck Tanoh wrote:
> Hello everybody,
>
> I've created a Wikipedia page for BioCatalogue: 
> http://en.wikipedia.org/wiki/BioCatalogue .
> I need to update the logo though.
>
> Feel free to update or comment.
>
> Franck
>
> -- 
> "Science knows no country, because knowledge belongs to humanity, and 
> is the torch which illuminates the world." - Louis Pasteur
>


From jits at cs.man.ac.uk  Mon Oct  5 08:45:21 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 05 Oct 2009 13:45:21 +0100
Subject: [BioCatalogue-developers] wikipedia for BioCatalogue
In-Reply-To: <4AC9E06E.8040805@ebi.ac.uk>
References: <d0ee827d0910050256h54b73503y78044b894904878c@mail.gmail.com>
	<4AC9E06E.8040805@ebi.ac.uk>
Message-ID: <4AC9EA61.2070809@cs.man.ac.uk>

Good point Eric.

I've noticed that the BioCatalogue page is pretty much a copy from the
myExperiment page - http://en.wikipedia.org/wiki/MyExperiment :-P

Might be worth adding to the BioCatalogue page a mention the
BioCatalogue project is related to the myExperiment project.

Cheers,
Jits


Eric Nzuobontane wrote:
> Hi Franck, it is a good step and believe the wikipedia entry will
> bring quite a few people to the catalogue. Since this is very public,
> we should carefully monitor what goes on there so that it does not
> become a dis-service to the catalogue. The REST API is not released
> yet, so I believe we should not be writing about it just yet.
>
> Eric
>
>
> Franck Tanoh wrote:
>> Hello everybody,
>>
>> I've created a Wikipedia page for BioCatalogue:
>> http://en.wikipedia.org/wiki/BioCatalogue .
>> I need to update the logo though.
>>
>> Feel free to update or comment.
>>
>> Franck
>>
>> -- 
>> "Science knows no country, because knowledge belongs to humanity, and
>> is the torch which illuminates the world." - Louis Pasteur
>>
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From noreply at rubyforge.org  Mon Oct  5 12:22:21 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  5 Oct 2009 12:22:21 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2807] long lines out of the box
Message-ID: <20091005162221.B262A1858202@rubyforge.org>

Task #2807 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: long lines out of the box 
Complete: 0%
Status: Open

Description: the format of services with long description is not properly handled. The description is out of the 'box' with long line crossing the entire screen. e.g. see service description and example input for the following service: 
http://www.biocatalogue.org/services/2069-genesilicometaserversoapservice_324691

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2807&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Oct  5 12:27:41 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  5 Oct 2009 12:27:41 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2808] To limit the number of
	similar service displayed by default
Message-ID: <20091005162741.D8E601858202@rubyforge.org>

Task #2808 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: To limit the number of similar service displayed by default
Complete: 0%
Status: Open

Description: Need to limit the number of similar services displayed. e.g display the first 10 only. 
The list is sometimes quite long...the following service has 38 similar services: http://www.biocatalogue.org/services/2069-genesilicometaserversoapservice_32469

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2808&group_id=6901&group_project_id=12540

From jits at cs.man.ac.uk  Tue Oct  6 12:32:31 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 06 Oct 2009 17:32:31 +0100
Subject: [BioCatalogue-developers] wikipedia for BioCatalogue
In-Reply-To: <d0ee827d0910060924w3e0db328q88d4b532ae237b8f@mail.gmail.com>
References: <d0ee827d0910050256h54b73503y78044b894904878c@mail.gmail.com>	
	<4AC9E06E.8040805@ebi.ac.uk> <4AC9EA61.2070809@cs.man.ac.uk>
	<d0ee827d0910060924w3e0db328q88d4b532ae237b8f@mail.gmail.com>
Message-ID: <4ACB711F.3070102@cs.man.ac.uk>

Nice one, thanks Franck.

Jits

Franck Tanoh wrote:
> >I've noticed that the BioCatalogue page is pretty much a copy from the
> >myExperiment page - http://en.wikipedia.org/wiki/MyExperiment :-P
> It's the family :-)
>
> >Might be worth adding to the BioCatalogue page a mention the
> >BioCatalogue project is related to the myExperiment project.
> Done. I've also removed the bit about the API.
>
> cheers,
> Franck
>
> 2009/10/5 Jiten Bhagat <jits at cs.man.ac.uk <mailto:jits at cs.man.ac.uk>>
>
>     Good point Eric.
>
>     I've noticed that the BioCatalogue page is pretty much a copy from the
>     myExperiment page - http://en.wikipedia.org/wiki/MyExperiment :-P
>
>     Might be worth adding to the BioCatalogue page a mention the
>     BioCatalogue project is related to the myExperiment project.
>
>     Cheers,
>     Jits
>
>
>     Eric Nzuobontane wrote:
>     > Hi Franck, it is a good step and believe the wikipedia entry will
>     > bring quite a few people to the catalogue. Since this is very
>     public,
>     > we should carefully monitor what goes on there so that it does not
>     > become a dis-service to the catalogue. The REST API is not released
>     > yet, so I believe we should not be writing about it just yet.
>     >
>     > Eric
>     >
>     >
>     > Franck Tanoh wrote:
>     >> Hello everybody,
>     >>
>     >> I've created a Wikipedia page for BioCatalogue:
>     >> http://en.wikipedia.org/wiki/BioCatalogue .
>     >> I need to update the logo though.
>     >>
>     >> Feel free to update or comment.
>     >>
>     >> Franck
>     >>
>     >> --
>     >> "Science knows no country, because knowledge belongs to
>     humanity, and
>     >> is the torch which illuminates the world." - Louis Pasteur
>     >>
>     >
>     > _______________________________________________
>     > BioCatalogue-developers mailing list
>     > BioCatalogue-developers at rubyforge.org
>     <mailto:BioCatalogue-developers at rubyforge.org>
>     > http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>
>
>
>
> -- 
> "Science knows no country, because knowledge belongs to humanity, and
> is the torch which illuminates the world." - Louis Pasteur


From noreply at rubyforge.org  Tue Oct  6 13:09:19 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  6 Oct 2009 13:09:19 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2808] To limit the number of
	similar service displayed by default
Message-ID: <20091006170919.3134E18582D1@rubyforge.org>

Task #2808 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: To limit the number of similar service displayed by default
Complete: 100%
Status: Closed

Description: Need to limit the number of similar services displayed. e.g display the first 10 only. 
The list is sometimes quite long...the following service has 38 similar services: http://www.biocatalogue.org/services/2069-genesilicometaserversoapservice_32469

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-06 17:09
By: jits

Comment:
Done, limited to 10 for now.

I'll do more work in the future on this, to be able to expand/collapse, and show/hide more info etc etc

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2808&group_id=6901&group_project_id=12540

From jits at cs.man.ac.uk  Wed Oct  7 06:35:18 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 07 Oct 2009 11:35:18 +0100
Subject: [BioCatalogue-developers] Adding indexes to the activity_logs table
	to improve query performances
Message-ID: <4ACC6EE6.8060402@cs.man.ac.uk>

Hi,

This is hugely relevant to the event logging work that Sergey and I did
for myExperiment (what's happening with that anyways?)

If you haven't already, I suggest adding a few indexes for the
activity_logs table. More info below...

In the BioCatalogue we are using an extended version of the
activity_logs mechanism to store all kinds of events. Right now I use
this mainly to calculate how many times a service has been viewed. For
one service with just under 100 view counts this query was taking
between 200 and 300 milliseconds to complete. After adding some indexes
it now takes between 50 to 70 milliseconds.

Pasted after this email are the indexes I added, for reference (note
that the "format" index is specific to the BioCatalogue extensions to
the activity_logs).

Just a thought to improve the performance of the event logging branch,
as I know performance is one of the main concerns that is stopping it
from being released...

Jits

---

class AddIndexesToActivityLogs < ActiveRecord::Migration
  def self.up
    add_index :activity_logs, [ "action" ], :name => "act_logs_action_index"
    add_index :activity_logs, [ "activity_loggable_type",
"activity_loggable_id" ], :name => "act_logs_act_loggable_index"
    add_index :activity_logs, [ "culprit_type", "culprit_id" ], :name =>
"act_logs_culprit_index"
    add_index :activity_logs, [ "referenced_type", "referenced_id" ],
:name => "act_logs_referenced_index"
    add_index :activity_logs, [ "format" ], :name => "act_logs_format_index"
  end

  def self.down
    remove_index :activity_logs, :name => "act_logs_action_index"
    remove_index :activity_logs, :name => "act_logs_act_loggable_index"
    remove_index :activity_logs, :name => "act_logs_culprit_index"
    remove_index :activity_logs, :name => "act_logs_referenced_index"
    remove_index :activity_logs, :name => "act_logs_format_index"
  end
end

From jits at cs.man.ac.uk  Wed Oct  7 06:43:35 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 07 Oct 2009 11:43:35 +0100
Subject: [BioCatalogue-developers] Adding indexes to the activity_logs
	table to improve query performances
In-Reply-To: <4ACC6EE6.8060402@cs.man.ac.uk>
References: <4ACC6EE6.8060402@cs.man.ac.uk>
Message-ID: <4ACC70D7.8070109@cs.man.ac.uk>

Oops, it's actually changed from 200-300ms to 5-7ms (!) Note that this
is just the query time, and with an activity_logs table with 132K+ records.

Jits



Jiten Bhagat wrote:
> Hi,
>
> This is hugely relevant to the event logging work that Sergey and I did
> for myExperiment (what's happening with that anyways?)
>
> If you haven't already, I suggest adding a few indexes for the
> activity_logs table. More info below...
>
> In the BioCatalogue we are using an extended version of the
> activity_logs mechanism to store all kinds of events. Right now I use
> this mainly to calculate how many times a service has been viewed. For
> one service with just under 100 view counts this query was taking
> between 200 and 300 milliseconds to complete. After adding some indexes
> it now takes between 50 to 70 milliseconds.
>
> Pasted after this email are the indexes I added, for reference (note
> that the "format" index is specific to the BioCatalogue extensions to
> the activity_logs).
>
> Just a thought to improve the performance of the event logging branch,
> as I know performance is one of the main concerns that is stopping it
> from being released...
>
> Jits
>
> ---
>
> class AddIndexesToActivityLogs < ActiveRecord::Migration
>   def self.up
>     add_index :activity_logs, [ "action" ], :name => "act_logs_action_index"
>     add_index :activity_logs, [ "activity_loggable_type",
> "activity_loggable_id" ], :name => "act_logs_act_loggable_index"
>     add_index :activity_logs, [ "culprit_type", "culprit_id" ], :name =>
> "act_logs_culprit_index"
>     add_index :activity_logs, [ "referenced_type", "referenced_id" ],
> :name => "act_logs_referenced_index"
>     add_index :activity_logs, [ "format" ], :name => "act_logs_format_index"
>   end
>
>   def self.down
>     remove_index :activity_logs, :name => "act_logs_action_index"
>     remove_index :activity_logs, :name => "act_logs_act_loggable_index"
>     remove_index :activity_logs, :name => "act_logs_culprit_index"
>     remove_index :activity_logs, :name => "act_logs_referenced_index"
>     remove_index :activity_logs, :name => "act_logs_format_index"
>   end
> end
>
>   


From jits at cs.man.ac.uk  Wed Oct  7 08:59:16 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 07 Oct 2009 13:59:16 +0100
Subject: [BioCatalogue-developers] [myexperiment-hackers] Adding indexes
 to the activity_logs table to	improve query performances
In-Reply-To: <EMEW3|07b48e7e3ca2270c5c3ba07dfaa3158al96Bsx03dtm|ecs.soton.ac.uk|.64.0910071149430.8263@login.ecs.soton.ac.uk>
References: <4ACC6EE6.8060402@cs.man.ac.uk>	<Pine.LNX.4.64.0910071149430.8263@login.ecs.soton.ac.uk>
	<EMEW3|07b48e7e3ca2270c5c3ba07dfaa3158al96Bsx03dtm|ecs.soton.ac.uk|.64.0910071149430.8263@login.ecs.soton.ac.uk>
Message-ID: <4ACC90A4.7070707@cs.man.ac.uk>

Ah, great! Thanks Dan.

Jits


Danius Michaelides wrote:
> On Wed, 7 Oct 2009, Jiten Bhagat wrote:
>
>> Hi,
>>
>> This is hugely relevant to the event logging work that Sergey and I did
>> for myExperiment (what's happening with that anyways?)
>>
>> If you haven't already, I suggest adding a few indexes for the
>> activity_logs table. More info below...
>>
>> In the BioCatalogue we are using an extended version of the
>> activity_logs mechanism to store all kinds of events. Right now I use
>> this mainly to calculate how many times a service has been viewed. For
>> one service with just under 100 view counts this query was taking
>> between 200 and 300 milliseconds to complete. After adding some indexes
>> it now takes between 50 to 70 milliseconds.
>>
>> Pasted after this email are the indexes I added, for reference (note
>> that the "format" index is specific to the BioCatalogue extensions to
>> the activity_logs).
>>
>> Just a thought to improve the performance of the event logging branch,
>> as I know performance is one of the main concerns that is stopping it
>> from being released...
>
> I added indexes to the myexp event_logging branch awhile ago:
>
> add_index :activity_logs, [ "activity_loggable_type",
> "activity_loggable_id" ] ...
> add_index :activity_logs, [ "referenced_type", "referenced_id" ] ...
> add_index :activity_logs, [ "culprit_type", "culprit_id" ] ...
>
> No index for "action" - i guess coz i couldnt see any queries using it.
>
> But yeah, big improvement, just be careful not to make indexes that dont
> get used, as there's obviously a performance hit when inserting.
> Danius
>
>
> _______________________________________________
> myexperiment-hackers mailing list
> myexperiment-hackers at nongnu.org
> http://lists.nongnu.org/mailman/listinfo/myexperiment-hackers


From dtm at ecs.soton.ac.uk  Wed Oct  7 06:54:49 2009
From: dtm at ecs.soton.ac.uk (Danius Michaelides)
Date: Wed, 7 Oct 2009 11:54:49 +0100 (BST)
Subject: [BioCatalogue-developers] [myexperiment-hackers] Adding indexes
 to the activity_logs table to	improve query performances
In-Reply-To: <4ACC6EE6.8060402@cs.man.ac.uk>
References: <4ACC6EE6.8060402@cs.man.ac.uk>
	<Pine.LNX.4.64.0910071149430.8263@login.ecs.soton.ac.uk>
Message-ID: <EMEW3|07b48e7e3ca2270c5c3ba07dfaa3158al96Bsx03dtm|ecs.soton.ac.uk|.64.0910071149430.8263@login.ecs.soton.ac.uk>

On Wed, 7 Oct 2009, Jiten Bhagat wrote:

> Hi,
>
> This is hugely relevant to the event logging work that Sergey and I did
> for myExperiment (what's happening with that anyways?)
>
> If you haven't already, I suggest adding a few indexes for the
> activity_logs table. More info below...
>
> In the BioCatalogue we are using an extended version of the
> activity_logs mechanism to store all kinds of events. Right now I use
> this mainly to calculate how many times a service has been viewed. For
> one service with just under 100 view counts this query was taking
> between 200 and 300 milliseconds to complete. After adding some indexes
> it now takes between 50 to 70 milliseconds.
>
> Pasted after this email are the indexes I added, for reference (note
> that the "format" index is specific to the BioCatalogue extensions to
> the activity_logs).
>
> Just a thought to improve the performance of the event logging branch,
> as I know performance is one of the main concerns that is stopping it
> from being released...

I added indexes to the myexp event_logging branch awhile ago:

add_index :activity_logs, [ "activity_loggable_type", "activity_loggable_id" ] ...
add_index :activity_logs, [ "referenced_type", "referenced_id" ] ...
add_index :activity_logs, [ "culprit_type", "culprit_id" ] ...

No index for "action" - i guess coz i couldnt see any queries using it.

But yeah, big improvement, just be careful not to make indexes that dont
get used, as there's obviously a performance hit when inserting.
Danius

From noreply at rubyforge.org  Wed Oct  7 12:00:51 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  7 Oct 2009 12:00:51 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2812] User profile tab persistance
Message-ID: <20091007160051.2EAE418582FE@rubyforge.org>

Task #2812 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: User profile tab persistance
Complete: 0%
Status: Open

Description: When a page is clicked in the user profile (when browsing through the user's submitted services, for example), when the new page is rendered it takes you back to the profile tab instead of the tab you were viewing.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2812&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Wed Oct  7 12:01:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  7 Oct 2009 12:01:09 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2813] Annotations plugin: add
	limit= to annotation finder methods
Message-ID: <20091007160109.E22FC1858305@rubyforge.org>

Task #2813 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Annotations plugin: add limit= to annotation finder methods
Complete: 0%
Status: Open

Description: Currently methods like annotations_with_attribute will return all objects. Sometimes you only want the last one or a subset. So add the option to have a limit.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2813&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Oct  8 04:51:08 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  8 Oct 2009 04:51:08 -0400 (EDT)
Subject: [BioCatalogue-developers] [ biocatalogue-Bugs-26258 ] account
	confirmation email points to localhost
Message-ID: <20091008085108.24233185824A@rubyforge.org>

Bugs item #26258, was opened at 2009-06-17 10:48
You can respond by visiting: 
http://rubyforge.org/tracker/?func=detail&atid=26756&aid=26258&group_id=6901

Category: None
Group: None
>Status: Closed
>Resolution: Accepted
Priority: 3
Submitted By: Nobody (None)
>Assigned to: Jiten Bhagat (jits)
Summary: account confirmation email points to localhost

Initial Comment:
Content of the email I just received:

Please, click on the following link to activate your account.
http://localhost:3005/activate_account/ff874b7dfa115620b077d24cf7f1553640294951

----------------------------------------------------------------------

>Comment By: Jiten Bhagat (jits)
Date: 2009-10-08 08:51

Message:
This has been fixed.

Thanks for reporting!

