From noreply at rubyforge.org  Mon Feb  1 09:10:55 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  1 Feb 2010 09:10:55 -0500 (EST)
Subject: [BioCatalogue-developers] [1436]
 branches/integration-jan10/app/helpers/application_helper.rb: Minor textual
 update
Message-ID: <20100201141055.826B61588033@rubyforge.org>

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From noreply at rubyforge.org  Mon Feb  1 10:54:18 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  1 Feb 2010 10:54:18 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2902] Broken links in the feta
	imports
Message-ID: <20100201155418.17E7218582D6@rubyforge.org>

Task #2902 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Broken links in the feta imports 
Complete: 0%
Status: Open

Description: Revisit links from the feta import. Some (example workflows listed in the other annotation in biocat) don't work anymore:
http://www.mygrid.org.uk/feta/mygrid/example_workflow/DDBJ/blast/extractPosition_workflow.xml (blast should be capital BLAST)
http://www.mygrid.org.uk/feta/mygrid/example_workflow/DDBJ/blast/getSupportDatabaseList_workflow.xml (doesn't exit) 

-------------------------------------------------------
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From noreply at rubyforge.org  Mon Feb  1 10:56:18 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  1 Feb 2010 10:56:18 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2903] automatically check all the
	links in biocat
Message-ID: <20100201155618.2D22918582D4@rubyforge.org>

Task #2903 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: automatically check all the links in biocat
Complete: 0%
Status: Open

Description: Use existing tools to check the availability of all external links within the biocat. Then display an icon near those which don't exist anymore. 

-------------------------------------------------------
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From noreply at rubyforge.org  Mon Feb  1 11:02:18 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  1 Feb 2010 11:02:18 -0500 (EST)
Subject: [BioCatalogue-developers] [1437] branches/integration-jan10: UI
	work and fixes for monitoring
Message-ID: <20100201160218.63FC71588033@rubyforge.org>

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From noreply at rubyforge.org  Mon Feb  1 12:06:16 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  1 Feb 2010 12:06:16 -0500 (EST)
Subject: [BioCatalogue-developers] [1438] branches/integration-jan10: -
 added support to add and delete parameter constraints
Message-ID: <20100201170617.0822E1588066@rubyforge.org>

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From noreply at rubyforge.org  Mon Feb  1 12:43:39 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  1 Feb 2010 12:43:39 -0500 (EST)
Subject: [BioCatalogue-developers] [1439]
 branches/integration-jan10/lib/bio_catalogue/monitoring/status.rb: Bugfix
 for last checked for statuses
Message-ID: <20100201174339.CB7F81588067@rubyforge.org>

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From noreply at rubyforge.org  Mon Feb  1 13:04:26 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  1 Feb 2010 13:04:26 -0500 (EST)
Subject: [BioCatalogue-developers] [1440] branches/integration-jan10: REST
 API Work: Added < latestMonitoringStatus> to the core elements for
 <service>
Message-ID: <20100201180426.754E9158806A@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb  2 05:07:16 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 05:07:16 -0500 (EST)
Subject: [BioCatalogue-developers] [1441]
 branches/integration-jan10/public/images/small-query-sphere-50.png: small
 version of unchecked status image
Message-ID: <20100202100717.0CB0B1588071@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb  2 05:12:34 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 05:12:34 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2450] wsdl parsing should handle
	external schemas
Message-ID: <20100202101234.1F7C918582F4@rubyforge.org>

Task #2450 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: wsdl parsing should handle external schemas
Complete: 0%
Status: Closed

Description: Many wsdls defined they types in an external xml schema. This is currently being ignored in the parsing process

Follow-Ups:

-------------------------------------------------------
Date: 2010-02-02 10:12
By: ebontane

Comment:
With the integration of the EMBRACE parser, BioCatalogue now parses types in external schemas

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2450&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Feb  2 05:14:12 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 05:14:12 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2733] allow the submitter to
	select a display name for a service
Message-ID: <20100202101412.B2C5918582F4@rubyforge.org>

Task #2733 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: allow the submitter to select a display name for a service
Complete: 0%
Status: Closed

Description: <<I have a suggestion -- you allow people to add name aliases for services, but it would be really useful if you could tag one as the primary display name.

I wouldn't be surprised if quite a lot of the services out there have fairly unfriendly names in the WSDLs.

The EMBRACE Registry lets you enter a title for the service, which is what comes up in the human-readable web page, rather than the computer-readable name from the WSDL.>>
posted by Andrew  on the Biocat support list

Follow-Ups:

-------------------------------------------------------
Date: 2010-02-02 10:14
By: ebontane

Comment:
User can now add alternative display names for services

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2733&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Feb  2 05:17:12 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 05:17:12 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2733] allow the submitter to
	select a display name for a service
Message-ID: <20100202101712.BF6E918582F4@rubyforge.org>

Task #2733 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: allow the submitter to select a display name for a service
Complete: 70%
Status: Closed

Description: <<I have a suggestion -- you allow people to add name aliases for services, but it would be really useful if you could tag one as the primary display name.

I wouldn't be surprised if quite a lot of the services out there have fairly unfriendly names in the WSDLs.

The EMBRACE Registry lets you enter a title for the service, which is what comes up in the human-readable web page, rather than the computer-readable name from the WSDL.>>
posted by Andrew  on the Biocat support list

Follow-Ups:

-------------------------------------------------------
Date: 2010-02-02 10:17
By: jits

Comment:
As mentioned, this now exists, but in the form of "promoting" an alternative name to a preferred display name.

Now need the ability to directly set a preferred display name.

-------------------------------------------------------
Date: 2010-02-02 10:14
By: ebontane

Comment:
User can now add alternative display names for services

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2733&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Feb  2 07:06:14 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 07:06:14 -0500 (EST)
Subject: [BioCatalogue-developers] [1442] branches/integration-jan10/app:
	Various fixes for users:
Message-ID: <20100202120614.DCE931588071@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb  2 09:24:38 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 09:24:38 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2904] Investigate how rollbacks in
	transactions affect Solr
Message-ID: <20100202142438.35FFB185828E@rubyforge.org>

Task #2904 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Investigate how rollbacks in transactions affect Solr
Complete: 0%
Status: Open

Description: When transactions rollback, what happens to anything that was indexed in Solr during the transaction???

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2904&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Feb  2 09:54:07 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 09:54:07 -0500 (EST)
Subject: [BioCatalogue-developers] [1443] branches/integration-jan10:
 Updated the EMBRACE import script to import the names of services from
 EMBRACE as preferred display_name annotations .
Message-ID: <20100202145407.AECF518582F8@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb  2 10:37:39 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 10:37:39 -0500 (EST)
Subject: [BioCatalogue-developers] [1444]
 branches/integration-jan10/lib/bio_catalogue/monitoring/status.rb: bugfix
 for the test result unchecked status
Message-ID: <20100202153740.0B4FC18582F4@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb  2 11:14:27 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 11:14:27 -0500 (EST)
Subject: [BioCatalogue-developers] [1445]
 branches/integration-jan10/script/biocatalogue/embrace_import.rb: Various
 updates to the EMBRACE import script to take into account things like
 EMBRACE original IDs and submitters .
Message-ID: <20100202161427.CE8321858301@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb  2 11:46:35 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 11:46:35 -0500 (EST)
Subject: [BioCatalogue-developers] [1446]
 branches/integration-jan10/test/unit/annotation_test.rb: Test for the
 alternative_name to display_name process
Message-ID: <20100202164635.9B29D18582EC@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb  2 11:51:36 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 11:51:36 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2905] Add cancel button to vaious
	forms
Message-ID: <20100202165136.4B40818582EC@rubyforge.org>

Task #2905 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Add cancel button to vaious forms
Complete: 0%
Status: Open

Description: Potentially using...
<input type="button" name="Cancel" value="Cancel" onclick="window.location = 'yourpage.html' " />

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2905&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Feb  2 11:55:11 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 11:55:11 -0500 (EST)
Subject: [BioCatalogue-developers] [1447]
 branches/integration-jan10/test/unit/lib/: Added a new 'lib' folder under
 test/unit/ for unit tests for the Modules etc in lib/
Message-ID: <20100202165511.343E215B8028@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb  2 11:59:40 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 11:59:40 -0500 (EST)
Subject: [BioCatalogue-developers] [1448] branches/integration-jan10/app: -
 added functionality to edit constraints
Message-ID: <20100202165940.899111858301@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb  2 12:42:01 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 12:42:01 -0500 (EST)
Subject: [BioCatalogue-developers] [1449] branches/integration-jan10: REST
 API work: Initial implementation of the /lookup endpoint.
Message-ID: <20100202174201.2B0F018582FF@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb  2 13:02:51 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 13:02:51 -0500 (EST)
Subject: [BioCatalogue-developers] [1450]
 branches/integration-jan10/app/helpers/api_helper.rb: Bugfix: filter value
 names weren't meant to be lowercased!
Message-ID: <20100202180251.2CF8215B8028@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb  2 13:57:59 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  2 Feb 2010 13:57:59 -0500 (EST)
Subject: [BioCatalogue-developers] [1451] branches/integration-jan10: REST
 API work: various updates to the / tags and /tag endpoints to bring it in
 line with the rest of the API design .
Message-ID: <20100202185759.8A12A15B8028@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  3 04:44:00 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  3 Feb 2010 04:44:00 -0500 (EST)
Subject: [BioCatalogue-developers] [1452]
 branches/integration-jan10/app/views/rest_parameters/
 edit_constraint_popup.html.erb: file that was omitted in my last commit
Message-ID: <20100203094400.331D018582CA@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  3 05:20:30 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  3 Feb 2010 05:20:30 -0500 (EST)
Subject: [BioCatalogue-developers] [1453]
 branches/integration-jan10/app/controllers/search_controller.rb: Better
 error handling for Serach By Data controller logic.
Message-ID: <20100203102031.45A621858289@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  3 05:23:24 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  3 Feb 2010 05:23:24 -0500 (EST)
Subject: [BioCatalogue-developers] [1454]
 branches/integration-jan10/app/controllers/users_controller.rb: Pre-emptive
 returns for when error_to_home is called.
Message-ID: <20100203102324.462721858289@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  3 05:57:23 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  3 Feb 2010 05:57:23 -0500 (EST)
Subject: [BioCatalogue-developers] [1455] branches/integration-jan10:
 Consolidated (and made more consistent) the way paging works.
Message-ID: <20100203105723.1FBC718582D6@rubyforge.org>

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From ytanoh at cs.man.ac.uk  Wed Feb  3 05:58:12 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 3 Feb 2010 10:58:12 +0000
Subject: [BioCatalogue-developers] category updates
Message-ID: <d0ee827d1002030258jb8e8d63i3951e2c6f9dfaee3@mail.gmail.com>

Hi Jits,

I've updated the categories ... see file attached
The updates are:
- changed  'Structure Prediction [7]'  to 'Protein Structure Prediction[7]
- changed 'Secondary Structure [8]' to 'Protein Secondary Structure [8]'
-changed 'Tertiary Structure [9]' to 'Protein Tertiary Structure [9]'
- added 3 new category:
     Nucleotide Structure Prediction [ ]
       --Nucleotide Secondary Structure [ ]
       --Nucleotide Tertiary Structure [ ]

Please change the existing category with the new one.