Jits

----------------------------------------------------------------------

You can respond by visiting: 
http://rubyforge.org/tracker/?func=detail&atid=26756&aid=26258&group_id=6901

From noreply at rubyforge.org  Thu Oct  8 07:19:07 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  8 Oct 2009 07:19:07 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2805] Track when users were last
	active
Message-ID: <20091008111907.729EC1858253@rubyforge.org>

Task #2805 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Track when users were last active
Complete: 80%
Status: Open

Description: Add a "last_active" field to users model and on every request update the user model (but only the one field) to show when a user was last active.

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-08 11:19
By: fbacall

Comment:
Last active field added to mode, updated every time a page is viewed. Bypasses callbacks + validation when field updated. Needs further testing.

Revision #1122

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2805&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Oct  8 07:21:44 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  8 Oct 2009 07:21:44 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2790] Add a "Services I have
	annotated" tab in user profile
Message-ID: <20091008112153.9ACEA185826F@rubyforge.org>

Task #2790 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Add a "Services I have annotated" tab in user profile
Complete: 80%
Status: Open

Description: At the moment there is now way to see what services someone has annotated.

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-08 11:21
By: fbacall

Comment:
"Serviced annotated" tab added to profile. Takes ~5 secs to load profile/page, ~1.5 secs after caching. Need to work out what to do with annotated + submitted services sharing page variable.

Revision 1130

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2790&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Oct  8 08:39:19 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  8 Oct 2009 08:39:19 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2814] Search module has
	discrepancies between "any" and scoped searches
Message-ID: <20091008123919.EC3371858279@rubyforge.org>

Task #2814 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Search module has discrepancies between "any" and scoped searches
Complete: 0%
Status: Open

Description: At the moment, the models that are searched on are defined:

@@models_for_search_scopes

This has a major issue - if the collections are not in "sync", in terms of mappings of results, then the counts of results from the "all" search and the scoped searches will not match up! Sort this out....

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2814&group_id=6901&group_project_id=12540

From jits at cs.man.ac.uk  Thu Oct  8 08:46:15 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Thu, 08 Oct 2009 13:46:15 +0100
Subject: [BioCatalogue-developers] Merging of the REST API branch
Message-ID: <4ACDDF17.9020507@cs.man.ac.uk>

Hi all,

Just to let you know, if you are working on anything in the REST API
branch (Finn and Mannie in particular) then please commit all work by
4pm today as I intend to merge this branch into trunk and then
discontinue at.

It's likely I will create a second REST API branch (with a different
name) to continue with the REST API development. The current REST API
branch has evolved to include a lot more changes than just the REST API
work, unfortunately. This was due to some very important refactorings I
have been making.

Cheers,
Jits

From noreply at rubyforge.org  Thu Oct  8 09:54:16 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  8 Oct 2009 09:54:16 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2815] Update prototype libraries
	(especially for IE8 support)
Message-ID: <20091008135416.6C4EB185827B@rubyforge.org>

Task #2815 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Update prototype libraries (especially for IE8 support)
Complete: 0%
Status: Open

Description: At the moment the Prototype library we use is quite old and newer versions have better IE8 compatibility.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2815&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Oct  8 10:12:57 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  8 Oct 2009 10:12:57 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2807] long lines out of the box
Message-ID: <20091008141257.DD6AE1858253@rubyforge.org>

Task #2807 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: long lines out of the box 
Complete: 50%
Status: Open

Description: the format of services with long description is not properly handled. The description is out of the 'box' with long line crossing the entire screen. e.g. see service description and example input for the following service: 
http://www.biocatalogue.org/services/2069-genesilicometaserversoapservice_324691

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-08 14:12
By: fbacall

Comment:
Added scrollbar when box overflows. Need to workout how to best make only the description scroll.

Revision 1135

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2807&group_id=6901&group_project_id=12540

From jits at cs.man.ac.uk  Thu Oct  8 20:22:14 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 09 Oct 2009 01:22:14 +0100
Subject: [BioCatalogue-developers] Faster Search!
Message-ID: <4ACE8236.8000606@cs.man.ac.uk>

Hi guys,

I've committed some changes to search that I am very excited about (I
know, I know, I need to get out more...)

I've now managed to bring down search performance to less than a second
even on heavy searches like "ebi". This includes getting the search
results from Solr, figuring out what associated objects are relevant,
and rendering the view.

You can check it out now on the sandbox -
http://www.sandbox.biocatalogue.org. Note that this is running on an old
P4 3.0GHz with 2GB of RAM (I've given the Solr process half of that RAM,
which helps). A search for "ebi" used to take 3 to 4 seconds and now it
takes 1 to 1.2 seconds (!) I'm hoping that this is good enough now :-)

If you're interested in the gory details...

Firstly, I implemented the "simple" listings view. BUT this only gave
between 10-15% improvement.

The massive perf boost has came from my latest change - modifying the
models, acts_as_solr plugin and the search module to store the
associations at index time as extra fields in Solr, and then using these
at query time instead of doing all the mapping stuff I had implemented
before (although the mapping stuff is still there as a fall back and is
required at index time).

NOTE: this does mean that Solr will need to be restarted and then
reindexed when we get to the live release. This reindexing process now
takes a longer, partly because I have added some sleeps in the code so
as not to push the Solr server to breaking point at index time, but all
this for gains at query time.

Cheers,
Jits

From jits at cs.man.ac.uk  Thu Oct  8 20:24:56 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 09 Oct 2009 01:24:56 +0100
Subject: [BioCatalogue-developers] Faster Search!
In-Reply-To: <4ACE8236.8000606@cs.man.ac.uk>
References: <4ACE8236.8000606@cs.man.ac.uk>
Message-ID: <4ACE82D8.3020304@cs.man.ac.uk>

Note that initial hits might be slow as the caches "warm up"...

And I forgot to say - please do give feedback and report any issues.

Thanks,
Jits


Jiten Bhagat wrote:
> Hi guys,
>
> I've committed some changes to search that I am very excited about (I
> know, I know, I need to get out more...)
>
> I've now managed to bring down search performance to less than a second
> even on heavy searches like "ebi". This includes getting the search
> results from Solr, figuring out what associated objects are relevant,
> and rendering the view.
>
> You can check it out now on the sandbox -
> http://www.sandbox.biocatalogue.org. Note that this is running on an old
> P4 3.0GHz with 2GB of RAM (I've given the Solr process half of that RAM,
> which helps). A search for "ebi" used to take 3 to 4 seconds and now it
> takes 1 to 1.2 seconds (!) I'm hoping that this is good enough now :-)
>
> If you're interested in the gory details...
>
> Firstly, I implemented the "simple" listings view. BUT this only gave
> between 10-15% improvement.
>
> The massive perf boost has came from my latest change - modifying the
> models, acts_as_solr plugin and the search module to store the
> associations at index time as extra fields in Solr, and then using these
> at query time instead of doing all the mapping stuff I had implemented
> before (although the mapping stuff is still there as a fall back and is
> required at index time).
>
> NOTE: this does mean that Solr will need to be restarted and then
> reindexed when we get to the live release. This reindexing process now
> takes a longer, partly because I have added some sleeps in the code so
> as not to push the Solr server to breaking point at index time, but all
> this for gains at query time.
>
> Cheers,
> Jits
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From noreply at rubyforge.org  Thu Oct  8 20:32:01 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  8 Oct 2009 20:32:01 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2788] More profiling on search
Message-ID: <20091009003201.284FE1858287@rubyforge.org>

Task #2788 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: More profiling on search
Complete: 100%
Status: Closed

Description: Need to do more profiling and optimisations on the search, from the solr retrieval to mapping to building the views.

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-09 00:32
By: jits

Comment:
This has been revamped and performance greatly improved in revision 1138...

Firstly, by implementing "simple" listings view. BUT this only gave
between 10-15% improvement.

The big perf boost has came from modifying the
models, acts_as_solr plugin and the search module to store the
associations at index time as extra fields in Solr, and then using these
at query time instead of doing all the mapping stuff I had implemented
before (although the mapping stuff is still there as a fall back and is
required at index time).

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2788&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Oct  8 20:32:52 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  8 Oct 2009 20:32:52 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2787] Build a leaner list for the
	search results
Message-ID: <20091009003252.E6B681858285@rubyforge.org>

Task #2787 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Build a leaner list for the search results
Complete: 60%
Status: Open

Description: To improve on search results performance

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-09 00:32
By: jits

Comment:
Done, awating user feedback and further testing...

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2787&group_id=6901&group_project_id=12540

From tlaurent at ebi.ac.uk  Fri Oct  9 05:21:14 2009
From: tlaurent at ebi.ac.uk (Thomas Laurent)
Date: Fri, 09 Oct 2009 10:21:14 +0100
Subject: [BioCatalogue-developers] Faster Search!
In-Reply-To: <4ACE8236.8000606@cs.man.ac.uk>
References: <4ACE8236.8000606@cs.man.ac.uk>
Message-ID: <4ACF008A.3090404@ebi.ac.uk>

I love it Jits ! That's A LOT faster ! It makes a massive difference for 
the user experience. In my opinion it's probably one of the most 
important/crucial improvement made to the Biocatalogue since the 
beginning of the project.
I bow to you Jits ;-)

Thomas

Jiten Bhagat wrote:
> Hi guys,
> 
> I've committed some changes to search that I am very excited about (I
> know, I know, I need to get out more...)
> 
> I've now managed to bring down search performance to less than a second
> even on heavy searches like "ebi". This includes getting the search
> results from Solr, figuring out what associated objects are relevant,
> and rendering the view.
> 
> You can check it out now on the sandbox -
> http://www.sandbox.biocatalogue.org. Note that this is running on an old
> P4 3.0GHz with 2GB of RAM (I've given the Solr process half of that RAM,
> which helps). A search for "ebi" used to take 3 to 4 seconds and now it
> takes 1 to 1.2 seconds (!) I'm hoping that this is good enough now :-)
> 
> If you're interested in the gory details...
> 
> Firstly, I implemented the "simple" listings view. BUT this only gave
> between 10-15% improvement.
> 
> The massive perf boost has came from my latest change - modifying the
> models, acts_as_solr plugin and the search module to store the
> associations at index time as extra fields in Solr, and then using these
> at query time instead of doing all the mapping stuff I had implemented
> before (although the mapping stuff is still there as a fall back and is
> required at index time).
> 
> NOTE: this does mean that Solr will need to be restarted and then
> reindexed when we get to the live release. This reindexing process now
> takes a longer, partly because I have added some sleeps in the code so
> as not to push the Solr server to breaking point at index time, but all
> this for gains at query time.
> 
> Cheers,
> Jits
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers

From jits at cs.man.ac.uk  Fri Oct  9 06:06:27 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 09 Oct 2009 11:06:27 +0100
Subject: [BioCatalogue-developers] Faster Search!
In-Reply-To: <d0ee827d0910090200ja6ba40as91a33573ff8aa4d5@mail.gmail.com>
References: <4ACE8236.8000606@cs.man.ac.uk>
	<d0ee827d0910090200ja6ba40as91a33573ff8aa4d5@mail.gmail.com>
Message-ID: <4ACF0B23.4030208@cs.man.ac.uk>

Franck Tanoh wrote:
> Jits,
> Yep, search is very quick now, and i guess it will be quicker when we
> move to the biocat live ...well done!
> By the way the sandbox is :  http://sandbox.biocatalogue.org
> <http://www.sandbox.biocatalogue.org/> without the 'www'.

Ah yes! Thanks Franck.

I should not be allowed on a computer after 9pm!

Jits


>
> cheers,
> Franck
>
> 2009/10/9 Jiten Bhagat <jits at cs.man.ac.uk <mailto:jits at cs.man.ac.uk>>
>
>     Hi guys,
>
>     I've committed some changes to search that I am very excited about (I
>     know, I know, I need to get out more...)
>
>     I've now managed to bring down search performance to less than a
>     second
>     even on heavy searches like "ebi". This includes getting the search
>     results from Solr, figuring out what associated objects are relevant,
>     and rendering the view.
>
>     You can check it out now on the sandbox -
>     http://www.sandbox.biocatalogue.org. Note that this is running on
>     an old
>     P4 3.0GHz with 2GB of RAM (I've given the Solr process half of
>     that RAM,
>     which helps). A search for "ebi" used to take 3 to 4 seconds and
>     now it
>     takes 1 to 1.2 seconds (!) I'm hoping that this is good enough now :-)
>
>     If you're interested in the gory details...
>
>     Firstly, I implemented the "simple" listings view. BUT this only gave
>     between 10-15% improvement.
>
>     The massive perf boost has came from my latest change - modifying the
>     models, acts_as_solr plugin and the search module to store the
>     associations at index time as extra fields in Solr, and then using
>     these
>     at query time instead of doing all the mapping stuff I had implemented
>     before (although the mapping stuff is still there as a fall back
>     and is
>     required at index time).
>
>     NOTE: this does mean that Solr will need to be restarted and then
>     reindexed when we get to the live release. This reindexing process now
>     takes a longer, partly because I have added some sleeps in the code so
>     as not to push the Solr server to breaking point at index time,
>     but all
>     this for gains at query time.
>
>     Cheers,
>     Jits
>     _______________________________________________
>     BioCatalogue-developers mailing list
>     BioCatalogue-developers at rubyforge.org
>     <mailto:BioCatalogue-developers at rubyforge.org>
>     http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>
>
>
>
> -- 
> "Science knows no country, because knowledge belongs to humanity, and
> is the torch which illuminates the world." - Louis Pasteur


From jits at cs.man.ac.uk  Fri Oct  9 06:10:53 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 09 Oct 2009 11:10:53 +0100
Subject: [BioCatalogue-developers] Faster Search!
In-Reply-To: <4ACF008A.3090404@ebi.ac.uk>
References: <4ACE8236.8000606@cs.man.ac.uk> <4ACF008A.3090404@ebi.ac.uk>
Message-ID: <4ACF0C2D.2060907@cs.man.ac.uk>

Thomas Laurent wrote:
> I love it Jits ! That's A LOT faster ! It makes a massive difference
> for the user experience. In my opinion it's probably one of the most
> important/crucial improvement made to the Biocatalogue since the
> beginning of the project.

I completely agree with you Thomas and it was something you said along
the lines of this a little while back that really stuck in my head. I
wasn't the same person since then, but I'm getting back to normal now
that the situation has improved...

> I bow to you Jits ;-)

Hahaha... why thank you very much Thomas ;-)

Now if only I can improve the performance of the Operations tab for
services with millions of operations...

Jits

>
> Thomas
>
> Jiten Bhagat wrote:
>> Hi guys,
>>
>> I've committed some changes to search that I am very excited about (I
>> know, I know, I need to get out more...)
>>
>> I've now managed to bring down search performance to less than a second
>> even on heavy searches like "ebi". This includes getting the search
>> results from Solr, figuring out what associated objects are relevant,
>> and rendering the view.
>>
>> You can check it out now on the sandbox -
>> http://www.sandbox.biocatalogue.org. Note that this is running on an old
>> P4 3.0GHz with 2GB of RAM (I've given the Solr process half of that RAM,
>> which helps). A search for "ebi" used to take 3 to 4 seconds and now it
>> takes 1 to 1.2 seconds (!) I'm hoping that this is good enough now :-)
>>
>> If you're interested in the gory details...
>>
>> Firstly, I implemented the "simple" listings view. BUT this only gave
>> between 10-15% improvement.
>>
>> The massive perf boost has came from my latest change - modifying the
>> models, acts_as_solr plugin and the search module to store the
>> associations at index time as extra fields in Solr, and then using these
>> at query time instead of doing all the mapping stuff I had implemented
>> before (although the mapping stuff is still there as a fall back and is
>> required at index time).
>>
>> NOTE: this does mean that Solr will need to be restarted and then
>> reindexed when we get to the live release. This reindexing process now
>> takes a longer, partly because I have added some sleeps in the code so
>> as not to push the Solr server to breaking point at index time, but all
>> this for gains at query time.
>>
>> Cheers,
>> Jits
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From jits at cs.man.ac.uk  Fri Oct  9 06:15:54 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 09 Oct 2009 11:15:54 +0100
Subject: [BioCatalogue-developers] Faster Search!
In-Reply-To: <d0ee827d0910090200ja6ba40as91a33573ff8aa4d5@mail.gmail.com>
References: <4ACE8236.8000606@cs.man.ac.uk>
	<d0ee827d0910090200ja6ba40as91a33573ff8aa4d5@mail.gmail.com>
Message-ID: <4ACF0D5A.7040507@cs.man.ac.uk>

I've noticed that certain searches, like for "protein" take between 3-4
seconds. This isn't awful, but I'll look to see how I can improve this.

Please let me know if you come across any other queries that take longer
than 2 or so seconds.

Cheers,
Jits


Franck Tanoh wrote:
> Jits,
> Yep, search is very quick now, and i guess it will be quicker when we
> move to the biocat live ...well done!
> By the way the sandbox is :  http://sandbox.biocatalogue.org
> <http://www.sandbox.biocatalogue.org/> without the 'www'.
>
> cheers,
> Franck
>
> 2009/10/9 Jiten Bhagat <jits at cs.man.ac.uk <mailto:jits at cs.man.ac.uk>>
>
>     Hi guys,
>
>     I've committed some changes to search that I am very excited about (I
>     know, I know, I need to get out more...)
>
>     I've now managed to bring down search performance to less than a
>     second
>     even on heavy searches like "ebi". This includes getting the search
>     results from Solr, figuring out what associated objects are relevant,
>     and rendering the view.
>
>     You can check it out now on the sandbox -
>     http://www.sandbox.biocatalogue.org. Note that this is running on
>     an old
>     P4 3.0GHz with 2GB of RAM (I've given the Solr process half of
>     that RAM,
>     which helps). A search for "ebi" used to take 3 to 4 seconds and
>     now it
>     takes 1 to 1.2 seconds (!) I'm hoping that this is good enough now :-)
>
>     If you're interested in the gory details...
>
>     Firstly, I implemented the "simple" listings view. BUT this only gave
>     between 10-15% improvement.
>
>     The massive perf boost has came from my latest change - modifying the
>     models, acts_as_solr plugin and the search module to store the
>     associations at index time as extra fields in Solr, and then using
>     these
>     at query time instead of doing all the mapping stuff I had implemented
>     before (although the mapping stuff is still there as a fall back
>     and is
>     required at index time).
>
>     NOTE: this does mean that Solr will need to be restarted and then
>     reindexed when we get to the live release. This reindexing process now
>     takes a longer, partly because I have added some sleeps in the code so
>     as not to push the Solr server to breaking point at index time,
>     but all
>     this for gains at query time.
>
>     Cheers,
>     Jits
>     _______________________________________________
>     BioCatalogue-developers mailing list
>     BioCatalogue-developers at rubyforge.org
>     <mailto:BioCatalogue-developers at rubyforge.org>
>     http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>
>
>
>
> -- 
> "Science knows no country, because knowledge belongs to humanity, and
> is the torch which illuminates the world." - Louis Pasteur


From noreply at rubyforge.org  Fri Oct  9 09:59:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  9 Oct 2009 09:59:09 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2812] User profile tab persistance
Message-ID: <20091009135909.3C92D1D78828@rubyforge.org>

Task #2812 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: User profile tab persistance
Complete: 0%
Status: Deleted

Description: When a page is clicked in the user profile (when browsing through the user's submitted services, for example), when the new page is rendered it takes you back to the profile tab instead of the tab you were viewing.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2812&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Fri Oct  9 11:51:50 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  9 Oct 2009 11:51:50 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2645] Tab persistency on user
	profile
Message-ID: <20091009155151.082DE185826F@rubyforge.org>

Task #2645 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Tab persistency on user profile
Complete: 80%
Status: Open

Description: If  you go to a user's page and click on the "services submitted", if you go to the "next" page, the tab goes back to "Profile".