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 noreply at rubyforge.org  Wed Feb  3 06:42:43 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  3 Feb 2010 06:42:43 -0500 (EST)
Subject: [BioCatalogue-developers] [1456]
 branches/integration-jan10/config/initializers/mail.rb.pre: template action
 mailer configuration file to be used for local configuration .
Message-ID: <20100203114243.334F3185828E@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  3 06:44:40 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  3 Feb 2010 06:44:40 -0500 (EST)
Subject: [BioCatalogue-developers] [1457]
 branches/integration-jan10/config/initializers/mail.rb: deleted mail .rb
 from repository
Message-ID: <20100203114440.A4CBE18582D3@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  3 07:07:07 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  3 Feb 2010 07:07:07 -0500 (EST)
Subject: [BioCatalogue-developers] [1458]
	branches/integration-jan10/config/initializers/:
Message-ID: <20100203120707.5D43118582C3@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  3 08:13:01 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  3 Feb 2010 08:13:01 -0500 (EST)
Subject: [BioCatalogue-developers] [1459]
 branches/integration-jan10/config/initializers/mail.rb.pre: Fix for mail
 config template
Message-ID: <20100203131301.C8AB118582CE@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  3 09:07:07 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  3 Feb 2010 09:07:07 -0500 (EST)
Subject: [BioCatalogue-developers] [1460] branches/integration-jan10: REST
 API work: Added pageSize parameter to /services and /search XML outputs.
Message-ID: <20100203140707.F016C18582D3@rubyforge.org>

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From jits at cs.man.ac.uk  Wed Feb  3 09:20:05 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 03 Feb 2010 14:20:05 +0000
Subject: [BioCatalogue-developers] category updates
In-Reply-To: <d0ee827d1002030258jb8e8d63i3951e2c6f9dfaee3@mail.gmail.com>
References: <d0ee827d1002030258jb8e8d63i3951e2c6f9dfaee3@mail.gmail.com>
Message-ID: <4B698615.6090009@cs.man.ac.uk>

Franck Tanoh wrote:
> Hi Jits,
>
> I've updated the categories ... see file attached
> The updates are:
> - changed  'Structure Prediction [7]'  to 'Protein Structure Prediction[7]
> - changed 'Secondary Structure [8]' to 'Protein Secondary Structure [8]'
> -changed 'Tertiary Structure [9]' to 'Protein Tertiary Structure [9]'
> - added 3 new category:
>      Nucleotide Structure Prediction [ ]
>        --Nucleotide Secondary Structure [ ]
>        --Nucleotide Tertiary Structure [ ]
>
> Please change the existing category with the new one.
>   

I've updated the categories, in the current integration branch. This
will go out in next release.

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  Wed Feb  3 09:20:56 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  3 Feb 2010 09:20:56 -0500 (EST)
Subject: [BioCatalogue-developers] [1461]
 branches/integration-jan10/data/service_categories.yml: Updated the Service
 Categories (via Franck).
Message-ID: <20100203142056.3F6AC185828E@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  3 11:43:37 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  3 Feb 2010 11:43:37 -0500 (EST)
Subject: [BioCatalogue-developers] [1462]
 branches/integration-jan10/app/models/service.rb: Minor update for logging
 tweets
Message-ID: <20100203164337.A469A18582D8@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  3 12:13:46 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  3 Feb 2010 12:13:46 -0500 (EST)
Subject: [BioCatalogue-developers] [1463]
 branches/integration-jan10/test/functional/
 test_results_controller_test.rb: fix for functional tests
Message-ID: <20100203171346.2B00318582D8@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb  3 12:15:00 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed,  3 Feb 2010 12:15:00 -0500 (EST)
Subject: [BioCatalogue-developers] [1464]
 branches/integration-jan10/test/factories/service_tests.rb: completing fix
 for functional test commit
Message-ID: <20100203171500.BCB3718582DA@rubyforge.org>

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From jits at cs.man.ac.uk  Wed Feb  3 12:25:10 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 03 Feb 2010 17:25:10 +0000
Subject: [BioCatalogue-developers] Factories
Message-ID: <4B69B176.3080304@cs.man.ac.uk>

Mannie, Eric,

Under test/ we have both a factories.rb and a factories/ directory. We
need to stick to one convention for these. I would say stick to the
test/factories/ directory with individual files.

Please could someone consolidate these.

Cheers,
Jits

From jits at cs.man.ac.uk  Wed Feb  3 13:02:41 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 03 Feb 2010 18:02:41 +0000
Subject: [BioCatalogue-developers] Possibly useful for BioCatalogue
In-Reply-To: <op.u7kbtay2nbznux@littlesony.wireless.ubc.ca>
References: <op.u7kbtay2nbznux@littlesony.wireless.ubc.ca>
Message-ID: <4B69BA41.20804@cs.man.ac.uk>

Hi Mark,

This looks very useful! Thanks for letting us know about it.

This could also be very useful for our internal test for the REST API.

Cheers,
Jits



Mark Wilkinson wrote:
> Hi Jits and Carole!
>
> Eddie has just committed a module to CPAN that might be useful for you
> when it comes to service testing for biocatalogue.
>
> http://search.cpan.org/dist/XML-SemanticCompare/
>
> It compares two XML trees based on "content" - e.g. same attributes,
> different order, or whatever.  We use it for automated service testing
> of Moby services (comparing expected output with "live" output)
>
> Just wanted to let you know it was now available in case it was useful
> to you in any way.
>
> Cheers!
>
> Mark
>
>
>


From jerzyo at genesilico.pl  Wed Feb  3 13:34:15 2010
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Wed, 03 Feb 2010 19:34:15 +0100
Subject: [BioCatalogue-developers] Possibly useful for BioCatalogue
In-Reply-To: <4B69BA41.20804@cs.man.ac.uk>
References: <op.u7kbtay2nbznux@littlesony.wireless.ubc.ca>
	<4B69BA41.20804@cs.man.ac.uk>
Message-ID: <4B69C1A7.5010504@genesilico.pl>

And we could use it to extend search by data on XML files...

George

Jiten Bhagat wrote:
> Hi Mark,
>
> This looks very useful! Thanks for letting us know about it.
>
> This could also be very useful for our internal test for the REST API.
>
> Cheers,
> Jits
>
>
>
> Mark Wilkinson wrote:
>   
>> Hi Jits and Carole!
>>
>> Eddie has just committed a module to CPAN that might be useful for you
>> when it comes to service testing for biocatalogue.
>>
>> http://search.cpan.org/dist/XML-SemanticCompare/
>>
>> It compares two XML trees based on "content" - e.g. same attributes,
>> different order, or whatever.  We use it for automated service testing
>> of Moby services (comparing expected output with "live" output)
>>
>> Just wanted to let you know it was now available in case it was useful
>> to you in any way.
>>
>> Cheers!
>>
>> Mark
>>
>>
>>
>>     
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>
>
>
>   


From jerzyo at genesilico.pl  Thu Feb  4 02:56:51 2010
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Thu, 04 Feb 2010 08:56:51 +0100
Subject: [BioCatalogue-developers] MyExperiment Input data
Message-ID: <4B6A7DC3.6090102@genesilico.pl>

Hi

Franck, Is there anything interesting in the inputs I parsed from 
MyExperiment?

George

From mannie.tags at googlemail.com  Thu Feb  4 05:10:43 2010
From: mannie.tags at googlemail.com (Mannie Tagarira)
Date: Thu, 4 Feb 2010 10:10:43 +0000
Subject: [BioCatalogue-developers] Factories
In-Reply-To: <4B69B176.3080304@cs.man.ac.uk>
References: <4B69B176.3080304@cs.man.ac.uk>
Message-ID: <A2B86406-4233-4462-A009-A50E9F849E74@gmail.com>

Jits, Eric

Thanks for raising this, I take responsibility for this.  I noticed this a couple of days ago when I made my commit.  I will move it to follow the convention, but after I have re-factored some of the tests, etc.  Is that okay?

Thanks,
Mannie



On 3 Feb 2010, at 17:25, Jiten Bhagat wrote:

> Mannie, Eric,
> 
> Under test/ we have both a factories.rb and a factories/ directory. We
> need to stick to one convention for these. I would say stick to the
> test/factories/ directory with individual files.
> 
> Please could someone consolidate these.
> 
> 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  Thu Feb  4 05:16:04 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Thu, 04 Feb 2010 10:16:04 +0000
Subject: [BioCatalogue-developers] Factories
In-Reply-To: <A2B86406-4233-4462-A009-A50E9F849E74@gmail.com>
References: <4B69B176.3080304@cs.man.ac.uk>
	<A2B86406-4233-4462-A009-A50E9F849E74@gmail.com>
Message-ID: <4B6A9E64.1070005@cs.man.ac.uk>

Mannie Tagarira wrote:
> Jits, Eric
>
> Thanks for raising this, I take responsibility for this.  I noticed this a couple of days ago when I made my commit.  I will move it to follow the convention, but after I have re-factored some of the tests, etc.  Is that okay?
>   

Sure. Thanks Mannie.

Bear in mind this - we're all making various changes to the tests and
test infrastructure (I know I have lately), so it's important that
things are always kept running and done properly.

Cheers,
Jits


> Thanks,
> Mannie
>
>
>
> On 3 Feb 2010, at 17:25, Jiten Bhagat wrote:
>
>   
>> Mannie, Eric,
>>
>> Under test/ we have both a factories.rb and a factories/ directory. We
>> need to stick to one convention for these. I would say stick to the
>> test/factories/ directory with individual files.
>>
>> Please could someone consolidate these.
>>
>> Cheers,
>> Jits
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>     
>
>   


From ytanoh at cs.man.ac.uk  Thu Feb  4 05:18:23 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Thu, 4 Feb 2010 10:18:23 +0000
Subject: [BioCatalogue-developers] MyExperiment Input data
In-Reply-To: <4B6A7DC3.6090102@genesilico.pl>
References: <4B6A7DC3.6090102@genesilico.pl>
Message-ID: <d0ee827d1002040218o588e17b7re3797fc07be3076b@mail.gmail.com>

Yep, good stuff. We now need to think of a better way to export them
into biocat. Probably a generic script we can use again and again.
Can your Feta import script be customized for that?

Franck

On 4 February 2010 07:56, Jerzy Orlowski <jerzyo at genesilico.pl> wrote:
> Hi
>
> Franck, Is there anything interesting in the inputs I parsed from
> MyExperiment?
>
> George
> _______________________________________________
> BioCatalogue-developers mailing list
> 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 ericnzuo at ebi.ac.uk  Thu Feb  4 05:30:37 2010
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 04 Feb 2010 10:30:37 +0000
Subject: [BioCatalogue-developers] Factories
In-Reply-To: <4B6A9E64.1070005@cs.man.ac.uk>
References: <4B69B176.3080304@cs.man.ac.uk>	<A2B86406-4233-4462-A009-A50E9F849E74@gmail.com>
	<4B6A9E64.1070005@cs.man.ac.uk>
Message-ID: <4B6AA1CD.8010502@ebi.ac.uk>

That is my fault because I created the factories directory after Mannie 
had created the factories.rb file. The intention was to liase with 
Mannie to move everything into that directory as I thought it kept 
things a bit more modular.
Thanks for raising that Jits.

Eric


Jiten Bhagat wrote:
> Mannie Tagarira wrote:
>   
>> Jits, Eric
>>
>> Thanks for raising this, I take responsibility for this.  I noticed this a couple of days ago when I made my commit.  I will move it to follow the convention, but after I have re-factored some of the tests, etc.  Is that okay?
>>   
>>     
>
> Sure. Thanks Mannie.
>
> Bear in mind this - we're all making various changes to the tests and
> test infrastructure (I know I have lately), so it's important that
> things are always kept running and done properly.
>
> Cheers,
> Jits
>
>
>   
>> Thanks,
>> Mannie
>>
>>
>>
>> On 3 Feb 2010, at 17:25, Jiten Bhagat wrote:
>>
>>   
>>     
>>> Mannie, Eric,
>>>
>>> Under test/ we have both a factories.rb and a factories/ directory. We
>>> need to stick to one convention for these. I would say stick to the
>>> test/factories/ directory with individual files.
>>>
>>> Please could someone consolidate these.
>>>
>>> Cheers,
>>> Jits
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>     
>>>       
>>   
>>     
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   

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From jits at cs.man.ac.uk  Thu Feb  4 05:34:30 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Thu, 04 Feb 2010 10:34:30 +0000
Subject: [BioCatalogue-developers] Factories
In-Reply-To: <4B6AA1CD.8010502@ebi.ac.uk>
References: <4B69B176.3080304@cs.man.ac.uk>	<A2B86406-4233-4462-A009-A50E9F849E74@gmail.com>
	<4B6A9E64.1070005@cs.man.ac.uk> <4B6AA1CD.8010502@ebi.ac.uk>
Message-ID: <4B6AA2B6.9010104@cs.man.ac.uk>

> The intention was to liase with Mannie to move everything into that
> directory as I thought it kept things a bit more modular

Agreed! No problem :-) We have an opportunity right now to really make
our test environment consistent and effective.