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-09 15:51
By: fbacall

Comment:
The code to set the right tab on page load works fine, it's just the use_tab_cookie setting in the session returns false and so the code doesn't run. Need to look into the point of that setting... 

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2645&group_id=6901&group_project_id=12540

From ericnzuo at ebi.ac.uk  Mon Oct 12 04:56:59 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 12 Oct 2009 09:56:59 +0100
Subject: [BioCatalogue-developers] Faster Search!
In-Reply-To: <4ACF0D5A.7040507@cs.man.ac.uk>
References: <4ACE8236.8000606@cs.man.ac.uk>	<d0ee827d0910090200ja6ba40as91a33573ff8aa4d5@mail.gmail.com>
	<4ACF0D5A.7040507@cs.man.ac.uk>
Message-ID: <4AD2EF5B.7030108@ebi.ac.uk>

A bit late... but then it can't be too late to say this is a great 
improvement! It makes a massive difference and even without the 
improvement on the operations tab, it make a lot of sense to release 
this as soon as possible. My believe is that when a user clicks on a 
particular service, they already have an interest in it and are more 
likely to tolerate a few more seconds.  Congrats Jits!

Eric



Jiten Bhagat wrote:
> I've noticed that certain searches, like for "protein" take between 3-4
> seconds. This isn't awful, but I'll look to see how I can improve this.
>
> Please let me know if you come across any other queries that take longer
> than 2 or so seconds.
>
> Cheers,
> Jits
>
>
> Franck Tanoh wrote:
>   
>> Jits,
>> Yep, search is very quick now, and i guess it will be quicker when we
>> move to the biocat live ...well done!
>> By the way the sandbox is :  http://sandbox.biocatalogue.org
>> <http://www.sandbox.biocatalogue.org/> without the 'www'.
>>
>> cheers,
>> Franck
>>
>> 2009/10/9 Jiten Bhagat <jits at cs.man.ac.uk <mailto:jits at cs.man.ac.uk>>
>>
>>     Hi guys,
>>
>>     I've committed some changes to search that I am very excited about (I
>>     know, I know, I need to get out more...)
>>
>>     I've now managed to bring down search performance to less than a
>>     second
>>     even on heavy searches like "ebi". This includes getting the search
>>     results from Solr, figuring out what associated objects are relevant,
>>     and rendering the view.
>>
>>     You can check it out now on the sandbox -
>>     http://www.sandbox.biocatalogue.org. Note that this is running on
>>     an old
>>     P4 3.0GHz with 2GB of RAM (I've given the Solr process half of
>>     that RAM,
>>     which helps). A search for "ebi" used to take 3 to 4 seconds and
>>     now it
>>     takes 1 to 1.2 seconds (!) I'm hoping that this is good enough now :-)
>>
>>     If you're interested in the gory details...
>>
>>     Firstly, I implemented the "simple" listings view. BUT this only gave
>>     between 10-15% improvement.
>>
>>     The massive perf boost has came from my latest change - modifying the
>>     models, acts_as_solr plugin and the search module to store the
>>     associations at index time as extra fields in Solr, and then using
>>     these
>>     at query time instead of doing all the mapping stuff I had implemented
>>     before (although the mapping stuff is still there as a fall back
>>     and is
>>     required at index time).
>>
>>     NOTE: this does mean that Solr will need to be restarted and then
>>     reindexed when we get to the live release. This reindexing process now
>>     takes a longer, partly because I have added some sleeps in the code so
>>     as not to push the Solr server to breaking point at index time,
>>     but all
>>     this for gains at query time.
>>
>>     Cheers,
>>     Jits
>>     _______________________________________________
>>     BioCatalogue-developers mailing list
>>     BioCatalogue-developers at rubyforge.org
>>     <mailto:BioCatalogue-developers at rubyforge.org>
>>     http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>
>>
>>
>>
>> -- 
>> "Science knows no country, because knowledge belongs to humanity, and
>> is the torch which illuminates the world." - Louis Pasteur
>>     
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From jits at cs.man.ac.uk  Mon Oct 12 06:36:31 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 12 Oct 2009 11:36:31 +0100
Subject: [BioCatalogue-developers] Faster Search!
In-Reply-To: <4AD2EF5B.7030108@ebi.ac.uk>
References: <4ACE8236.8000606@cs.man.ac.uk>	<d0ee827d0910090200ja6ba40as91a33573ff8aa4d5@mail.gmail.com>
	<4ACF0D5A.7040507@cs.man.ac.uk> <4AD2EF5B.7030108@ebi.ac.uk>
Message-ID: <4AD306AF.3040401@cs.man.ac.uk>

Thanks Eric.

> My believe is that when a user clicks on a particular service, they
> already have an interest in it and are more likely to tolerate a few
> more seconds.

That's a fair point. Hopefully ;-)

Jits


Eric Nzuobontane wrote:
> A bit late... but then it can't be too late to say this is a great
> improvement! It makes a massive difference and even without the
> improvement on the operations tab, it make a lot of sense to release
> this as soon as possible. My believe is that when a user clicks on a
> particular service, they already have an interest in it and are more
> likely to tolerate a few more seconds.  Congrats Jits!
>
> Eric
>
>
>
> Jiten Bhagat wrote:
>> I've noticed that certain searches, like for "protein" take between 3-4
>> seconds. This isn't awful, but I'll look to see how I can improve this.
>>
>> Please let me know if you come across any other queries that take longer
>> than 2 or so seconds.
>>
>> Cheers,
>> Jits
>>
>>
>> Franck Tanoh wrote:
>>  
>>> Jits,
>>> Yep, search is very quick now, and i guess it will be quicker when we
>>> move to the biocat live ...well done!
>>> By the way the sandbox is :  http://sandbox.biocatalogue.org
>>> <http://www.sandbox.biocatalogue.org/> without the 'www'.
>>>
>>> cheers,
>>> Franck
>>>
>>> 2009/10/9 Jiten Bhagat <jits at cs.man.ac.uk <mailto:jits at cs.man.ac.uk>>
>>>
>>>     Hi guys,
>>>
>>>     I've committed some changes to search that I am very excited
>>> about (I
>>>     know, I know, I need to get out more...)
>>>
>>>     I've now managed to bring down search performance to less than a
>>>     second
>>>     even on heavy searches like "ebi". This includes getting the search
>>>     results from Solr, figuring out what associated objects are
>>> relevant,
>>>     and rendering the view.
>>>
>>>     You can check it out now on the sandbox -
>>>     http://www.sandbox.biocatalogue.org. Note that this is running on
>>>     an old
>>>     P4 3.0GHz with 2GB of RAM (I've given the Solr process half of
>>>     that RAM,
>>>     which helps). A search for "ebi" used to take 3 to 4 seconds and
>>>     now it
>>>     takes 1 to 1.2 seconds (!) I'm hoping that this is good enough
>>> now :-)
>>>
>>>     If you're interested in the gory details...
>>>
>>>     Firstly, I implemented the "simple" listings view. BUT this only
>>> gave
>>>     between 10-15% improvement.
>>>
>>>     The massive perf boost has came from my latest change -
>>> modifying the
>>>     models, acts_as_solr plugin and the search module to store the
>>>     associations at index time as extra fields in Solr, and then using
>>>     these
>>>     at query time instead of doing all the mapping stuff I had
>>> implemented
>>>     before (although the mapping stuff is still there as a fall back
>>>     and is
>>>     required at index time).
>>>
>>>     NOTE: this does mean that Solr will need to be restarted and then
>>>     reindexed when we get to the live release. This reindexing
>>> process now
>>>     takes a longer, partly because I have added some sleeps in the
>>> code so
>>>     as not to push the Solr server to breaking point at index time,
>>>     but all
>>>     this for gains at query time.
>>>
>>>     Cheers,
>>>     Jits
>>>     _______________________________________________
>>>     BioCatalogue-developers mailing list
>>>     BioCatalogue-developers at rubyforge.org
>>>     <mailto:BioCatalogue-developers at rubyforge.org>
>>>     http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>
>>>
>>>
>>>
>>> -- 
>>> "Science knows no country, because knowledge belongs to humanity, and
>>> is the torch which illuminates the world." - Louis Pasteur
>>>     
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>   
>



From jerzyo at genesilico.pl  Mon Oct 12 13:57:57 2009
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Mon, 12 Oct 2009 18:57:57 +0100
Subject: [BioCatalogue-developers] need some name for biocat jamboree
In-Reply-To: <d0ee827d0910120942i63991e17g4f8783688cb8562@mail.gmail.com>
References: <d0ee827d0909290802p700c2b83jcf603a5b60b69167@mail.gmail.com>	<4AC224ED.5030808@ebi.ac.uk>
	<d0ee827d0910120942i63991e17g4f8783688cb8562@mail.gmail.com>
Message-ID: <4AD36E25.1010004@genesilico.pl>

JamBioree 2009?

Franck Tanoh pisze:
> Rodrigo,
>
> I contacted : Ying Cheng, Chen Li and Mahmut Uludag.
> Chen and Mahmut pointed me to their colleagues. As a result i have 3 
> people coming from the EBI which is enough for the mini jamboree. 
>
> Cheers,
> Franck
> -
>
> 2009/9/29 Rodrigo Lopez <rls at ebi.ac.uk <mailto:rls at ebi.ac.uk>>
>
>     List of potential contacts:
>
>     Bruno Aranda: baranda at ebi.ac.uk <mailto:baranda at ebi.ac.uk>
>     Ying Cheng: ycheng at ebi.ac.uk <mailto:ycheng at ebi.ac.uk>
>     Phil Jones: pjones at ebi.ac.uk <mailto:pjones at ebi.ac.uk>
>     Richard Cote: rcote at ebi.ac.uk <mailto:rcote at ebi.ac.uk>
>     Alan Horne: hornead at ebi.ac.uk <mailto:hornead at ebi.ac.uk>
>     Chen Li: chenli at ebi.ac.uk <mailto:chenli at ebi.ac.uk>
>     Mahmut Uludag: uludag at ebi.ac.uk <mailto:uludag at ebi.ac.uk>
>     Misha Kapushesky: ostolop at ebi.ac.uk <mailto:ostolop at ebi.ac.uk>
>     Paula de Matos: pmatos at ebi.ac.uk <mailto:pmatos at ebi.ac.uk>
>     Sam Patient: spatient at ebi.ac.uk <mailto:spatient at ebi.ac.uk>
>
>     Note: Some of the above are coordinators and the invitation should
>     imply that if they cannot attend themselves, then to nominate
>     someone. I'd be surprised if you get more than 3 positive replies
>     for the initial jamboree. People are *very* busy these days...
>
>     R:)
>
>
>     Franck Tanoh wrote:
>
>         Hi,
>
>         I want to invite one or 2 persons from the EBI for the annotation
>         jamboree on Nov 27.
>         Any suggestion please?
>
>         cheers,
>         Franck
>
>
>
>
> -- 
> "Science knows no country, because knowledge belongs to humanity, and 
> is the torch which illuminates the world." - Louis Pasteur
>
>
> ------------------------------------------------------------------------
>
> Scanned for malicious content. See headers for details.
> ------------------------------------------------------------------------
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From noreply at rubyforge.org  Tue Oct 13 08:52:40 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 13 Oct 2009 08:52:40 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2645] Tab persistency on user
	profile
Message-ID: <20091013125240.E8B0E1779935@rubyforge.org>

Task #2645 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Tab persistency on user profile
Complete: 90%
Status: Open

Description: If  you go to a user's page and click on the "services submitted", if you go to the "next" page, the tab goes back to "Profile".

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-13 12:52
By: fbacall

Comment:
Added appropriate filter to user_controller. Issue with tracking pages for each tab.

-------------------------------------------------------
Date: 2009-10-09 15:51
By: fbacall

Comment:
The code to set the right tab on page load works fine, it's just the use_tab_cookie setting in the session returns false and so the code doesn't run. Need to look into the point of that setting... 

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2645&group_id=6901&group_project_id=12540

From jits at cs.man.ac.uk  Fri Oct 16 12:39:38 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 16 Oct 2009 17:39:38 +0100
Subject: [BioCatalogue-developers] Faster Search!
In-Reply-To: <4ACF0D5A.7040507@cs.man.ac.uk>
References: <4ACE8236.8000606@cs.man.ac.uk>	<d0ee827d0910090200ja6ba40as91a33573ff8aa4d5@mail.gmail.com>
	<4ACF0D5A.7040507@cs.man.ac.uk>
Message-ID: <4AD8A1CA.5060509@cs.man.ac.uk>

Hi,

Just a quick update on this - by implementing a config option to disable
the post Solr object mapping, I have brought the search for "protein"
down from 3-4 seconds to 1.0-1.3 seconds.

I've done this config option so it's a falback... just in case disabling
it causes any issues (eg: not all relevant search results are being
returned because not all relevant associated object IDs are being
indexed/retrieved in Solr properly).

Let me know if you notice any other slowdowns.

Cheers,
Jits


Jiten Bhagat wrote:
> I've noticed that certain searches, like for "protein" take between 3-4
> seconds. This isn't awful, but I'll look to see how I can improve this.
>
> Please let me know if you come across any other queries that take longer
> than 2 or so seconds.
>
> Cheers,
> Jits
>
>
> Franck Tanoh wrote:
>   
>> Jits,
>> Yep, search is very quick now, and i guess it will be quicker when we
>> move to the biocat live ...well done!
>> By the way the sandbox is :  http://sandbox.biocatalogue.org
>> <http://www.sandbox.biocatalogue.org/> without the 'www'.
>>
>> cheers,
>> Franck
>>
>> 2009/10/9 Jiten Bhagat <jits at cs.man.ac.uk <mailto:jits at cs.man.ac.uk>>
>>
>>     Hi guys,
>>
>>     I've committed some changes to search that I am very excited about (I
>>     know, I know, I need to get out more...)
>>
>>     I've now managed to bring down search performance to less than a
>>     second
>>     even on heavy searches like "ebi". This includes getting the search
>>     results from Solr, figuring out what associated objects are relevant,
>>     and rendering the view.
>>
>>     You can check it out now on the sandbox -
>>     http://www.sandbox.biocatalogue.org. Note that this is running on
>>     an old
>>     P4 3.0GHz with 2GB of RAM (I've given the Solr process half of
>>     that RAM,
>>     which helps). A search for "ebi" used to take 3 to 4 seconds and
>>     now it
>>     takes 1 to 1.2 seconds (!) I'm hoping that this is good enough now :-)
>>
>>     If you're interested in the gory details...
>>
>>     Firstly, I implemented the "simple" listings view. BUT this only gave
>>     between 10-15% improvement.
>>
>>     The massive perf boost has came from my latest change - modifying the
>>     models, acts_as_solr plugin and the search module to store the
>>     associations at index time as extra fields in Solr, and then using
>>     these
>>     at query time instead of doing all the mapping stuff I had implemented
>>     before (although the mapping stuff is still there as a fall back
>>     and is
>>     required at index time).
>>
>>     NOTE: this does mean that Solr will need to be restarted and then
>>     reindexed when we get to the live release. This reindexing process now
>>     takes a longer, partly because I have added some sleeps in the code so
>>     as not to push the Solr server to breaking point at index time,
>>     but all
>>     this for gains at query time.
>>
>>     Cheers,
>>     Jits
>>     _______________________________________________
>>     BioCatalogue-developers mailing list
>>     BioCatalogue-developers at rubyforge.org
>>     <mailto:BioCatalogue-developers at rubyforge.org>
>>     http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>
>>
>>
>>
>> -- 
>> "Science knows no country, because knowledge belongs to humanity, and
>> is the torch which illuminates the world." - Louis Pasteur
>>     
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From MAILER-DAEMON at ebi.ac.uk  Sun Oct 18 07:07:31 2009
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Sun, 18 Oct 2009 12:07:31 +0100
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <200910181107.n9IB7VFu032307@spike.ebi.ac.uk>

The original message was received at Sun, 18 Oct 2009 12:05:54 +0100
from pweb-4a.ebi.ac.uk [172.18.1.109]

   ----- The following addresses had permanent fatal errors -----
<biocatalogue-developers at rubyforge.org>
    (reason: 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network)

   ----- Transcript of session follows -----
... while talking to rubyforge.org.:
>>> DATA
<<< 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network
550 5.1.1 <biocatalogue-developers at rubyforge.org>... User unknown
<<< 554 5.5.1 Error: no valid recipients
-------------- next part --------------
An embedded message was scrubbed...
From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
Subject: [Production ERROR] services#index
	(ActiveRecord::PreparedStatementInvalid) "wrong number of bind
	variables (0 for 3) in: `service_providers`.`name` IN
	('interviewer.inha.ac.kr]/?_PHPLIB[libdir]=http://www.difusion.com.mx/altair/libraries/openid/Auth/OpenID/.ht/one??')"
Date: Sun, 18 Oct 2009 12:05:53 +0100
Size: 14460
URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091018/d9337734/attachment-0001.mht>

From MAILER-DAEMON at ebi.ac.uk  Mon Oct 19 03:39:11 2009
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Mon, 19 Oct 2009 08:39:11 +0100
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <200910190739.n9J7dBO4022595@spike.ebi.ac.uk>

The original message was received at Mon, 19 Oct 2009 08:37:37 +0100
from pweb-4a.ebi.ac.uk [172.18.1.109]

   ----- The following addresses had permanent fatal errors -----
<biocatalogue-developers at rubyforge.org>
    (reason: 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network)

   ----- Transcript of session follows -----
... while talking to rubyforge.org.:
>>> DATA
<<< 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network
550 5.1.1 <biocatalogue-developers at rubyforge.org>... User unknown
<<< 554 5.5.1 Error: no valid recipients
-------------- next part --------------
An embedded message was scrubbed...
From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
Subject: [Production ERROR] services#index
	(ActiveRecord::PreparedStatementInvalid) "wrong number of bind
	variables (0 for 1) in: `service_providers`.`name` IN
	('interviewer.inha.ac.kr]///?_SERVER[DOCUMENT_ROOT]=http://buro16.ru/////id2.txt')"
Date: Mon, 19 Oct 2009 08:37:37 +0100
Size: 14020
URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091019/6f992fa0/attachment.mht>

From ericnzuo at ebi.ac.uk  Mon Oct 19 05:01:59 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 19 Oct 2009 10:01:59 +0100
Subject: [BioCatalogue-developers] annual report follow-up
Message-ID: <4ADC2B07.2050409@ebi.ac.uk>

Hi Guys,
As agreed in the last meeting, we need to come up with a set of 
statistics that will help Carole compile next annual report. From 
reading the previous report I came up with a set of questions which I 
think answering will help us come up with the numbers/graphs/tables.