Another thing I am considering which I will run past you guys later:
Factories are painfully low for building large datasets (eg: loads of
"tag" annotations). So using a CSV format fixtures file might be the way
forward for that.

Jits


Eric Nzuobontane wrote:
> That is my fault because I created the factories directory after
> Mannie had created the factories.rb file. The intention was to liase
> with Mannie to move everything into that directory as I thought it
> kept things a bit more modular.
> Thanks for raising that Jits.
>
> Eric
>
>
> Jiten Bhagat wrote:
>> Mannie Tagarira wrote:
>>  
>>> Jits, Eric
>>>
>>> Thanks for raising this, I take responsibility for this.  I noticed
>>> this a couple of days ago when I made my commit.  I will move it to
>>> follow the convention, but after I have re-factored some of the
>>> tests, etc.  Is that okay?
>>>       
>>
>> Sure. Thanks Mannie.
>>
>> Bear in mind this - we're all making various changes to the tests and
>> test infrastructure (I know I have lately), so it's important that
>> things are always kept running and done properly.
>>
>> Cheers,
>> Jits
>>
>>
>>  
>>> Thanks,
>>> Mannie
>>>
>>>
>>>
>>> On 3 Feb 2010, at 17:25, Jiten Bhagat wrote:
>>>
>>>      
>>>> Mannie, Eric,
>>>>
>>>> Under test/ we have both a factories.rb and a factories/ directory. We
>>>> need to stick to one convention for these. I would say stick to the
>>>> test/factories/ directory with individual files.
>>>>
>>>> Please could someone consolidate these.
>>>>
>>>> Cheers,
>>>> Jits
>>>> _______________________________________________
>>>> BioCatalogue-developers mailing list
>>>> BioCatalogue-developers at rubyforge.org
>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>>           
>>>       
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>   
>


From noreply at rubyforge.org  Thu Feb  4 05:40:49 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  4 Feb 2010 05:40:49 -0500 (EST)
Subject: [BioCatalogue-developers] [1465] branches/integration-jan10: Some
 tests for the BioCatalogue::Tags:: get_tags method.
Message-ID: <20100204104049.D77FC18582E0@rubyforge.org>

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From jerzyo at genesilico.pl  Thu Feb  4 05:55:32 2010
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Thu, 04 Feb 2010 11:55:32 +0100
Subject: [BioCatalogue-developers] MyExperiment Input data
In-Reply-To: <d0ee827d1002040218o588e17b7re3797fc07be3076b@mail.gmail.com>
References: <4B6A7DC3.6090102@genesilico.pl>
	<d0ee827d1002040218o588e17b7re3797fc07be3076b@mail.gmail.com>
Message-ID: <4B6AA7A4.8020200@genesilico.pl>

Sure.

However, it needs to be checked manually before:
1. Some sevices might be not from life sciences
2. Some services might be not in biocatalogue (and needed to be created)
3. Some services might be dead
Once these 3 issues are solved, we can use the script

George

Franck Tanoh wrote:
> Yep, good stuff. We now need to think of a better way to export them
> into biocat. Probably a generic script we can use again and again.
> Can your Feta import script be customized for that?
>
> Franck
>
> On 4 February 2010 07:56, Jerzy Orlowski <jerzyo at genesilico.pl> wrote:
>   
>> Hi
>>
>> Franck, Is there anything interesting in the inputs I parsed from
>> MyExperiment?
>>
>> George
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>
>>     
>
>
>
>   


From jits at cs.man.ac.uk  Thu Feb  4 06:05:46 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Thu, 04 Feb 2010 11:05:46 +0000
Subject: [BioCatalogue-developers] Factories
In-Reply-To: <4B6AA2B6.9010104@cs.man.ac.uk>
References: <4B69B176.3080304@cs.man.ac.uk>	<A2B86406-4233-4462-A009-A50E9F849E74@gmail.com>	<4B6A9E64.1070005@cs.man.ac.uk>
	<4B6AA1CD.8010502@ebi.ac.uk> <4B6AA2B6.9010104@cs.man.ac.uk>
Message-ID: <4B6AAA0A.50103@cs.man.ac.uk>

Whilst we're on testing... let's ensure we keep this page up to date:

http://www.biocatalogue.org/wiki/doku.php?id=development:codebase_testing

Cheers,
Jits


Jiten Bhagat wrote:
>> The intention was to liase with Mannie to move everything into that
>> directory as I thought it kept things a bit more modular
>>     
>
> Agreed! No problem :-) We have an opportunity right now to really make
> our test environment consistent and effective.
>
> Another thing I am considering which I will run past you guys later:
> Factories are painfully low for building large datasets (eg: loads of
> "tag" annotations). So using a CSV format fixtures file might be the way
> forward for that.
>
> Jits
>
>
> Eric Nzuobontane wrote:
>   
>> That is my fault because I created the factories directory after
>> Mannie had created the factories.rb file. The intention was to liase
>> with Mannie to move everything into that directory as I thought it
>> kept things a bit more modular.
>> Thanks for raising that Jits.
>>
>> Eric
>>
>>
>> Jiten Bhagat wrote:
>>     
>>> Mannie Tagarira wrote:
>>>  
>>>       
>>>> Jits, Eric
>>>>
>>>> Thanks for raising this, I take responsibility for this.  I noticed
>>>> this a couple of days ago when I made my commit.  I will move it to
>>>> follow the convention, but after I have re-factored some of the
>>>> tests, etc.  Is that okay?
>>>>       
>>>>         
>>> Sure. Thanks Mannie.
>>>
>>> Bear in mind this - we're all making various changes to the tests and
>>> test infrastructure (I know I have lately), so it's important that
>>> things are always kept running and done properly.
>>>
>>> Cheers,
>>> Jits
>>>
>>>
>>>  
>>>       
>>>> Thanks,
>>>> Mannie
>>>>
>>>>
>>>>
>>>> On 3 Feb 2010, at 17:25, Jiten Bhagat wrote:
>>>>
>>>>      
>>>>         
>>>>> Mannie, Eric,
>>>>>
>>>>> Under test/ we have both a factories.rb and a factories/ directory. We
>>>>> need to stick to one convention for these. I would say stick to the
>>>>> test/factories/ directory with individual files.
>>>>>
>>>>> Please could someone consolidate these.
>>>>>
>>>>> Cheers,
>>>>> Jits
>>>>> _______________________________________________
>>>>> BioCatalogue-developers mailing list
>>>>> BioCatalogue-developers at rubyforge.org
>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>>>           
>>>>>           
>>>>       
>>>>         
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>   
>>>       
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From noreply at rubyforge.org  Thu Feb  4 06:22:53 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  4 Feb 2010 06:22:53 -0500 (EST)
Subject: [BioCatalogue-developers] [1466]
 branches/integration-jan10/vendor/embrace_scripts/src: removed unnecessary
 file and renamed script that creates script execution directories
Message-ID: <20100204112253.351DA1858289@rubyforge.org>