Since it is a 5 page report, I believe we may need not as many 
tables/graphs... What do you guys thing are the most important table to 
produce so that we can see who is best place to produce them.

Eric


Some Questions to be answered by the stats for reports
======================================

1) Any evidence to show we did stop wasteful reinvention?
2) Any evidence to show we helped people find what is out there?
3) Evidence on the comprehensivity of the catalogue. Maybe stats on the 
services by domain for example?
4) Evidence of a wide user base, expert curators, service providers...?
5) Evidence(stats on) user annotations, annotations from other registries?
6) Evidence sustainability and improvement of backend infrastructure?
7) Evidence of out reach activities and indexing by search engines?
8) Evidence of service curation compliance with our annotation model?
9) Who are the major service providers?
10) Google analytics now wired in. What do we learn from its reports?
11) Collaboration with other projects : OMII-UK, myExperiment, seekda, 
EMBRACE, BioSapiens
12) Talk & and publications since the last report?
13) Community engagement going from  the pilot launch in December 2008 
to the full launch in July 2009.
14) SAB meetings & recommendations since the last report?

Eric



From MAILER-DAEMON at ebi.ac.uk  Mon Oct 19 06:03:07 2009
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Mon, 19 Oct 2009 11:03:07 +0100
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <200910191003.n9JA37F0010262@spike.ebi.ac.uk>

The original message was received at Mon, 19 Oct 2009 11:01:31 +0100
from pweb-3b.ebi.ac.uk [172.18.1.108]

   ----- The following addresses had permanent fatal errors -----
<biocatalogue-developers at rubyforge.org>
    (reason: 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network)

   ----- Transcript of session follows -----
... while talking to rubyforge.org.:
>>> DATA
<<< 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network
550 5.1.1 <biocatalogue-developers at rubyforge.org>... User unknown
<<< 554 5.5.1 Error: no valid recipients
-------------- next part --------------
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From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
Subject: [Production ERROR] services#index
	(ActiveRecord::PreparedStatementInvalid) "wrong number of bind
	variables (0 for 1) in: `service_providers`.`name` IN
	('mrs.cmbi.ru.nl]//ru/catalogue/?_SERVER[DOCUMENT_ROOT]=http://vandanashourie.com/logicampus-2.0.3/id.txt')"
Date: Mon, 19 Oct 2009 11:01:31 +0100
Size: 14316
URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091019/ec6f2044/attachment-0001.mht>

From MAILER-DAEMON at ebi.ac.uk  Mon Oct 19 06:25:41 2009
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Mon, 19 Oct 2009 11:25:41 +0100
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <200910191025.n9JAPfIM012945@spike.ebi.ac.uk>

The original message was received at Mon, 19 Oct 2009 11:24:06 +0100
from pweb-3b.ebi.ac.uk [172.18.1.108]

   ----- The following addresses had permanent fatal errors -----
<biocatalogue-developers at rubyforge.org>
    (reason: 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network)

   ----- Transcript of session follows -----
... while talking to rubyforge.org.:
>>> DATA
<<< 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network
550 5.1.1 <biocatalogue-developers at rubyforge.org>... User unknown
<<< 554 5.5.1 Error: no valid recipients
-------------- next part --------------
An embedded message was scrubbed...
From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
Subject: [Production ERROR] services#index
	(ActiveRecord::PreparedStatementInvalid) "wrong number of bind
	variables (0 for 1) in: `service_providers`.`name` IN
	('www.hsls.pitt.edu]//ru/catalogue/?_SERVER[DOCUMENT_ROOT]=http://vandanashourie.com/logicampus-2.0.3/id.txt')"
Date: Mon, 19 Oct 2009 11:24:06 +0100
Size: 14345
URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091019/c971d07a/attachment.mht>

From MAILER-DAEMON at ebi.ac.uk  Mon Oct 19 07:01:17 2009
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Mon, 19 Oct 2009 12:01:17 +0100
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <200910191101.n9JB1HdJ017416@spike.ebi.ac.uk>

The original message was received at Mon, 19 Oct 2009 11:59:44 +0100
from pweb-3b.ebi.ac.uk [172.18.1.108]

   ----- The following addresses had permanent fatal errors -----
<biocatalogue-developers at rubyforge.org>
    (reason: 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network)

   ----- Transcript of session follows -----
... while talking to rubyforge.org.:
>>> DATA
<<< 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network
550 5.1.1 <biocatalogue-developers at rubyforge.org>... User unknown
<<< 554 5.5.1 Error: no valid recipients
-------------- next part --------------
An embedded message was scrubbed...
From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
Subject: [Production ERROR] application#show (ActionView::TemplateError)
	"undefined method `name' for nil:NilClass"
Date: Mon, 19 Oct 2009 11:59:44 +0100
Size: 9795
URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091019/d1dfc608/attachment.mht>

From noreply at rubyforge.org  Mon Oct 19 09:27:18 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 19 Oct 2009 09:27:18 -0400 (EDT)
Subject: [BioCatalogue-developers] [1170] branches/jerzy/: getting new branch
Message-ID: <20091019132718.60746185828D@rubyforge.org>

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From noreply at rubyforge.org  Mon Oct 19 09:28:14 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 19 Oct 2009 09:28:14 -0400 (EDT)
Subject: [BioCatalogue-developers] [1171] branches/jerzy/: branch for jerzy
	for adding raw text input search
Message-ID: <20091019132814.7133F185828D@rubyforge.org>

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From MAILER-DAEMON at ebi.ac.uk  Mon Oct 19 11:23:34 2009
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Mon, 19 Oct 2009 16:23:34 +0100
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <200910191523.n9JFNYkF020121@spike.ebi.ac.uk>

The original message was received at Mon, 19 Oct 2009 16:22:00 +0100
from pweb-3b.ebi.ac.uk [172.18.1.108]

   ----- The following addresses had permanent fatal errors -----
<biocatalogue-developers at rubyforge.org>
    (reason: 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network)

   ----- Transcript of session follows -----
... while talking to rubyforge.org.:
>>> DATA
<<< 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network
550 5.1.1 <biocatalogue-developers at rubyforge.org>... User unknown
<<< 554 5.5.1 Error: no valid recipients
-------------- next part --------------
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From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
Subject: [Production ERROR] sessions#create
	(ActionController::InvalidAuthenticityToken)
	"ActionController::InvalidAuthenticityToken"
Date: Mon, 19 Oct 2009 16:22:00 +0100
Size: 13630
URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091019/c10a552e/attachment.mht>

From noreply at rubyforge.org  Mon Oct 19 11:42:35 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 19 Oct 2009 11:42:35 -0400 (EDT)
Subject: [BioCatalogue-developers] [1172] trunk/public/2009/xml/rest: Added
 the xlink. xsd file from the Taverna 1 Server codebase,
 in the hope that this will work with JAXB.
Message-ID: <20091019154235.35D3A1858282@rubyforge.org>

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From noreply at rubyforge.org  Mon Oct 19 11:59:48 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 19 Oct 2009 11:59:48 -0400 (EDT)
Subject: [BioCatalogue-developers] [1173]
	trunk/public/2009/xml/rest/schema-v1.xsd: Minor fix
Message-ID: <20091019155948.B34C418581EF@rubyforge.org>

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From noreply at rubyforge.org  Mon Oct 19 12:22:29 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 19 Oct 2009 12:22:29 -0400 (EDT)
Subject: [BioCatalogue-developers] [1174]
 trunk/app/views/users/show.html.erb: Bugfix - edit account/ profile button
 should only be shown for the current user's profile page.
Message-ID: <20091019162230.00F821858267@rubyforge.org>

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From noreply at rubyforge.org  Mon Oct 19 12:31:28 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 19 Oct 2009 12:31:28 -0400 (EDT)
Subject: [BioCatalogue-developers] [1175] trunk/app: Implemented the ability
 to delete a service from the catalogue.
Message-ID: <20091019163128.E3BF8185828D@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 20 04:55:01 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 20 Oct 2009 04:55:01 -0400 (EDT)
Subject: [BioCatalogue-developers] [1176] branches/rest-services-support:
 first iteration of the UI mockup for rest support;
 also fixed some fixtures to allow for functional tests
Message-ID: <20091020085501.D727A18582BF@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 20 06:10:36 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 20 Oct 2009 06:10:36 -0400 (EDT)
Subject: [BioCatalogue-developers] [1177] trunk: Merged the changes Mannie
 made for functional tests, from the rest-services-support branch,
 revision 1158.
Message-ID: <20091020101036.257FC18582CB@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 20 06:11:08 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 20 Oct 2009 06:11:08 -0400 (EDT)
Subject: [BioCatalogue-developers] [1178] branches/rest-services-support/:
 Deleting in order to recreate from latest trunk
Message-ID: <20091020101108.8AF4918582CB@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 20 06:11:50 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 20 Oct 2009 06:11:50 -0400 (EDT)
Subject: [BioCatalogue-developers] [1179] branches/rest-services-support/:
 New branch for the REST services support.
Message-ID: <20091020101150.D4ED318582BC@rubyforge.org>

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From jits at cs.man.ac.uk  Tue Oct 20 08:39:26 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 20 Oct 2009 13:39:26 +0100
Subject: [BioCatalogue-developers] annual report follow-up
In-Reply-To: <4ADC2B07.2050409@ebi.ac.uk>
References: <4ADC2B07.2050409@ebi.ac.uk>
Message-ID: <4ADDAF7E.3090808@cs.man.ac.uk>

Hi Eric,

This is a very useful list to work off of.

I forgot what we agreed on yesterday in terms of the break down of who
does what for the stats...

Jits


Eric Nzuobontane wrote:
> Hi Guys,
> As agreed in the last meeting, we need to come up with a set of
> statistics that will help Carole compile next annual report. From
> reading the previous report I came up with a set of questions which I
> think answering will help us come up with the numbers/graphs/tables.
>
> Since it is a 5 page report, I believe we may need not as many
> tables/graphs... What do you guys thing are the most important table
> to produce so that we can see who is best place to produce them.
>
> Eric
>
>
> Some Questions to be answered by the stats for reports
> ======================================
>
> 1) Any evidence to show we did stop wasteful reinvention?
> 2) Any evidence to show we helped people find what is out there?
> 3) Evidence on the comprehensivity of the catalogue. Maybe stats on
> the services by domain for example?
> 4) Evidence of a wide user base, expert curators, service providers...?
> 5) Evidence(stats on) user annotations, annotations from other
> registries?
> 6) Evidence sustainability and improvement of backend infrastructure?
> 7) Evidence of out reach activities and indexing by search engines?
> 8) Evidence of service curation compliance with our annotation model?
> 9) Who are the major service providers?
> 10) Google analytics now wired in. What do we learn from its reports?
> 11) Collaboration with other projects : OMII-UK, myExperiment, seekda,
> EMBRACE, BioSapiens
> 12) Talk & and publications since the last report?
> 13) Community engagement going from  the pilot launch in December 2008
> to the full launch in July 2009.
> 14) SAB meetings & recommendations since the last report?
>
> Eric
>
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From noreply at rubyforge.org  Tue Oct 20 11:59:04 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 20 Oct 2009 11:59:04 -0400 (EDT)
Subject: [BioCatalogue-developers] [1180] trunk: Fixed / stats and made into
 completely into an asynchronous task.
Message-ID: <20091020155904.D3FEB1D7882B@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 20 12:37:07 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 20 Oct 2009 12:37:07 -0400 (EDT)
Subject: [BioCatalogue-developers] [1181] trunk: Style and layout changes
	for the stats page.
Message-ID: <20091020163707.BD6311D7882B@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 20 13:06:39 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 20 Oct 2009 13:06:39 -0400 (EDT)
Subject: [BioCatalogue-developers] [1182] trunk: Style fix for buttons
Message-ID: <20091020170639.C6FF318582C1@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 20 13:41:05 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 20 Oct 2009 13:41:05 -0400 (EDT)
Subject: [BioCatalogue-developers] [1183] trunk: Better error handling for
	the WSDL parsing stuff.
Message-ID: <20091020174105.29B8E18582C1@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 20 13:41:27 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 20 Oct 2009 13:41:27 -0400 (EDT)
Subject: [BioCatalogue-developers] [1184] branches/rest-api/: Deleted old
	branch
Message-ID: <20091020174127.806F8185826F@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 20 13:41:50 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 20 Oct 2009 13:41:50 -0400 (EDT)
Subject: [BioCatalogue-developers] [1185] branches/actsassolr_upgrade/:
	Deleting old branch
Message-ID: <20091020174150.B82E11D7882B@rubyforge.org>

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From jits at cs.man.ac.uk  Wed Oct 21 05:20:23 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 21 Oct 2009 10:20:23 +0100
Subject: [BioCatalogue-developers] WSDL Parsing
Message-ID: <4ADED257.3030300@cs.man.ac.uk>

Hi Eric,

I've been trying to set up the WSDLUtils service on my computer but it
didn't work the first time. The solution turned out to be this:

<http://blog.namran.net/2009/03/10/php-fatal-error-class-domdocument-not-found-in-blabla/>

You might want to add this to the readme file and wiki page.

Cheers,
Jits

PS: I also get these errors but they don't seem to be show stoppers -

[Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Warning: 
Call-time pass-by-reference has been deprecated in
/var/www/WSDLUtils/ValidatorWrapper.php on line 35
[Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Warning: 
Call-time pass-by-reference has been deprecated in
/var/www/WSDLUtils/ValidatorWrapper.php on line 64
[Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Notice: 
Undefined index:  wsdl_uri in /var/www/WSDLUtils/WSDLUtils.php on line 16
[Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Notice: 
Undefined index:  wsdl_uri in /var/www/WSDLUtils/WSDLUtils.php on line 18
[Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Notice: 
Undefined index:  method in /var/www/WSDLUtils/WSDLUtils.php on line 27
[Wed Oct 21 10:18:51 2009] [error] [client 127.0.0.1] PHP Warning: 
DOMDocument::load(): supplied argument is not a valid Stream-Context
resource in /var/www/WSDLUtils/WSDLParser/WSDLXmlSchemaParser.php on line 24


From noreply at rubyforge.org  Wed Oct 21 05:42:18 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 21 Oct 2009 05:42:18 -0400 (EDT)
Subject: [BioCatalogue-developers] [1186] trunk/lib/bio_catalogue/util.rb:
 Bugfix for the util method that parses out metadata for Solr from a Hash
Message-ID: <20091021094219.1EE571D78831@rubyforge.org>

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From jits at cs.man.ac.uk  Wed Oct 21 10:47:07 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 21 Oct 2009 15:47:07 +0100
Subject: [BioCatalogue-developers] new terms and conditions
In-Reply-To: <d0ee827d0909300400g7e976bb5xc869b9d45815db81@mail.gmail.com>
References: <d0ee827d0909300400g7e976bb5xc869b9d45815db81@mail.gmail.com>
Message-ID: <4ADF1EEB.60200@cs.man.ac.uk>

Where can I get the latest version from?

Jits


Franck Tanoh wrote:
> Hi guys,
> please, do update our terms and conditions when doing the next release.
>
> cheers,
> Franck
>
>   


From ytanoh at cs.man.ac.uk  Wed Oct 21 11:34:26 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 21 Oct 2009 16:34:26 +0100
Subject: [BioCatalogue-developers] new terms and conditions
In-Reply-To: <4ADF1EEB.60200@cs.man.ac.uk>
References: <d0ee827d0909300400g7e976bb5xc869b9d45815db81@mail.gmail.com>
	<4ADF1EEB.60200@cs.man.ac.uk>
Message-ID: <28F05E71-D196-4CF1-ADB4-53D2DB05A317@cs.man.ac.uk>

It is in dropbox (other directory)

Franck

On 21 Oct 2009, at 15:47, Jiten Bhagat wrote:

> Where can I get the latest version from?
>
> Jits
>
>
> Franck Tanoh wrote:
>> Hi guys,
>> please, do update our terms and conditions when doing the next  
>> release.
>>
>> cheers,
>> Franck
>>
>>
>


From noreply at rubyforge.org  Wed Oct 21 11:41:34 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 21 Oct 2009 11:41:34 -0400 (EDT)
Subject: [BioCatalogue-developers] [1187] trunk/app: Added rel= nofollow to
 any user contributed links that are shown in the UI.
Message-ID: <20091021154134.72CAC1D78847@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Thu Oct 22 03:34:03 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 22 Oct 2009 08:34:03 +0100
Subject: [BioCatalogue-developers] WSDL Parsing
In-Reply-To: <4ADED257.3030300@cs.man.ac.uk>
References: <4ADED257.3030300@cs.man.ac.uk>
Message-ID: <4AE00AEB.5070208@ebi.ac.uk>

Hi Jits,
Thanks for the information. I guess maybe because that may have already 
been installed on my mac and the test server where I have tried the 
parser so far, I did not know about the problem.
So apart from getting it to work, is it working as expected? Are there 
thing we should do differently?