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From MAILER-DAEMON at ebi.ac.uk  Thu Feb  4 08:41:06 2010
From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem)
Date: Thu, 4 Feb 2010 13:41:06 GMT
Subject: [BioCatalogue-developers] Returned mail: see transcript for details
Message-ID: <201002041341.o14Df6r4009814@wolin.ebi.ac.uk>

The original message was received at Thu, 4 Feb 2010 13:41:06 GMT
from spike.ebi.ac.uk [193.62.196.9]

   ----- The following addresses had permanent fatal errors -----
<ericnzuo at wolin.ebi.ac.uk>
    (reason: 550 5.1.1 User unknown)
ericnzuo at imap.ebi.ac.uk
    (reason: 550 5.1.1 User unknown)
    (expanded from: <ericnzuo at wolin.ebi.ac.uk>)

   ----- Transcript of session follows -----
550 5.1.1 ericnzuo at imap.ebi.ac.uk... User unknown
550 5.1.1 <ericnzuo at wolin.ebi.ac.uk>... User unknown
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From: BioCatalogue Errors <biocatalogue-developers at rubyforge.org>
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	"ActionController::InvalidAuthenticityToken"
Date: Thu, 4 Feb 2010 13:40:26 +0000
Size: 38288
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From ytanoh at cs.man.ac.uk  Thu Feb  4 09:23:39 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Thu, 4 Feb 2010 14:23:39 +0000
Subject: [BioCatalogue-developers] MyExperiment Input data
In-Reply-To: <4B6AA7A4.8020200@genesilico.pl>
References: <4B6A7DC3.6090102@genesilico.pl>
	<d0ee827d1002040218o588e17b7re3797fc07be3076b@mail.gmail.com>
	<4B6AA7A4.8020200@genesilico.pl>
Message-ID: <d0ee827d1002040623q3a25f17aweb3f2de10b84e3d8@mail.gmail.com>

Hum, might as well do everything manually... How about we use the
script first then manually check the services the script will flag?
At least that will hopefully reduce the number of services to be curated.

Franck

On 4 February 2010 10:55, Jerzy Orlowski <jerzyo at genesilico.pl> wrote:
> Sure.
>
> However, it needs to be checked manually before:
> 1. Some sevices might be not from life sciences
> 2. Some services might be not in biocatalogue (and needed to be created)
> 3. Some services might be dead
> Once these 3 issues are solved, we can use the script
>
> George
>
> Franck Tanoh wrote:
>>
>> Yep, good stuff. We now need to think of a better way to export them
>> into biocat. Probably a generic script we can use again and again.
>> Can your Feta import script be customized for that?
>>
>> Franck
>>
>> On 4 February 2010 07:56, Jerzy Orlowski <jerzyo at genesilico.pl> wrote:
>>
>>>
>>> Hi
>>>
>>> Franck, Is there anything interesting in the inputs I parsed from
>>> MyExperiment?
>>>
>>> George
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>
>>>
>>
>>
>>
>>
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>



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

From noreply at rubyforge.org  Thu Feb  4 09:29:13 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  4 Feb 2010 09:29:13 -0500 (EST)
Subject: [BioCatalogue-developers] [1467] branches/integration-jan10: REST
 API work: / tags is now paged in the same way that /services and /search
 is.
Message-ID: <20100204142913.80DC318582DE@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb  4 09:33:02 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  4 Feb 2010 09:33:02 -0500 (EST)
Subject: [BioCatalogue-developers] [1468]
 branches/integration-jan10/public/2009/xml/rest/schema-v1.xsd: REST API
 work: fix to schema for previous work.
Message-ID: <20100204143303.0597E18582E1@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb  4 11:45:21 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  4 Feb 2010 11:45:21 -0500 (EST)
Subject: [BioCatalogue-developers] [1469] branches/integration-jan10: REST
 API work: implemented the / service_providers endpoint.
Message-ID: <20100204164521.9239E1588062@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb  4 11:51:07 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  4 Feb 2010 11:51:07 -0500 (EST)
Subject: [BioCatalogue-developers] [1470] branches/integration-jan10/app:
 REST API work: moved the sort parameters into a generic partial that can be
 used for all collection resources .
Message-ID: <20100204165107.6A0D618582C9@rubyforge.org>

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From ytanoh at cs.man.ac.uk  Thu Feb  4 11:51:11 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Thu, 4 Feb 2010 16:51:11 +0000
Subject: [BioCatalogue-developers] Some annotation issues....
Message-ID: <d0ee827d1002040851ief2ce36oc73976b7220478a6@mail.gmail.com>

Hi guys,
I've come across these issues which make the annotation of service in
the catalogue not a pleasant journey :-(
-Operations pages takes too long to load (even a service with 4 operation)
-Need to revisit the operation page UI, it's now impossible to have an
overview of that page, too much 'scrolling' to find descriptions
etc... I have some ideas we can discuss
-Can we make sure any external links within the site open in a new tab
or window? Otherwise it's difficult to get back to where you where
before accessing that external page. I can list these if necessary.
-Need a way to mark a service as deprecated...I've come across loads
of operations (not service) which are still in the wsdl file but no
more used.
-Can we collapse the example field, some example are very long.