Eric



Jiten Bhagat wrote:
> Hi Eric,
>
> I've been trying to set up the WSDLUtils service on my computer but it
> didn't work the first time. The solution turned out to be this:
>
> <http://blog.namran.net/2009/03/10/php-fatal-error-class-domdocument-not-found-in-blabla/>
>
> You might want to add this to the readme file and wiki page.
>
> Cheers,
> Jits
>
> PS: I also get these errors but they don't seem to be show stoppers -
>
> [Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Warning: 
> Call-time pass-by-reference has been deprecated in
> /var/www/WSDLUtils/ValidatorWrapper.php on line 35
> [Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Warning: 
> Call-time pass-by-reference has been deprecated in
> /var/www/WSDLUtils/ValidatorWrapper.php on line 64
> [Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Notice: 
> Undefined index:  wsdl_uri in /var/www/WSDLUtils/WSDLUtils.php on line 16
> [Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Notice: 
> Undefined index:  wsdl_uri in /var/www/WSDLUtils/WSDLUtils.php on line 18
> [Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Notice: 
> Undefined index:  method in /var/www/WSDLUtils/WSDLUtils.php on line 27
> [Wed Oct 21 10:18:51 2009] [error] [client 127.0.0.1] PHP Warning: 
> DOMDocument::load(): supplied argument is not a valid Stream-Context
> resource in /var/www/WSDLUtils/WSDLParser/WSDLXmlSchemaParser.php on line 24
>   


From ericnzuo at ebi.ac.uk  Fri Oct 23 04:32:55 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Fri, 23 Oct 2009 09:32:55 +0100
Subject: [BioCatalogue-developers] BBSRC report
Message-ID: <4AE16A37.3040605@ebi.ac.uk>

Hi Guys,
Please find attached a copy of the the stats for report I have been 
generating with Rodrigo's guidance. There are quite a few things in 
there but there are quite a few bits missing as well.
Some of the thing that need to be done include:
1) Making the report consistent over the period January 2009 -> October 
20th, with a marker for the date of the launch, July 1, 2009
2) Stats on the best/worst annotated services. I have written a little 
script to give me annotation counts per service. However this does not 
include provider descriptions. But it is fairly accurate. My first look 
at it shows that many of the annotations are from feta. I think we 
should have at least half of these services manually annotated by us.
3) Stats on Tag clouds, and some image of the tag cloud
4) 1-2 page report on activities like testing which are not available 
from the stats.

Eric


From ytanoh at cs.man.ac.uk  Fri Oct 23 05:02:18 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Fri, 23 Oct 2009 10:02:18 +0100
Subject: [BioCatalogue-developers] BBSRC report
In-Reply-To: <4AE16A37.3040605@ebi.ac.uk>
References: <4AE16A37.3040605@ebi.ac.uk>
Message-ID: <769BE973-F13B-4D59-A34F-A5547A663AE0@cs.man.ac.uk>

Hi Eric,

> Please find attached a copy of the the stats for report
nothing attached

> My first look at it shows that many of the annotations are from  
> feta. I think we should have at least half of these services  
> manually annotated by us.
not sure, I understand the second sentence, I manually curated all the  
annotation from feta.

Franck

On 23 Oct 2009, at 09:32, Eric Nzuobontane wrote:

> Hi Guys,
> Please find attached a copy of the the stats for report I have been  
> generating with Rodrigo's guidance. There are quite a few things in  
> there but there are quite a few bits missing as well.
> Some of the thing that need to be done include:
> 1) Making the report consistent over the period January 2009 ->  
> October 20th, with a marker for the date of the launch, July 1, 2009
> 2) Stats on the best/worst annotated services. I have written a  
> little script to give me annotation counts per service. However this  
> does not include provider descriptions. But it is fairly accurate.  
> My first look at it shows that many of the annotations are from  
> feta. I think we should have at least half of these services  
> manually annotated by us.
> 3) Stats on Tag clouds, and some image of the tag cloud
> 4) 1-2 page report on activities like testing which are not  
> available from the stats.
>
> Eric
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From jits at cs.man.ac.uk  Fri Oct 23 06:14:26 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 23 Oct 2009 11:14:26 +0100
Subject: [BioCatalogue-developers] WSDL Parsing
In-Reply-To: <4AE00AEB.5070208@ebi.ac.uk>
References: <4ADED257.3030300@cs.man.ac.uk> <4AE00AEB.5070208@ebi.ac.uk>
Message-ID: <4AE18202.9030408@cs.man.ac.uk>

Eric Nzuobontane wrote:
> Hi Jits,
> Thanks for the information. I guess maybe because that may have
> already been installed on my mac and the test server where I have
> tried the parser so far, I did not know about the problem.
> So apart from getting it to work, is it working as expected? Are there
> thing we should do differently?

It looks fine to me so far. I'm just building the UI for the
computational type details and then we can deploy this on the test server.

Cheers
Jits

>
> Eric
>
>
>
> Jiten Bhagat wrote:
>> Hi Eric,
>>
>> I've been trying to set up the WSDLUtils service on my computer but it
>> didn't work the first time. The solution turned out to be this:
>>
>> <http://blog.namran.net/2009/03/10/php-fatal-error-class-domdocument-not-found-in-blabla/>
>>
>>
>> You might want to add this to the readme file and wiki page.
>>
>> Cheers,
>> Jits
>>
>> PS: I also get these errors but they don't seem to be show stoppers -
>>
>> [Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Warning:
>> Call-time pass-by-reference has been deprecated in
>> /var/www/WSDLUtils/ValidatorWrapper.php on line 35
>> [Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Warning:
>> Call-time pass-by-reference has been deprecated in
>> /var/www/WSDLUtils/ValidatorWrapper.php on line 64
>> [Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Notice:
>> Undefined index:  wsdl_uri in /var/www/WSDLUtils/WSDLUtils.php on
>> line 16
>> [Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Notice:
>> Undefined index:  wsdl_uri in /var/www/WSDLUtils/WSDLUtils.php on
>> line 18
>> [Wed Oct 21 10:18:50 2009] [error] [client 127.0.0.1] PHP Notice:
>> Undefined index:  method in /var/www/WSDLUtils/WSDLUtils.php on line 27
>> [Wed Oct 21 10:18:51 2009] [error] [client 127.0.0.1] PHP Warning:
>> DOMDocument::load(): supplied argument is not a valid Stream-Context
>> resource in /var/www/WSDLUtils/WSDLParser/WSDLXmlSchemaParser.php on
>> line 24
>>   
>


From noreply at rubyforge.org  Fri Oct 23 06:41:01 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 23 Oct 2009 06:41:01 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2785] Refresh of Stats page
	generates exception
Message-ID: <20091023104101.61364158805C@rubyforge.org>

Task #2785 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Refresh of Stats page generates exception
Complete: 100%
Status: Closed

Description: Refreshing the stats page on the live site  throws an exception.  

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-23 10:41
By: jits

Comment:
Fixed, and now refresh is moved into a seperate background process (aka delayed job)

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2785&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Fri Oct 23 06:41:40 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 23 Oct 2009 06:41:40 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2635] Make stats calculations run
	as a background task
Message-ID: <20091023104141.05C05158805C@rubyforge.org>

Task #2635 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Make stats calculations run as a background task
Complete: 100%
Status: Closed

Description: Right now the stats run within a request. which is baaad. Make this run as an asynchronous background task instead.

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-23 10:41
By: jits

Comment:
Done

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2635&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Fri Oct 23 06:42:57 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 23 Oct 2009 06:42:57 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2825] Stats: better error handling
Message-ID: <20091023104257.DD472185827F@rubyforge.org>

Task #2825 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Stats: better error handling
Complete: 0%
Status: Open

Description: Since the stats are cached and only regenerated every now and then, the view that renders needs to take into account non-existent services etc etc

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2825&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Fri Oct 23 07:03:04 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 23 Oct 2009 07:03:04 -0400 (EDT)
Subject: [BioCatalogue-developers] [1188] trunk: Fixes for the stats page:
Message-ID: <20091023110304.2A8CE16782AF@rubyforge.org>

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From noreply at rubyforge.org  Fri Oct 23 07:03:33 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 23 Oct 2009 07:03:33 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2766] Stats should take into
	account unactivated vs activated users
Message-ID: <20091023110333.DF0EC185827F@rubyforge.org>

Task #2766 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Stats should take into account unactivated vs activated users
Complete: 100%
Status: Closed

Description: Check the stats generation code to make sure we distinguish between unactivated vs activated users

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-23 11:03
By: jits

Comment:
Fixed, in revision 1188

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2766&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Fri Oct 23 07:05:03 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 23 Oct 2009 07:05:03 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2826] Stats: add categories stats
Message-ID: <20091023110504.0391C158805C@rubyforge.org>

Task #2826 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Stats: add categories stats
Complete: 0%
Status: Open

Description: Like the number of services that each category has, etc

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2826&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Fri Oct 23 07:05:28 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 23 Oct 2009 07:05:28 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2827] Stats: add tags section
Message-ID: <20091023110528.70528158805C@rubyforge.org>

Task #2827 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Stats: add tags section
Complete: 0%
Status: Open

Description: Eg: the frequency of each tag, etc

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2827&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Fri Oct 23 07:16:31 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 23 Oct 2009 07:16:31 -0400 (EDT)
Subject: [BioCatalogue-developers] [1189] trunk: Intial UI for displaying
 the computational type details of Soap Inputs and Outputs .
Message-ID: <20091023111632.2901F158805C@rubyforge.org>

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From noreply at rubyforge.org  Fri Oct 23 07:20:33 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 23 Oct 2009 07:20:33 -0400 (EDT)
Subject: [BioCatalogue-developers] [1190] trunk: Minor style refactoring and
	update.
Message-ID: <20091023112033.F2451158805C@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Fri Oct 23 08:58:32 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Fri, 23 Oct 2009 13:58:32 +0100
Subject: [BioCatalogue-developers] BBSRC report
In-Reply-To: <d0ee827d0910230437r33d4ce54id494123e5ce0c991@mail.gmail.com>
References: <4AE16A37.3040605@ebi.ac.uk>	
	<769BE973-F13B-4D59-A34F-A5547A663AE0@cs.man.ac.uk>	
	<4AE173A4.1020900@ebi.ac.uk>
	<d0ee827d0910230437r33d4ce54id494123e5ce0c991@mail.gmail.com>
Message-ID: <4AE1A878.7040102@ebi.ac.uk>


>
> good report, Carole may not need all info but we can use it as a 
> skeleton to gather usage trend of the biocat. Can be useful for talk, 
> demo, presentation etc. I'm thinking we can have this on the wiki and 
> update the number and possibly picture on a monthly basis.
Agreed, this report should be a guidance to the stats that we need 
produce. We could develop a suit of tools that could generate them on 
the fly.

> I don't think you need to list service without annotation in the 
> report...anyway there are so many of them.
No, see the latest version of the report
> As for writing a script to find the most annotated service, that can 
> be tricky because all the services don't have the same number of 
> operations and what we define by annotation is sometimes meaningless 
> for the user (things like xsd:int). 
> By the way what do you mean by 'most annotated service'? do you mean 
> service with annotations from different sources ( automation, several 
> user, ...). Or do you just mean services which have all their 
> component annotated? 
well, what I meant was services that have their components annotated. It 
would be interesting to see how the services I came up with as the most 
annotated compare with what you expect as annotations. One thing I note 
is that there is a strong correlation btw the number of annotations and 
the number of operations for a service. But hey, it not about the 
quality of annotations, rather the quantity. Quality will be hard to 
measure.
> if you mean the later, the list I sent yesterday is fine.
I produced the list from my script. Thanks!

Eric

>
> Franck
>
> 2009/10/23 Eric Nzuobontane <ericnzuo at ebi.ac.uk 
> <mailto:ericnzuo at ebi.ac.uk>>
>
>     attached now. Sorry about that!
>
>     OK, those annotations from feta are classed as coming from other
>     registries.  How feta relates to BioCatalogue is not very clear!.
>
>     Eric
>
>
>
>
>     Franck Tanoh wrote:
>
>         Hi Eric,
>
>             Please find attached a copy of the the stats for report
>
>         nothing attached
>
>             My first look at it shows that many of the annotations are
>             from feta. I think we should have at least half of these
>             services manually annotated by us.
>
>         not sure, I understand the second sentence, I manually curated
>         all the annotation from feta.
>
>         Franck
>
>         On 23 Oct 2009, at 09:32, Eric Nzuobontane wrote:
>
>             Hi Guys,
>             Please find attached a copy of the the stats for report I
>             have been generating with Rodrigo's guidance. There are
>             quite a few things in there but there are quite a few bits
>             missing as well.
>             Some of the thing that need to be done include:
>             1) Making the report consistent over the period January
>             2009 -> October 20th, with a marker for the date of the
>             launch, July 1, 2009
>             2) Stats on the best/worst annotated services. I have
>             written a little script to give me annotation counts per
>             service. However this does not include provider
>             descriptions. But it is fairly accurate. My first look at
>             it shows that many of the annotations are from feta. I
>             think we should have at least half of these services
>             manually annotated by us.
>             3) Stats on Tag clouds, and some image of the tag cloud
>             4) 1-2 page report on activities like testing which are
>             not available from the stats.
>
>             Eric
>
>             _______________________________________________
>             BioCatalogue-developers mailing list
>             BioCatalogue-developers at rubyforge.org
>             <mailto:BioCatalogue-developers at rubyforge.org>
>             http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>
>
>
>
>
> -- 
> "Science knows no country, because knowledge belongs to humanity, and 
> is the torch which illuminates the world." - Louis Pasteur


From noreply at rubyforge.org  Fri Oct 23 10:00:13 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 23 Oct 2009 10:00:13 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2828] flag services/annotation to
	be deleted
Message-ID: <20091023140014.4147316782B2@rubyforge.org>

Task #2828 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: flag services/annotation to be deleted 
Complete: 0%
Status: Open

Description: can we flag service or annotation before deletion. For example, keep them in the catalogue for 1 or week or 2 with the delete flag; then inform the submitter that his service/annotation is going to be deleted; 

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2828&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Fri Oct 23 10:07:13 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 23 Oct 2009 10:07:13 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2829] unable to see all search
	result
Message-ID: <20091023140713.734FA16782B1@rubyforge.org>

Task #2829 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: unable to see all search result 
Complete: 0%
Status: Open

Description: when i do a search with the provider name such as 'dev.biordf.net' or 'www.ebi.ac.uk', i'm unable to view all the search result. there is a 'Unable to Process Requested Data' when i try to access page 3, 4 etc...

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2829&group_id=6901&group_project_id=12540

From ytanoh at cs.man.ac.uk  Fri Oct 23 10:09:39 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Fri, 23 Oct 2009 15:09:39 +0100
Subject: [BioCatalogue-developers] BBSRC report
In-Reply-To: <4AE1A878.7040102@ebi.ac.uk>
References: <4AE16A37.3040605@ebi.ac.uk>	
	<769BE973-F13B-4D59-A34F-A5547A663AE0@cs.man.ac.uk>	
	<4AE173A4.1020900@ebi.ac.uk>
	<d0ee827d0910230437r33d4ce54id494123e5ce0c991@mail.gmail.com>
	<4AE1A878.7040102@ebi.ac.uk>
Message-ID: <FA060E59-4ED3-43D2-B546-4B894E44A44F@cs.man.ac.uk>

Eric,

please, do not forget to send the file on the main list for Carole.

Franck

On 23 Oct 2009, at 13:58, Eric Nzuobontane wrote:

>
>>
>> good report, Carole may not need all info but we can use it as a  
>> skeleton to gather usage trend of the biocat. Can be useful for  
>> talk, demo, presentation etc. I'm thinking we can have this on the  
>> wiki and update the number and possibly picture on a monthly basis.
> Agreed, this report should be a guidance to the stats that we need  
> produce. We could develop a suit of tools that could generate them  
> on the fly.
>
>> I don't think you need to list service without annotation in the  
>> report...anyway there are so many of them.
> No, see the latest version of the report
>> As for writing a script to find the most annotated service, that  
>> can be tricky because all the services don't have the same number  
>> of operations and what we define by annotation is sometimes  
>> meaningless for the user (things like xsd:int). By the way what do  
>> you mean by 'most annotated service'? do you mean service with  
>> annotations from different sources ( automation, several  
>> user, ...). Or do you just mean services which have all their  
>> component annotated?
> well, what I meant was services that have their components  
> annotated. It would be interesting to see how the services I came up  
> with as the most annotated compare with what you expect as  
> annotations. One thing I note is that there is a strong correlation  
> btw the number of annotations and the number of operations for a  
> service. But hey, it not about the quality of annotations, rather  
> the quantity. Quality will be hard to measure.
>> if you mean the later, the list I sent yesterday is fine.
> I produced the list from my script. Thanks!
>
> Eric
>
>>
>> Franck
>>
>> 2009/10/23 Eric Nzuobontane <ericnzuo at ebi.ac.uk <mailto:ericnzuo at ebi.ac.uk 
>> >>
>>
>>    attached now. Sorry about that!
>>
>>    OK, those annotations from feta are classed as coming from other
>>    registries.  How feta relates to BioCatalogue is not very clear!.
>>
>>    Eric
>>
>>
>>
>>
>>    Franck Tanoh wrote:
>>
>>        Hi Eric,
>>
>>            Please find attached a copy of the the stats for report
>>
>>        nothing attached
>>
>>            My first look at it shows that many of the annotations are
>>            from feta. I think we should have at least half of these
>>            services manually annotated by us.
>>
>>        not sure, I understand the second sentence, I manually curated
>>        all the annotation from feta.
>>
>>        Franck
>>
>>        On 23 Oct 2009, at 09:32, Eric Nzuobontane wrote:
>>
>>            Hi Guys,
>>            Please find attached a copy of the the stats for report I
>>            have been generating with Rodrigo's guidance. There are
>>            quite a few things in there but there are quite a few bits
>>            missing as well.
>>            Some of the thing that need to be done include:
>>            1) Making the report consistent over the period January
>>            2009 -> October 20th, with a marker for the date of the
>>            launch, July 1, 2009
>>            2) Stats on the best/worst annotated services. I have
>>            written a little script to give me annotation counts per
>>            service. However this does not include provider
>>            descriptions. But it is fairly accurate. My first look at
>>            it shows that many of the annotations are from feta. I
>>            think we should have at least half of these services
>>            manually annotated by us.
>>            3) Stats on Tag clouds, and some image of the tag cloud
>>            4) 1-2 page report on activities like testing which are
>>            not available from the stats.
>>
>>            Eric
>>
>>            _______________________________________________
>>            BioCatalogue-developers mailing list
>>            BioCatalogue-developers at rubyforge.org
>>            <mailto:BioCatalogue-developers at rubyforge.org>
>>            http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>
>>
>>
>>
>>
>> -- 
>> "Science knows no country, because knowledge belongs to humanity,  
>> and is the torch which illuminates the world." - Louis Pasteur
>


From noreply at rubyforge.org  Fri Oct 23 11:35:44 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 23 Oct 2009 11:35:44 -0400 (EDT)
Subject: [BioCatalogue-developers] [1191]
 branches/rest-services-support/app/views/rest_services/new.html.erb:
 updated UI for rest service support
Message-ID: <20091023153544.94F4318582C2@rubyforge.org>

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From MAILER-DAEMON at ebi.ac.uk  Sun Oct 25 04:49:33 2009
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Sun, 25 Oct 2009 08:49:33 GMT
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <200910250849.n9P8nX1p021190@spike.ebi.ac.uk>

The original message was received at Sun, 25 Oct 2009 08:47:58 GMT
from pweb-3b.ebi.ac.uk [172.18.1.108]

   ----- The following addresses had permanent fatal errors -----
<biocatalogue-developers at rubyforge.org>
    (reason: 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network)

   ----- Transcript of session follows -----
... while talking to rubyforge.org.:
>>> DATA
<<< 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network
550 5.1.1 <biocatalogue-developers at rubyforge.org>... User unknown
<<< 554 5.5.1 Error: no valid recipients
-------------- next part --------------
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From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
Subject: [Production ERROR] services#index
	(ActiveRecord::PreparedStatementInvalid) "wrong number of bind
	variables (0 for 2) in: `service_providers`.`name` IN ('duoshare.com',
	'interviewer.inha.ac.kr]//?_SERVER[DOCUMENT_ROOT]=http://www.parrocchialucrezia.it/components/com_joomlalib/standalone/id.txt?')"
Date: Sun, 25 Oct 2009 08:47:57 +0000
Size: 14751
URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091025/13e121fa/attachment.mht>

From noreply at rubyforge.org  Sun Oct 25 16:11:07 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 25 Oct 2009 16:11:07 -0400 (EDT)
Subject: [BioCatalogue-developers] [1192] trunk: Work on stats page:
Message-ID: <20091025201107.4638B1588060@rubyforge.org>

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From noreply at rubyforge.org  Sun Oct 25 18:17:58 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 25 Oct 2009 18:17:58 -0400 (EDT)
Subject: [BioCatalogue-developers] [1193] trunk: Further revamp of the stats
	page:
Message-ID: <20091025221759.0BDFF1588060@rubyforge.org>

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From noreply at rubyforge.org  Sun Oct 25 19:14:05 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 25 Oct 2009 19:14:05 -0400 (EDT)
Subject: [BioCatalogue-developers] [1194] trunk: Added tags section to stats
	page.
Message-ID: <20091025231405.3F86D185826F@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Mon Oct 26 07:43:27 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 26 Oct 2009 11:43:27 +0000
Subject: [BioCatalogue-developers] is service relevant to BioCatalogue?
Message-ID: <4AE58B5F.1010103@ebi.ac.uk>

Hi Franck,
I wonder if http://www.biocatalogue.org/services/2072-postmlservice_474910
relevant to biocatalogue. Could you verify this?

Eric


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From ytanoh at cs.man.ac.uk  Mon Oct 26 07:56:49 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Mon, 26 Oct 2009 11:56:49 +0000
Subject: [BioCatalogue-developers] is service relevant to BioCatalogue?
In-Reply-To: <4AE58B5F.1010103@ebi.ac.uk>
References: <4AE58B5F.1010103@ebi.ac.uk>
Message-ID: <909566BB-9AA1-481F-9D5B-B283749B6066@cs.man.ac.uk>

Eric,

Did you get any on the e-mails i sent regarding that service? ...see  
below.
It is not a life science service, i've been trying to get it removed  
or flagged since last week.

Franck


On 26 Oct 2009, at 11:43, Eric Nzuobontane wrote:

> Hi Franck,
> I wonder if http://www.biocatalogue.org/services/2072-postmlservice_474910
> relevant to biocatalogue. Could you verify this?
>
> Eric
>
>
> <ericnzuo.vcf>

Hi guys,

I want to email the guy who submitted the following service that his  
service may be removed because not life science related.
Can i get his e-mail?
http://www.biocatalogue.org/services/2072-postmlservice_474910

Franck

-- 
"Science knows no country, because knowledge belongs to humanity, and  
is the torch which illuminates the world." - Louis Pasteur

2009/10/22 Franck Tanoh <ytanoh at cs.man.ac.uk>
Hi guys,

The following service has nothing to do with Life Science: http://www.biocatalogue.org/services/2072-postmlservice_474910
I plan to email the submitter. My request is, can we flag service or  
annotation before deletion. For example, keep them in the catalogue  
for 1 or week or 2 with the delete flag. We could then inform the  
submitter that his service/annotation is going to be deleted; users of  
the catalogue will be aware of the 'fate' of that service or  
annotation. That's how Wikipedia does it.

Cheers,
Franck

-- 
"Science knows no country, because knowledge belongs to humanity, and  
is the torch which illuminates the world." - Louis Pasteur

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From ericnzuo at ebi.ac.uk  Mon Oct 26 08:02:07 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 26 Oct 2009 12:02:07 +0000
Subject: [BioCatalogue-developers] is service relevant to BioCatalogue?
In-Reply-To: <909566BB-9AA1-481F-9D5B-B283749B6066@cs.man.ac.uk>
References: <4AE58B5F.1010103@ebi.ac.uk>
	<909566BB-9AA1-481F-9D5B-B283749B6066@cs.man.ac.uk>
Message-ID: <4AE58FBF.9040403@ebi.ac.uk>

I think I missed those mails. Anyway, did you do as you suggested? I 
mean informing people that it will be removed so that we can go ahead 
with removing it today?

Eric

Franck Tanoh wrote:
> Eric, 
>
> Did you get any on the e-mails i sent regarding that service? ...see 
> below. 
> It is not a life science service, i've been trying to get it removed 
> or flagged since last week. 
>
> Franck
>
>
> On 26 Oct 2009, at 11:43, Eric Nzuobontane wrote:
>
>> Hi Franck,
>> I wonder if 
>> http://www.biocatalogue.org/services/2072-postmlservice_474910
>> relevant to biocatalogue. Could you verify this?
>>
>> Eric
>>
>>
>> <ericnzuo.vcf>
>
> Hi guys, 
>
> I want to email the guy who submitted the following service that his 
> service may be removed because not life science related. 
> Can i get his e-mail? 
> http://www.biocatalogue.org/services/2072-postmlservice_474910 
>
> Franck
>
> -- 
> "Science knows no country, because knowledge belongs to humanity, and 
> is the torch which illuminates the world." - Louis Pasteur
>
> 2009/10/22 Franck Tanoh <ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>>
>
>     Hi guys, 
>
>     The following service has nothing to do with Life
>     Science: http://www.biocatalogue.org/services/2072-postmlservice_474910
>     I plan to email the submitter. My request is, can we flag service
>     or annotation before deletion. For example, keep them in the
>     catalogue for 1 or week or 2 with the delete flag. We could then
>     inform the submitter that his service/annotation is going to be
>     deleted; users of the catalogue will be aware of the 'fate' of
>     that service or annotation. That's how Wikipedia does it. 
>
>     Cheers, 
>     Franck
>
>     -- 
>     "Science knows no country, because knowledge belongs to humanity,
>     and is the torch which illuminates the world." - Louis Pasteur
>
>

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From ytanoh at cs.man.ac.uk  Mon Oct 26 08:11:54 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Mon, 26 Oct 2009 12:11:54 +0000
Subject: [BioCatalogue-developers] is service relevant to BioCatalogue?
In-Reply-To: <4AE58FBF.9040403@ebi.ac.uk>
References: <4AE58B5F.1010103@ebi.ac.uk>
	<909566BB-9AA1-481F-9D5B-B283749B6066@cs.man.ac.uk>
	<4AE58FBF.9040403@ebi.ac.uk>
Message-ID: <5A57E88D-4CA5-47C4-A17A-53EE3337683E@cs.man.ac.uk>


> I think I missed those mails.
are you still on the contact list? Or do my e-mails go into you spam  
box :-( ?

> Anyway, did you do as you suggested? I mean informing people that it  
> will be removed so that we can go ahead with removing it today?
i sent you an e-mail this morning (cced jits).. doesn't look like you  
got it.
this is what I wrote:
<<Hi Eric,
Jits says,  it's illegal to email the submitter myself :-( .... but  
you as sys admin, you could if the user ticked the box about receiving  
notification.
Can you double check that and email him please?  The problem with the  
service is that it has nothing to do with life science.
Cheers,
Franck >>

Franck

On 26 Oct 2009, at 12:02, Eric Nzuobontane wrote:

> I think I missed those mails. Anyway, did you do as you suggested? I  
> mean informing people that it will be removed so that we can go  
> ahead with removing it today?
>
> Eric
>
> Franck Tanoh wrote:
>> Eric,
>> Did you get any on the e-mails i sent regarding that  
>> service? ...see below. It is not a life science service, i've been  
>> trying to get it removed or flagged since last week.
>> Franck
>>
>>
>> On 26 Oct 2009, at 11:43, Eric Nzuobontane wrote:
>>
>>> Hi Franck,
>>> I wonder if http://www.biocatalogue.org/services/2072-postmlservice_474910
>>> relevant to biocatalogue. Could you verify this?
>>>
>>> Eric
>>>
>>>
>>> <ericnzuo.vcf>
>>
>> Hi guys,
>> I want to email the guy who submitted the following service that  
>> his service may be removed because not life science related. Can i  
>> get his e-mail? http://www.biocatalogue.org/services/2072-postmlservice_474910
>> Franck
>>
>> -- 
>> "Science knows no country, because knowledge belongs to humanity,  
>> and is the torch which illuminates the world." - Louis Pasteur
>>
>> 2009/10/22 Franck Tanoh <ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk 
>> >>
>>
>>    Hi guys,
>>    The following service has nothing to do with Life
>>    Science: http://www.biocatalogue.org/services/2072-postmlservice_474910
>>    I plan to email the submitter. My request is, can we flag service
>>    or annotation before deletion. For example, keep them in the
>>    catalogue for 1 or week or 2 with the delete flag. We could then
>>    inform the submitter that his service/annotation is going to be
>>    deleted; users of the catalogue will be aware of the 'fate' of
>>    that service or annotation. That's how Wikipedia does it.
>>    Cheers,     Franck
>>
>>    --     "Science knows no country, because knowledge belongs to  
>> humanity,
>>    and is the torch which illuminates the world." - Louis Pasteur
>>
>>
>
> <ericnzuo.vcf>


From noreply at rubyforge.org  Mon Oct 26 09:21:19 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 26 Oct 2009 09:21:19 -0400 (EDT)
Subject: [BioCatalogue-developers] [1195] trunk/config/routes.rb: Fix for
	search.
Message-ID: <20091026132119.CA52A19782A2@rubyforge.org>

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From noreply at rubyforge.org  Mon Oct 26 09:21:36 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 26 Oct 2009 09:21:36 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2829] unable to see all search
	result
Message-ID: <20091026132136.CF527159807D@rubyforge.org>

Task #2829 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: unable to see all search result 
Complete: 100%
Status: Closed

Description: when i do a search with the provider name such as 'dev.biordf.net' or 'www.ebi.ac.uk', i'm unable to view all the search result. there is a 'Unable to Process Requested Data' when i try to access page 3, 4 etc...

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-26 13:21
By: jits

Comment:
Done, in revision 1195.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2829&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Oct 26 09:28:26 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 26 Oct 2009 09:28:26 -0400 (EDT)
Subject: [BioCatalogue-developers] [1196]
 trunk/config/initializers/biocat_main.rb: Updated error mailer
 configuration to include 400 errors.
Message-ID: <20091026132826.E04DB19782A2@rubyforge.org>

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From noreply at rubyforge.org  Mon Oct 26 09:30:00 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 26 Oct 2009 09:30:00 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2752] Better REST services support
Message-ID: <20091026133000.971001598078@rubyforge.org>

Task #2752 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Better REST services support
Complete: 0%
Status: Open

Description: 1. Parameterized URLs:

"Having said that, we are very keen on having some basic functionality in place for this. So would the ability to add parameterised URLs together with some test parameters be useful in meeting your needs? This is something we could potentially release quicker. "

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2752&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Oct 26 09:30:28 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 26 Oct 2009 09:30:28 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2634] Work on synonyms for search
Message-ID: <20091026133028.7E9621598079@rubyforge.org>

Task #2634 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Work on synonyms for search
Complete: 100%
Status: Closed

Description: Work on synonyms for search

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-26 13:30
By: jits

Comment:
Done

-------------------------------------------------------
Date: 2009-06-16 11:30
By: jits

Comment:
Franck to go through pseudo synonyms one more time.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2634&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Oct 26 09:32:23 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 26 Oct 2009 09:32:23 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2682] Main URL rewrite for main
	biocatalogue site
Message-ID: <20091026133223.A700D19782A2@rubyforge.org>

Task #2682 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Main URL rewrite for main biocatalogue site
Complete: 0%
Status: Open

Description: Ensure that http://biocatalogue.org always rewrites to http://www.biocatalogue.org.

This is crucial to the functioning of things like Disqus and bookmarking, as they work on absolute URLs.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2682&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Oct 26 09:33:22 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 26 Oct 2009 09:33:22 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2682] Main URL rewrite for main
	biocatalogue site
Message-ID: <20091026133322.23A751598079@rubyforge.org>

Task #2682 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Main URL rewrite for main biocatalogue site
Complete: 100%
Status: Closed

Description: Ensure that http://biocatalogue.org always rewrites to http://www.biocatalogue.org.

This is crucial to the functioning of things like Disqus and bookmarking, as they work on absolute URLs.

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-26 13:33
By: jits

Comment:
This seems to have been done.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2682&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Oct 26 09:34:16 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 26 Oct 2009 09:34:16 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2719] get to the same page after
	logging
Message-ID: <20091026133416.579AC1598079@rubyforge.org>

Task #2719 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: get to the same page after logging 
Complete: 0%
Status: Deleted

Description: link without logging, the logging form appears asking me to logging before i carry on. Once i enter ma logging details, i expect the site to take me to the description page so that i can add my description. 

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-26 13:34
By: jits

Comment:
I think this problem doesn't exist anymore

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2719&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Oct 26 09:35:10 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 26 Oct 2009 09:35:10 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2710] Add other types of
	annotations to service show page
Message-ID: <20091026133510.AF51B1598079@rubyforge.org>

Task #2710 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Add other types of annotations to service show page
Complete: 100%
Status: Closed

Description: Things like "usage conditions", "cost" etc etc

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-26 13:35
By: jits

Comment:
Done for now

-------------------------------------------------------
Date: 2009-06-23 14:41
By: jits

Comment:
Cost, licenses and contact info added.

Not sure about "usage conditions" yet.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2710&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Oct 26 09:36:14 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 26 Oct 2009 09:36:14 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2720] get to the same page after
	logging
Message-ID: <20091026133614.5DC7E1598079@rubyforge.org>

Task #2720 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: get to the same page after logging 
Complete: 0%
Status: Deleted

Description: To return to the same page when you sign in. e.g. I select the description link without logging, the logging form appears asking me to logging before i carry on. Once i enter ma logging details, i expect the site to take me to the description page so that i can add my description. 

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-26 13:36
By: jits

Comment:
I think this problem doesn't exist anymore

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2720&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Oct 26 09:38:25 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 26 Oct 2009 09:38:25 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2783] Check UI for instances of
	non activated users showing up
Message-ID: <20091026133825.33DC91598078@rubyforge.org>

Task #2783 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Check UI for instances of non activated users showing up
Complete: 100%
Status: Closed

Description: There is a potential bug!

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-26 13:38
By: jits

Comment:
A default scope has been added to the User model to hopefully prevent unactivated users from showing up.

-------------------------------------------------------
Date: 2009-09-08 14:54
By: jits

Comment:
An initial check has been done. However, a proper audit needs to take place at some point.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2783&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Oct 26 09:39:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 26 Oct 2009 09:39:09 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2778] possibility to add
	annotation inline to the page ...
Message-ID: <20091026133909.95CD41858277@rubyforge.org>

Task #2778 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: possibility to add annotation inline to the page ...
Complete: 50%
Status: Open

Description: I've really had a bad and frustrating experiment trying to annotate the operation of this service (http://www.biocatalogue.org/services/2048-wsblastpgpservice_414364#operations).
Anytime i submit a description the page just goes back to the top. i have to scroll down to find where i was and what i've just added.
 Can the page just return to the field i have added the description to when i click submit? Please double check...

Franck

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-26 13:39
By: jits

Comment:
Inline forms to add annotations have been added.