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  Fri Feb  5 04:33:38 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 05 Feb 2010 09:33:38 +0000
Subject: [BioCatalogue-developers] Some annotation issues....
In-Reply-To: <d0ee827d1002040851ief2ce36oc73976b7220478a6@mail.gmail.com>
References: <d0ee827d1002040851ief2ce36oc73976b7220478a6@mail.gmail.com>
Message-ID: <4B6BE5F2.9030100@cs.man.ac.uk>

Franck,

Good points! Keep pestering us about this... I will try and do some of
these for the next release. Especially a new Operations UI.

Cheers,
Jits


Franck Tanoh wrote:
> Hi guys,
> I've come across these issues which make the annotation of service in
> the catalogue not a pleasant journey :-(
> -Operations pages takes too long to load (even a service with 4 operation)
> -Need to revisit the operation page UI, it's now impossible to have an
> overview of that page, too much 'scrolling' to find descriptions
> etc... I have some ideas we can discuss
> -Can we make sure any external links within the site open in a new tab
> or window? Otherwise it's difficult to get back to where you where
> before accessing that external page. I can list these if necessary.
> -Need a way to mark a service as deprecated...I've come across loads
> of operations (not service) which are still in the wsdl file but no
> more used.
> -Can we collapse the example field, some example are very long.
>
> Franck
>
>   


From noreply at rubyforge.org  Fri Feb  5 05:27:26 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 05:27:26 -0500 (EST)
Subject: [BioCatalogue-developers] [1471]
 branches/integration-jan10/app/views/services/show.xml.builder: REST API
 work: bugfix for /services/{id} when <summary> is included.
Message-ID: <20100205102727.17E2F1858282@rubyforge.org>

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From jits at cs.man.ac.uk  Fri Feb  5 05:42:45 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 05 Feb 2010 10:42:45 +0000
Subject: [BioCatalogue-developers] Some annotation issues....
In-Reply-To: <d0ee827d1002040851ief2ce36oc73976b7220478a6@mail.gmail.com>
References: <d0ee827d1002040851ief2ce36oc73976b7220478a6@mail.gmail.com>
Message-ID: <4B6BF625.7090204@cs.man.ac.uk>

Can we add something else to this list pleae:

We need to discuss the notion of "preferred annotations", ie: when
showing a simple listing, or needing to show just one "description" etc,
what do we choose, and what's the priority order? The one from the WSDL
first? Or one from an expert curator??

One to discuss further!

Cheers,
Jits


Franck Tanoh wrote:
> Hi guys,
> I've come across these issues which make the annotation of service in
> the catalogue not a pleasant journey :-(
> -Operations pages takes too long to load (even a service with 4 operation)
> -Need to revisit the operation page UI, it's now impossible to have an
> overview of that page, too much 'scrolling' to find descriptions
> etc... I have some ideas we can discuss
> -Can we make sure any external links within the site open in a new tab
> or window? Otherwise it's difficult to get back to where you where
> before accessing that external page. I can list these if necessary.
> -Need a way to mark a service as deprecated...I've come across loads
> of operations (not service) which are still in the wsdl file but no
> more used.
> -Can we collapse the example field, some example are very long.
>
> Franck
>
>   


From noreply at rubyforge.org  Fri Feb  5 05:51:42 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 05:51:42 -0500 (EST)
Subject: [BioCatalogue-developers] [1472] branches/integration-jan10: REST
	API work:
Message-ID: <20100205105142.6EB9118582C9@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  5 05:58:05 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 05:58:05 -0500 (EST)
Subject: [BioCatalogue-developers] [1473]
 branches/integration-jan10/lib/bio_catalogue/util.rb: REST API work:
 renamed 'wsdl_url' to 'wsdl_location' (for /lookup)
Message-ID: <20100205105805.8DFA11858289@rubyforge.org>

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From ytanoh at cs.man.ac.uk  Fri Feb  5 06:36:42 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Fri, 5 Feb 2010 11:36:42 +0000
Subject: [BioCatalogue-developers] Some annotation issues....
In-Reply-To: <4B6BF625.7090204@cs.man.ac.uk>
References: <d0ee827d1002040851ief2ce36oc73976b7220478a6@mail.gmail.com>
	<4B6BF625.7090204@cs.man.ac.uk>
Message-ID: <d0ee827d1002050336x2d20b24bt397c3fae59d8d811@mail.gmail.com>

Hi,
I'll add it to the list but so far our policy has been to show the
provider description first then the curators then members.  what i
think will be extremely useful is the possibility if necessary for the
curator to swap the order.

Franck

On 5 February 2010 10:42, Jiten Bhagat <jits at cs.man.ac.uk> wrote:
> Can we add something else to this list pleae:
>
> We need to discuss the notion of "preferred annotations", ie: when
> showing a simple listing, or needing to show just one "description" etc,
> what do we choose, and what's the priority order? The one from the WSDL
> first? Or one from an expert curator??
>
> One to discuss further!
>
> Cheers,
> Jits
>
>
> Franck Tanoh wrote:
>> Hi guys,
>> I've come across these issues which make the annotation of service in
>> the catalogue not a pleasant journey :-(
>> -Operations pages takes too long to load (even a service with 4 operation)
>> -Need to revisit the operation page UI, it's now impossible to have an
>> overview of that page, too much 'scrolling' to find descriptions
>> etc... I have some ideas we can discuss
>> -Can we make sure any external links within the site open in a new tab
>> or window? Otherwise it's difficult to get back to where you where
>> before accessing that external page. I can list these if necessary.
>> -Need a way to mark a service as deprecated...I've come across loads
>> of operations (not service) which are still in the wsdl file but no
>> more used.
>> -Can we collapse the example field, some example are very long.
>>
>> 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  Fri Feb  5 06:41:25 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 05 Feb 2010 11:41:25 +0000
Subject: [BioCatalogue-developers] Some annotation issues....
In-Reply-To: <d0ee827d1002050336x2d20b24bt397c3fae59d8d811@mail.gmail.com>
References: <d0ee827d1002040851ief2ce36oc73976b7220478a6@mail.gmail.com>	
	<4B6BF625.7090204@cs.man.ac.uk>
	<d0ee827d1002050336x2d20b24bt397c3fae59d8d811@mail.gmail.com>
Message-ID: <4B6C03E5.6080105@cs.man.ac.uk>

My point is not so much about the ordering of *multiple* annotations
(thought that's also another important point), but when a *single*,
*preferred* description etc is required to be shown.