This needs to go through user testing now.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2778&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Oct 26 10:19:10 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 26 Oct 2009 10:19:10 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2827] Stats: add tags section
Message-ID: <20091026141910.7E4551588060@rubyforge.org>

Task #2827 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Stats: add tags section
Complete: 100%
Status: Closed

Description: Eg: the frequency of each tag, etc

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-26 14:19
By: jits

Comment:
Done

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2827&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Oct 26 10:21:20 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 26 Oct 2009 10:21:20 -0400 (EDT)
Subject: [BioCatalogue-developers] [1197]
 trunk/app/views/soaplab_servers/_soaplab_server_box.html.erb: Minor textual
 change.
Message-ID: <20091026142120.1C5061858277@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Mon Oct 26 14:25:53 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 26 Oct 2009 18:25:53 +0000
Subject: [BioCatalogue-developers] [Fwd: rexml/formater/]
Message-ID: <4AE5E9B1.3010302@ebi.ac.uk>


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From MAILER-DAEMON at ebi.ac.uk  Tue Oct 27 05:55:57 2009
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Tue, 27 Oct 2009 09:55:57 GMT
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <200910270955.n9R9tvRD027417@spike.ebi.ac.uk>

The original message was received at Tue, 27 Oct 2009 09:54:23 GMT
from pweb-4a.ebi.ac.uk [172.18.1.109]

   ----- The following addresses had permanent fatal errors -----
<biocatalogue-developers at rubyforge.org>
    (reason: 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network)

   ----- Transcript of session follows -----
... while talking to rubyforge.org.:
>>> DATA
<<< 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network
550 5.1.1 <biocatalogue-developers at rubyforge.org>... User unknown
<<< 554 5.5.1 Error: no valid recipients
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From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
Subject: [Production ERROR] sessions#create
	(ActionController::InvalidAuthenticityToken)
	"ActionController::InvalidAuthenticityToken"
Date: Tue, 27 Oct 2009 09:54:23 +0000
Size: 13643
URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091027/1540cea2/attachment.mht>

From noreply at rubyforge.org  Tue Oct 27 06:39:38 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 27 Oct 2009 06:39:38 -0400 (EDT)
Subject: [BioCatalogue-developers] [1198] branches/codebase-testing/:
	Removed old branch
Message-ID: <20091027103938.230831858293@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 27 06:58:39 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 27 Oct 2009 06:58:39 -0400 (EDT)
Subject: [BioCatalogue-developers] [1199]
 trunk/lib/bio_catalogue/wsdl_utils_output_parser.rb: provide work around
 for when the rexml/formatter package is not available.
Message-ID: <20091027105839.4238018582BC@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 27 07:04:40 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 27 Oct 2009 07:04:40 -0400 (EDT)
Subject: [BioCatalogue-developers] [1200] branches/codebase-testing/: New
	branch for codebase testing work
Message-ID: <20091027110440.A0A581D7885A@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 27 07:37:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 27 Oct 2009 07:37:09 -0400 (EDT)
Subject: [BioCatalogue-developers] [1201]
 trunk/lib/bio_catalogue/wsdl_utils_output_parser.rb: catch file load
 exception which is not caught as a standard exception.
Message-ID: <20091027113709.E94941D7885A@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 27 07:40:30 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 27 Oct 2009 07:40:30 -0400 (EDT)
Subject: [BioCatalogue-developers] [1202]
	trunk/lib/bio_catalogue/wsdl_utils_output_parser.rb:
Message-ID: <20091027114030.E518E1D78860@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 27 08:19:33 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 27 Oct 2009 08:19:33 -0400 (EDT)
Subject: [BioCatalogue-developers] [1203] trunk: REST API work: added
 <locations> to the /services/{id}/ summary endpoint and other similar
 updates.
Message-ID: <20091027121933.3B0481588060@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 27 10:08:11 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 27 Oct 2009 10:08:11 -0400 (EDT)
Subject: [BioCatalogue-developers] [1204]
 trunk/lib/bio_catalogue/wsdl_utils_output_parser.rb: enable rexml parsing
 to work without rexml/formatter package
Message-ID: <20091027140811.CF6F71588060@rubyforge.org>

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From noreply at rubyforge.org  Tue Oct 27 11:02:22 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 27 Oct 2009 11:02:22 -0400 (EDT)
Subject: [BioCatalogue-developers] [1205] branches/rest-services-support:
 created a seperation to allow for monitoring of rest services
Message-ID: <20091027150222.E468A1588060@rubyforge.org>

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From MAILER-DAEMON at ebi.ac.uk  Tue Oct 27 11:55:39 2009
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Tue, 27 Oct 2009 15:55:39 GMT
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <200910271555.n9RFtdAr015717@spike.ebi.ac.uk>

The original message was received at Tue, 27 Oct 2009 15:54:06 GMT
from pweb-4a.ebi.ac.uk [172.18.1.109]

   ----- The following addresses had permanent fatal errors -----
<biocatalogue-developers at rubyforge.org>
    (reason: 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network)

   ----- Transcript of session follows -----
... while talking to rubyforge.org.:
>>> DATA
<<< 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network
550 5.1.1 <biocatalogue-developers at rubyforge.org>... User unknown
<<< 554 5.5.1 Error: no valid recipients
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From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
Subject: [Production ERROR] application#show (ActionView::TemplateError)
	"undefined method `display_name' for nil:NilClass"
Date: Tue, 27 Oct 2009 15:54:06 +0000
Size: 9623
URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091027/6407cfa5/attachment.mht>

From noreply at rubyforge.org  Tue Oct 27 12:31:07 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 27 Oct 2009 12:31:07 -0400 (EDT)
Subject: [BioCatalogue-developers] [1206] trunk/app/models/soap_service.rb:
 fixed bug in building soap service ports
Message-ID: <20091027163107.A41C215B8025@rubyforge.org>

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URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091027/ed51086a/attachment.html>

From ytanoh at cs.man.ac.uk  Wed Oct 28 07:24:22 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 28 Oct 2009 11:24:22 +0000
Subject: [BioCatalogue-developers] some note after running through the test
	site
Message-ID: <d0ee827d0910280424y25b5bc3bt951917e84800ea2e@mail.gmail.com>

Hi guys,

Good job for the updates.
Here are the issues i came across when running through the site:
1-unable to sign in with my openid
2-unable to sign in with my google id.
3-can't see simple view/ advance view when i search for service. these
options are only seen when i browse.
Default view when i search is 'simple view' ... i would prefer an
'advance view'. for a good first impression on casual or first time
users.
3-can't edit my account or profile... <something went wrong> type message
4-feedback seem to work without entering the security number when the
message section is empty
5-we need a better error message when user forget to enter the
security number...now we have
 <your message has not been submitted. the message length was not
entered correctly>
6-Number of similar service per service is limited to 10 without the
possibility to see the rest if there are more than 10.
7-i can see 'delete' and 'edit' on other people annotation. looks like
a can delete other users annotation. but couldn't  when i try. can you
hide these buttons. i should only see them for my annotations.
8-is soaplab improvement or complex type service metadata support part
of this release? didn't notice anything new

Will have another go.

cheers,
Franck

-- 
 "Science knows no country, because knowledge belongs to humanity, and
is the torch which illuminates the world." - Louis Pasteur

From jits at cs.man.ac.uk  Wed Oct 28 07:57:34 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 28 Oct 2009 11:57:34 +0000
Subject: [BioCatalogue-developers] some note after running through the
 test	site
In-Reply-To: <d0ee827d0910280424y25b5bc3bt951917e84800ea2e@mail.gmail.com>
References: <d0ee827d0910280424y25b5bc3bt951917e84800ea2e@mail.gmail.com>
Message-ID: <4AE831AE.5040702@cs.man.ac.uk>

Thanks Franck. We'll take a look at these.

Jits


Franck Tanoh wrote:
> Hi guys,
>
> Good job for the updates.
> Here are the issues i came across when running through the site:
> 1-unable to sign in with my openid
> 2-unable to sign in with my google id.
> 3-can't see simple view/ advance view when i search for service. these
> options are only seen when i browse.
> Default view when i search is 'simple view' ... i would prefer an
> 'advance view'. for a good first impression on casual or first time
> users.
> 3-can't edit my account or profile... <something went wrong> type message
> 4-feedback seem to work without entering the security number when the
> message section is empty
> 5-we need a better error message when user forget to enter the
> security number...now we have
>  <your message has not been submitted. the message length was not
> entered correctly>
> 6-Number of similar service per service is limited to 10 without the
> possibility to see the rest if there are more than 10.
> 7-i can see 'delete' and 'edit' on other people annotation. looks like
> a can delete other users annotation. but couldn't  when i try. can you
> hide these buttons. i should only see them for my annotations.
> 8-is soaplab improvement or complex type service metadata support part
> of this release? didn't notice anything new
>
> Will have another go.
>
> cheers,
> Franck
>
>   


From MAILER-DAEMON at ebi.ac.uk  Wed Oct 28 09:28:39 2009
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Wed, 28 Oct 2009 13:28:39 GMT
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <200910281328.n9SDSdLQ010861@spike.ebi.ac.uk>

The original message was received at Wed, 28 Oct 2009 13:27:04 GMT
from pweb-3b.ebi.ac.uk [172.18.1.108]

   ----- The following addresses had permanent fatal errors -----
<biocatalogue-developers at rubyforge.org>
    (reason: 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network)

   ----- Transcript of session follows -----
... while talking to rubyforge.org.:
>>> DATA
<<< 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network
550 5.1.1 <biocatalogue-developers at rubyforge.org>... User unknown
<<< 554 5.5.1 Error: no valid recipients
-------------- next part --------------
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From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
Subject: [Production ERROR] application#show (ActionView::TemplateError)
	"undefined method `display_name' for nil:NilClass"
Date: Wed, 28 Oct 2009 13:27:04 +0000
Size: 9624
URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091028/74af8409/attachment-0001.mht>

From noreply at rubyforge.org  Wed Oct 28 10:08:20 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 28 Oct 2009 10:08:20 -0400 (EDT)
Subject: [BioCatalogue-developers] [1207] trunk: Bugfix - reverted the use
 of the default scope in the User model to restrict by activated users (see
 revision 1188) as this was breaking all User.new calls.
Message-ID: <20091028140820.C71981588064@rubyforge.org>

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From noreply at rubyforge.org  Wed Oct 28 10:15:42 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 28 Oct 2009 10:15:42 -0400 (EDT)
Subject: [BioCatalogue-developers] [1208]
 trunk/app/controllers/users_controller.rb: Added extra checks for
 unactivated users showing up in the UI.
Message-ID: <20091028141542.3B4791588065@rubyforge.org>

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From noreply at rubyforge.org  Wed Oct 28 10:27:44 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 28 Oct 2009 10:27:44 -0400 (EDT)
Subject: [BioCatalogue-developers] [1209] trunk: Bugfixes for the password
	reset mechanism.
Message-ID: <20091028142744.327971588065@rubyforge.org>

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From noreply at rubyforge.org  Wed Oct 28 10:32:28 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 28 Oct 2009 10:32:28 -0400 (EDT)
Subject: [BioCatalogue-developers] [1210]
 trunk/app/controllers/application_controller.rb: Bugfix for checking who
 can edit/delete annotations.
Message-ID: <20091028143228.4B0161588065@rubyforge.org>

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From noreply at rubyforge.org  Wed Oct 28 10:38:33 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 28 Oct 2009 10:38:33 -0400 (EDT)
Subject: [BioCatalogue-developers] [1211] trunk/app: Various fixes for the
	contact page.
Message-ID: <20091028143833.D762B1588067@rubyforge.org>

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From noreply at rubyforge.org  Wed Oct 28 10:40:05 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 28 Oct 2009 10:40:05 -0400 (EDT)
Subject: [BioCatalogue-developers] [1212]
 trunk/app/controllers/contact_controller.rb: Minor fix for flash message
 showing across page requests.
Message-ID: <20091028144005.A712C1588066@rubyforge.org>

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From noreply at rubyforge.org  Wed Oct 28 10:50:20 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 28 Oct 2009 10:50:20 -0400 (EDT)
Subject: [BioCatalogue-developers] [1213] trunk/app: Now up to 100 similar
 services can be shown,
 with a default of 10 shown initially and the option of expanding to see all
 .
Message-ID: <20091028145021.104CC18581EF@rubyforge.org>

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From MAILER-DAEMON at ebi.ac.uk  Wed Oct 28 10:52:39 2009
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Wed, 28 Oct 2009 14:52:39 GMT
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <200910281452.n9SEqdDs018868@spike.ebi.ac.uk>

The original message was received at Wed, 28 Oct 2009 14:51:05 GMT
from pweb-4a.ebi.ac.uk [172.18.1.109]

   ----- The following addresses had permanent fatal errors -----
<biocatalogue-developers at rubyforge.org>
    (reason: 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network)

   ----- Transcript of session follows -----
... while talking to rubyforge.org.:
>>> DATA
<<< 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network
550 5.1.1 <biocatalogue-developers at rubyforge.org>... User unknown
<<< 554 5.5.1 Error: no valid recipients
-------------- next part --------------
An embedded message was scrubbed...
From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
Subject: [Production ERROR] application#show (ActionView::TemplateError)
	"undefined method `display_name' for nil:NilClass"
Date: Wed, 28 Oct 2009 14:51:05 +0000
Size: 9623
URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091028/c1c73b32/attachment.mht>

From noreply at rubyforge.org  Wed Oct 28 11:26:49 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 28 Oct 2009 11:26:49 -0400 (EDT)
Subject: [BioCatalogue-developers] [1214] trunk: Added the ability to switch
 between simple/ detailed views of search results.
Message-ID: <20091028152649.D70FF1588065@rubyforge.org>

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From noreply at rubyforge.org  Wed Oct 28 11:30:49 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 28 Oct 2009 11:30:49 -0400 (EDT)
Subject: [BioCatalogue-developers] [1215]
 trunk/app/views/search/show.html.erb: Minor tweak to layout on search page.
Message-ID: <20091028153049.3874A1588065@rubyforge.org>

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From noreply at rubyforge.org  Wed Oct 28 12:36:27 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 28 Oct 2009 12:36:27 -0400 (EDT)
Subject: [BioCatalogue-developers] [1216]
 trunk/app/views/widgets/_login_box.html.erb: minimal wording change for
 login box
Message-ID: <20091028163627.2DFB51588065@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Thu Oct 29 05:31:34 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 29 Oct 2009 09:31:34 +0000
Subject: [BioCatalogue-developers] Fwd: importing test script data
In-Reply-To: <5006E065-CAE6-4957-87C6-E1A5C839B6D0@number23.org>
References: <1C6EA717-21F9-46ED-B8B5-F49ED715E11E@manchester.ac.uk>
	<5006E065-CAE6-4957-87C6-E1A5C839B6D0@number23.org>
Message-ID: <4AE960F6.5000902@ebi.ac.uk>

Hi Phil,

Can I have a recent dump of the embrace database please.

Thanks,

Eric




Philip McDermott wrote:
> The field is body in the table DE_node_revisions, and you look that up 
> via the node id (nid).
>
> E.g.
>
> select * from DE_node where title="mkdomTest";
>
> +------+------+----------------+----------+-----------+-----+--------+------------+------------+---------+---------+----------+--------+------+-----------+ 
>
> | nid  | vid  | type           | language | title     | uid | status | 
> created    | changed    | comment | promote | moderate | sticky | tnid 
> | translate |
> +------+------+----------------+----------+-----------+-----+--------+------------+------------+---------+---------+----------+--------+------+-----------+ 
>
> | 1900 | 1900 | webservicetest |          | mkdomTest |  30 |      1 | 
> 1243951795 | 1243951795 |       2 |       0 |        0 |      0 |    0 
> |         0 |
> +------+------+----------------+----------+-----------+-----+--------+------------+------------+---------+---------+----------+--------+------+-----------+ 
>
> 1 row in set (0.00 sec)
>
>
> select body from DE_node_revisions where nid="1900";
>
> | This is a test for the MkDom2 webservice. It uses perl and SOAPlite. 
> It includes a test using a short fasta file (7 sequences) as input and 
> checks whether :
> <ul>
> <li>the output is not empty</li>
> <li>the first output element is in correct xdom format and contains 7 
> elements</li>
> <li>the second output element (the log file) indicates a normal end of 
> the program</li>
> <li>the third output element is in correct srs format and contains 4 
> domain families</li>
> <li>the last output element is a valid url to webdom (domain 
> visualization)</li>
> </ul> |
>
>
> Cheers
>
> Phil
>
>
>
> Begin forwarded message:
>
>> From: Philip McDermott <philip.mcdermott at manchester.ac.uk>
>> Date: 21 October 2009 17:28:57 BST
>> To: ericnzuo at ebi.ac.uk
>> Cc: Steve Pettifer <steve.pettifer at manchester.ac.uk>
>> Subject: Re: importing test script data
>>
>> Hi Eric,
>>
>> In answer to your questions:
>>
>> 1) type_id
>> This is the type of the test (Python, Perl, DAS etc.)
>>
>> 2) locality_id
>> This field isn't used.
>>
>> 3) pseudo
>> This was used by us for pseudo-tests but we aren't aware this is 
>> something supported in BioCatalogue so you shouldn't need it.
>>
>> 4)wsdl_operation
>> This field isn't used.
>>
>>> where the description of the test scripts are stored.
>> These are stored in the standard Drupal description field for the 
>> test, which I think is 'body'. You'll have to look up the correct 
>> drupal node via the id field. I'll have a look into it to make sure I 
>> gave you all that info originally.
>>
>> Cheers
>>
>> Phil
>>
>>
>>
>> On 20 Oct 2009, at 09:00, Steve Pettifer wrote:
>>
>>> Hi Phil,
>>>
>>> can you answer Eric's questions please..?
>>>
>>> Ta
>>>
>>> Steve
>>>
>>>
>>> Begin forwarded message:
>>>
>>>> From: Eric Nzuobontane <ericnzuo at ebi.ac.uk>
>>>> Date: 12 October 2009 10:31:32 GMT+01:00
>>>> To: Steve Pettifer <steve.pettifer at manchester.ac.uk>
>>>> Subject: importing test script data
>>>>
>>>> Hi Steve,
>>>>
>>>> I am doing a test a import of the test script data from embrace 
>>>> into biocat database. Looking at the 'DE_ws_table', which is the 
>>>> database table that holds the test data, there are some field in 
>>>> there that I do not understand and I am not sure if they are 
>>>> relevant for the import.
>>>> These are:
>>>> 1) type_id
>>>> 2) locality_id
>>>> 3) pseudo
>>>> 4)wsdl_operation
>>>>
>>>> Looking at the data I see that the wsdl_operation field apparently 
>>>> was not used (all entries are empty strings!), the locality and 
>>>> type ids all have value of 1. pseudo does have values of 1 & 0. 
>>>> Could you tell me how these fields I used so that I may ascertain 
>>>> if they are relevant for the import?
>>>> Thanks!
>>>> Eric
>>>>
>>> <ericnzuo.vcf>
>>>
>>


From noreply at rubyforge.org  Thu Oct 29 06:13:29 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 29 Oct 2009 06:13:29 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2833] Have the ability to download
	annotations
Message-ID: <20091029101329.58BA315B8026@rubyforge.org>

Task #2833 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Have the ability to download annotations
Complete: 0%
Status: Open

Description: This is especially useful for things like Examples where users want the exact text that is in the annotation.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2833&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Oct 29 10:34:15 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 29 Oct 2009 10:34:15 -0400 (EDT)
Subject: [BioCatalogue-developers] [1217] trunk: Various improvements to
	examples annotations:
Message-ID: <20091029143416.067941588073@rubyforge.org>

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From noreply at rubyforge.org  Thu Oct 29 10:38:24 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 29 Oct 2009 10:38:24 -0400 (EDT)
Subject: [BioCatalogue-developers] [1218]
 trunk/app/views/annotations/_examples.html.erb: Style updates for example
 annotations
Message-ID: <20091029143824.B74F718582BF@rubyforge.org>

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From noreply at rubyforge.org  Thu Oct 29 10:47:54 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 29 Oct 2009 10:47:54 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2833] Have the ability to download
	annotations
Message-ID: <20091029144754.DE2521588063@rubyforge.org>

Task #2833 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Have the ability to download annotations
Complete: 100%
Status: Closed

Description: This is especially useful for things like Examples where users want the exact text that is in the annotation.

Follow-Ups:

-------------------------------------------------------
Date: 2009-10-29 14:47
By: jits

Comment:
Done, in revision 1217

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2833&group_id=6901&group_project_id=12540

From MAILER-DAEMON at ebi.ac.uk  Thu Oct 29 11:42:06 2009
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Thu, 29 Oct 2009 15:42:06 GMT
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <200910291542.n9TFg6Nu006165@spike.ebi.ac.uk>

The original message was received at Thu, 29 Oct 2009 15:40:33 GMT
from pweb-3b.ebi.ac.uk [172.18.1.108]

   ----- The following addresses had permanent fatal errors -----
<biocatalogue-developers at rubyforge.org>
    (reason: 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network)

   ----- Transcript of session follows -----
... while talking to rubyforge.org.:
>>> DATA
<<< 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network
550 5.1.1 <biocatalogue-developers at rubyforge.org>... User unknown
<<< 554 5.5.1 Error: no valid recipients
-------------- next part --------------
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From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
Subject: [Production ERROR] sessions#create
	(ActionController::InvalidAuthenticityToken)
	"ActionController::InvalidAuthenticityToken"
Date: Thu, 29 Oct 2009 15:40:33 +0000
Size: 12471
URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091029/12892bb1/attachment.mht>

From noreply at rubyforge.org  Thu Oct 29 11:59:14 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 29 Oct 2009 11:59:14 -0400 (EDT)
Subject: [BioCatalogue-developers] [1219]
 trunk/app/views/annotations/_name_aliases.html.erb: Minor textual changes
Message-ID: <20091029155914.3B8A518582BC@rubyforge.org>

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From noreply at rubyforge.org  Thu Oct 29 12:11:22 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 29 Oct 2009 12:11:22 -0400 (EDT)
Subject: [BioCatalogue-developers] [1220] trunk: REST API work: changed
 <names> in /services/{id}/summary to < alternativeNames>
Message-ID: <20091029161122.8C7111588063@rubyforge.org>

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From MAILER-DAEMON at ebi.ac.uk  Fri Oct 30 04:19:22 2009
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Fri, 30 Oct 2009 08:19:22 GMT
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <200910300819.n9U8JMBB024888@spike.ebi.ac.uk>

The original message was received at Fri, 30 Oct 2009 08:17:48 GMT
from pweb-4a.ebi.ac.uk [172.18.1.109]

   ----- The following addresses had permanent fatal errors -----
<biocatalogue-developers at rubyforge.org>
    (reason: 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network)

   ----- Transcript of session follows -----
... while talking to rubyforge.org.:
>>> DATA
<<< 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network
550 5.1.1 <biocatalogue-developers at rubyforge.org>... User unknown
<<< 554 5.5.1 Error: no valid recipients
-------------- next part --------------
An embedded message was scrubbed...
From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
Subject: [Production ERROR] sessions#create
	(ActionController::InvalidAuthenticityToken)
	"ActionController::InvalidAuthenticityToken"
Date: Fri, 30 Oct 2009 08:17:48 +0000
Size: 12326
URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091030/7dd39a90/attachment.mht>

From noreply at rubyforge.org  Fri Oct 30 06:16:39 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 30 Oct 2009 06:16:39 -0400 (EDT)
Subject: [BioCatalogue-developers] [1221] trunk: Better error logging.
Message-ID: <20091030101639.385D6159803F@rubyforge.org>

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From noreply at rubyforge.org  Fri Oct 30 06:55:57 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 30 Oct 2009 06:55:57 -0400 (EDT)
Subject: [BioCatalogue-developers] [1222]
 trunk/vendor/gems/grosser-rpx_now-0.5.10/lib/rpx_now.rb: Fix for the use of
 a proxy, in the RPX integration code.
Message-ID: <20091030105557.1F13018581F3@rubyforge.org>

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From jits at cs.man.ac.uk  Fri Oct 30 07:11:46 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 30 Oct 2009 11:11:46 +0000
Subject: [BioCatalogue-developers] some note after running through the
 test	site
In-Reply-To: <d0ee827d0910280424y25b5bc3bt951917e84800ea2e@mail.gmail.com>
References: <d0ee827d0910280424y25b5bc3bt951917e84800ea2e@mail.gmail.com>
Message-ID: <4AEAC9F2.9090309@cs.man.ac.uk>

Franck Tanoh wrote:
> Hi guys,
>
> Good job for the updates.
> Here are the issues i came across when running through the site:
> 1-unable to sign in with my openid
>   

Fixed

> 2-unable to sign in with my google id.
>   

Fixed

> 3-can't see simple view/ advance view when i search for service. these
> options are only seen when i browse.
> Default view when i search is 'simple view' ... i would prefer an
> 'advance view'. for a good first impression on casual or first time
> users.
>   

Should be fixed (please test :-))

> 3-can't edit my account or profile... <something went wrong> type message
>   

Does this happen now?

> 4-feedback seem to work without entering the security number when the
> message section is empty
>   

Fixed

> 5-we need a better error message when user forget to enter the
> security number...now we have
>  <your message has not been submitted. the message length was not
> entered correctly>
>   

Better error message now.

> 6-Number of similar service per service is limited to 10 without the
> possibility to see the rest if there are more than 10.
>   

Now can show more than 10 as an expandable list.

> 7-i can see 'delete' and 'edit' on other people annotation. looks like
> a can delete other users annotation. but couldn't  when i try. can you
> hide these buttons. i should only see them for my annotations.
>   

Fixed

> 8-is soaplab improvement or complex type service metadata support part
> of this release? didn't notice anything new
>   

This will only come into effect for new services.

I believe Eric is writing a script to update the existing services?

> Will have another go.
>
>   

Cheers! And thanks for reporting... keep it coming ;-)

Cheers,
Jits

> cheers,
> Franck
>
>   


From jits at cs.man.ac.uk  Fri Oct 30 07:18:14 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 30 Oct 2009 11:18:14 +0000
Subject: [BioCatalogue-developers] some note after running through the
 test	site
In-Reply-To: <4AEAC9F2.9090309@cs.man.ac.uk>
References: <d0ee827d0910280424y25b5bc3bt951917e84800ea2e@mail.gmail.com>
	<4AEAC9F2.9090309@cs.man.ac.uk>
Message-ID: <4AEACB76.5090107@cs.man.ac.uk>

Oh, and regarding this...

> 3-can't see simple view/ advance view when i search for service. these
> options are only seen when i browse.
> Default view when i search is 'simple view' ... i would prefer an
> 'advance view'. for a good first impression on casual or first time
> users.

The decision was to show a simple listing by default, for performance
reasons, but give the user the option to see the detailed view. We could
still change this now given the other search improvements I have made.

Cheers,
Jits


Jiten Bhagat wrote:
> Franck Tanoh wrote:
>   
>> Hi guys,
>>
>> Good job for the updates.
>> Here are the issues i came across when running through the site:
>> 1-unable to sign in with my openid
>>   
>>     
>
> Fixed
>
>   
>> 2-unable to sign in with my google id.
>>   
>>     
>
> Fixed
>
>   
>> 3-can't see simple view/ advance view when i search for service. these
>> options are only seen when i browse.
>> Default view when i search is 'simple view' ... i would prefer an
>> 'advance view'. for a good first impression on casual or first time
>> users.
>>   
>>     
>
> Should be fixed (please test :-))
>
>   
>> 3-can't edit my account or profile... <something went wrong> type message
>>   
>>     
>
> Does this happen now?
>
>   
>> 4-feedback seem to work without entering the security number when the
>> message section is empty
>>   
>>     
>
> Fixed
>
>   
>> 5-we need a better error message when user forget to enter the
>> security number...now we have
>>  <your message has not been submitted. the message length was not
>> entered correctly>
>>   
>>     
>
> Better error message now.
>
>   
>> 6-Number of similar service per service is limited to 10 without the
>> possibility to see the rest if there are more than 10.
>>   
>>     
>
> Now can show more than 10 as an expandable list.
>
>   
>> 7-i can see 'delete' and 'edit' on other people annotation. looks like
>> a can delete other users annotation. but couldn't  when i try. can you
>> hide these buttons. i should only see them for my annotations.
>>   
>>     
>
> Fixed
>
>   
>> 8-is soaplab improvement or complex type service metadata support part
>> of this release? didn't notice anything new
>>   
>>     
>
> This will only come into effect for new services.
>
> I believe Eric is writing a script to update the existing services?
>
>   
>> Will have another go.
>>
>>   
>>     
>
> Cheers! And thanks for reporting... keep it coming ;-)
>
> Cheers,
> Jits
>
>   
>> cheers,
>> Franck
>>
>>   
>>     
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From noreply at rubyforge.org  Fri Oct 30 07:48:35 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 30 Oct 2009 07:48:35 -0400 (EDT)
Subject: [BioCatalogue-developers] [1223] trunk/app/views/services: REST API
 work: refactorings - stripped out the individual high level elements in the
 various /services endpoints into partials,
 so that they can easily be reused.
Message-ID: <20091030114836.0078E1858277@rubyforge.org>

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From noreply at rubyforge.org  Fri Oct 30 08:11:52 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 30 Oct 2009 08:11:52 -0400 (EDT)
Subject: [BioCatalogue-developers] [1224] trunk/app: REST API work:
Message-ID: <20091030121152.2476E1598031@rubyforge.org>

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From noreply at rubyforge.org  Fri Oct 30 08:55:22 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 30 Oct 2009 08:55:22 -0400 (EDT)
Subject: [BioCatalogue-developers] [1225] trunk: REST API work: now
 parameters have urlKey and (some have) urlValue attributes to help self
 document the API.
Message-ID: <20091030125522.962931588061@rubyforge.org>

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From noreply at rubyforge.org  Fri Oct 30 08:58:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 30 Oct 2009 08:58:09 -0400 (EDT)
Subject: [BioCatalogue-developers] [1226]
 trunk/public/2009/xml/rest/schema-v1.xsd: REST API work: minnor fix to
 schema for service summary.
Message-ID: <20091030125809.277181858249@rubyforge.org>

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From noreply at rubyforge.org  Fri Oct 30 10:28:16 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 30 Oct 2009 10:28:16 -0400 (EDT)
Subject: [BioCatalogue-developers] [1227] trunk/app/views: REST API work:
Message-ID: <20091030142816.6903D1858277@rubyforge.org>

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From noreply at rubyforge.org  Fri Oct 30 11:10:04 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 30 Oct 2009 11:10:04 -0400 (EDT)
Subject: [BioCatalogue-developers] [1228] trunk/app/views: REST API work:
Message-ID: <20091030151004.A720E1588066@rubyforge.org>

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From noreply at rubyforge.org  Fri Oct 30 11:14:18 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 30 Oct 2009 11:14:18 -0400 (EDT)
Subject: [BioCatalogue-developers] [1229] trunk: REST API work: fixed a few
 bugs and brought the schema up to date.
Message-ID: <20091030151418.AF20C1858282@rubyforge.org>

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From noreply at rubyforge.org  Fri Oct 30 11:37:15 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 30 Oct 2009 11:37:15 -0400 (EDT)
Subject: [BioCatalogue-developers] [1230]
 trunk/app/views/services/api/_related_links_for_service.xml.builder: Minor
 textual change
Message-ID: <20091030153716.137651588066@rubyforge.org>

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From noreply at rubyforge.org  Fri Oct 30 12:08:12 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 30 Oct 2009 12:08:12 -0400 (EDT)
Subject: [BioCatalogue-developers] [1231] trunk: Some refactorings for the
	annotations module.
Message-ID: <20091030160812.705E61588066@rubyforge.org>

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From noreply at rubyforge.org  Fri Oct 30 12:27:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 30 Oct 2009 12:27:09 -0400 (EDT)
Subject: [BioCatalogue-developers] [1232] trunk: REST API work: implemented
 the /services/{id}/ annotations endpoint,
 which returns back all the annotations for the service and it' s deployments,
 versions and version instances ( so not including annotations on the service
 technology parts like operations /inputs/outputs).
Message-ID: <20091030162710.171A41588066@rubyforge.org>

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From ytanoh at cs.man.ac.uk  Fri Oct 30 13:46:17 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Fri, 30 Oct 2009 17:46:17 +0000
Subject: [BioCatalogue-developers] some note after running through the
	test site
In-Reply-To: <4AEAC9F2.9090309@cs.man.ac.uk>
References: <d0ee827d0910280424y25b5bc3bt951917e84800ea2e@mail.gmail.com>
	<4AEAC9F2.9090309@cs.man.ac.uk>
Message-ID: <d0ee827d0910301046vce2b93co6f088244be7b5bcf@mail.gmail.com>

>> 8-is soaplab improvement or complex type service metadata support part
>> of this release? didn't notice anything new
>>> I believe Eric is writing a script to update the existing services?
Or we could simply remove and re-submit if it's too much hassle.

I've noticed that when you search for service the default view is
'simple view' but when you browse the default is the 'advance view'.
For Consistency, can we have one default view. If we want to keep the
simple view as default can we display more than 1 service description
+ the source.

Cheers,
Franck


>
> This will only come into effect for new services.

2009/10/30 Jiten Bhagat <jits at cs.man.ac.uk>:
> Franck Tanoh wrote:
>> Hi guys,
>>
>> Good job for the updates.
>> Here are the issues i came across when running through the site:
>> 1-unable to sign in with my openid
>>
>
> Fixed
>
>> 2-unable to sign in with my google id.
>>
>
> Fixed
>
>> 3-can't see simple view/ advance view when i search for service. these
>> options are only seen when i browse.
>> Default view when i search is 'simple view' ... i would prefer an
>> 'advance view'. for a good first impression on casual or first time
>> users.
>>
>
> Should be fixed (please test :-))
>
>> 3-can't edit my account or profile... <something went wrong> type message
>>
>
> Does this happen now?
>
>> 4-feedback seem to work without entering the security number when the
>> message section is empty
>>
>
> Fixed
>
>> 5-we need a better error message when user forget to enter the
>> security number...now we have
>> ?<your message has not been submitted. the message length was not
>> entered correctly>
>>
>
> Better error message now.
>
>> 6-Number of similar service per service is limited to 10 without the
>> possibility to see the rest if there are more than 10.
>>
>
> Now can show more than 10 as an expandable list.
>
>> 7-i can see 'delete' and 'edit' on other people annotation. looks like
>> a can delete other users annotation. but couldn't ?when i try. can you
>> hide these buttons. i should only see them for my annotations.
>>
>
> Fixed
>
>> 8-is soaplab improvement or complex type service metadata support part
>> of this release? didn't notice anything new
>>
>
> This will only come into effect for new services.
>
> I believe Eric is writing a script to update the existing services?
>
>> Will have another go.
>>
>>
>
> Cheers! And thanks for reporting... keep it coming ;-)
>
> Cheers,
> Jits
>
>> cheers,
>> Franck
>>
>>
>
>



-- 
 "Science knows no country, because knowledge belongs to humanity, and
is the torch which illuminates the world." - Louis Pasteur

From MAILER-DAEMON at ebi.ac.uk  Sat Oct 31 08:27:16 2009
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Sat, 31 Oct 2009 12:27:16 GMT
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <200910311227.n9VCRG2G024580@spike.ebi.ac.uk>

The original message was received at Sat, 31 Oct 2009 12:25:40 GMT
from pweb-4a.ebi.ac.uk [172.18.1.109]

   ----- The following addresses had permanent fatal errors -----
<biocatalogue-developers at rubyforge.org>
    (reason: 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network)

   ----- Transcript of session follows -----
... while talking to rubyforge.org.:
>>> DATA
<<< 550 5.7.1 <biocatalogue-developers at rubyforge.org>: Sender address rejected: Mail server in loopback network
550 5.1.1 <biocatalogue-developers at rubyforge.org>... User unknown
<<< 554 5.5.1 Error: no valid recipients
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From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
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	(ActionController::InvalidAuthenticityToken)
	"ActionController::InvalidAuthenticityToken"
Date: Sat, 31 Oct 2009 12:25:40 +0000
Size: 12411
URL: <http://rubyforge.org/mailman/private/biocatalogue-developers/attachments/20091031/abce86c7/attachment-0001.mht>