Jits


Franck Tanoh wrote:
> Hi,
> I'll add it to the list but so far our policy has been to show the
> provider description first then the curators then members.  what i
> think will be extremely useful is the possibility if necessary for the
> curator to swap the order.
>
> Franck
>
> On 5 February 2010 10:42, Jiten Bhagat <jits at cs.man.ac.uk> wrote:
>   
>> Can we add something else to this list pleae:
>>
>> We need to discuss the notion of "preferred annotations", ie: when
>> showing a simple listing, or needing to show just one "description" etc,
>> what do we choose, and what's the priority order? The one from the WSDL
>> first? Or one from an expert curator??
>>
>> One to discuss further!
>>
>> Cheers,
>> Jits
>>
>>
>> Franck Tanoh wrote:
>>     
>>> Hi guys,
>>> I've come across these issues which make the annotation of service in
>>> the catalogue not a pleasant journey :-(
>>> -Operations pages takes too long to load (even a service with 4 operation)
>>> -Need to revisit the operation page UI, it's now impossible to have an
>>> overview of that page, too much 'scrolling' to find descriptions
>>> etc... I have some ideas we can discuss
>>> -Can we make sure any external links within the site open in a new tab
>>> or window? Otherwise it's difficult to get back to where you where
>>> before accessing that external page. I can list these if necessary.
>>> -Need a way to mark a service as deprecated...I've come across loads
>>> of operations (not service) which are still in the wsdl file but no
>>> more used.
>>> -Can we collapse the example field, some example are very long.
>>>
>>> Franck
>>>
>>>
>>>       
>>     
>
>
>
>   


From noreply at rubyforge.org  Fri Feb  5 07:05:42 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 07:05:42 -0500 (EST)
Subject: [BioCatalogue-developers] [1474] branches/integration-jan10: REST
 API work: initial implementation of /soap_services/{id}
Message-ID: <20100205120542.75D9E1588062@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  5 07:20:26 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 07:20:26 -0500 (EST)
Subject: [BioCatalogue-developers] [1475] branches/integration-jan10: REST
 API work: renamed <submitter> to < originalSubmitter> in <service>
Message-ID: <20100205122026.811C6185828D@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  5 07:30:38 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 07:30:38 -0500 (EST)
Subject: [BioCatalogue-developers] [1476] branches/integration-jan10: REST
 API work: <version> is no longer an actual resource.
Message-ID: <20100205123038.7BD2F18582CA@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  5 10:42:41 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 10:42:41 -0500 (EST)
Subject: [BioCatalogue-developers] [1477] branches/integration-jan10: REST
 API work: major refactorings in the way the individual resource,
 results items etc are generated.
Message-ID: <20100205154241.C35671588062@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  5 11:00:34 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 11:00:34 -0500 (EST)
Subject: [BioCatalogue-developers] [1478]
 branches/integration-jan10/app/views/search/show.xml.builder: REST API
 work: slowly moving all search results to using the result_item partial
 mechanism (this time it was ServiceProviders).
Message-ID: <20100205160034.CA6561588033@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  5 11:07:18 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 11:07:18 -0500 (EST)
Subject: [BioCatalogue-developers] [1479] branches/integration-jan10: REST
 API work: using display_name was causing text to be double escaped ( since
 xml builders also escape).
Message-ID: <20100205160718.D2B3B1588033@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  5 11:58:48 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 11:58:48 -0500 (EST)
Subject: [BioCatalogue-developers] [1480] branches/integration-jan10: REST
	API work:
Message-ID: <20100205165848.75B6C18582CA@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  5 12:08:10 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 12:08:10 -0500 (EST)
Subject: [BioCatalogue-developers] [1481]
 branches/integration-jan10/public/2009/xml/rest/schema-v1.xsd: REST API
 work: updated the XSD - for all individual (ie: member) resources ,
 the <related> section is now optional in the schema.
Message-ID: <20100205170810.CFF3618582D6@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  5 12:17:55 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 12:17:55 -0500 (EST)
Subject: [BioCatalogue-developers] [1482] branches/integration-jan10: REST
 API work: fixes for the / categories and /categories/{id} endpoints.
Message-ID: <20100205171755.468E218582D7@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  5 12:32:12 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 12:32:12 -0500 (EST)
Subject: [BioCatalogue-developers] [1483] branches/integration-jan10: REST
 API work: more work on the categories API - added <totalItemsCount> as well
 as added a _core_elements partial.
Message-ID: <20100205173213.11E8718582D0@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  5 12:40:42 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 12:40:42 -0500 (EST)
Subject: [BioCatalogue-developers] [1484]
 branches/integration-jan10/app/views/tags: REST API work: /tags and
 /tags/{name} endpoints now follow the new partial structure.
Message-ID: <20100205174042.8EB9318582D7@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb  5 13:09:01 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri,  5 Feb 2010 13:09:01 -0500 (EST)
Subject: [BioCatalogue-developers] [1485] branches/integration-jan10: REST
 API work: added more fields to the <soapService> and <restService>
 resources.
Message-ID: <20100205180901.CBD6C185828D@rubyforge.org>

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From noreply at rubyforge.org  Sat Feb  6 08:22:42 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat,  6 Feb 2010 08:22:42 -0500 (EST)
Subject: [BioCatalogue-developers] [1486] branches/integration-jan10: REST
 API work: implemented / service_deployment/{id}.
Message-ID: <20100206132243.6DAF018582E4@rubyforge.org>

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From noreply at rubyforge.org  Sat Feb  6 08:33:14 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat,  6 Feb 2010 08:33:14 -0500 (EST)
Subject: [BioCatalogue-developers] [1487] branches/integration-jan10: REST
 API work: updated XSD for / service_deployments/{id} and some minor fixes.
Message-ID: <20100206133314.5A66518582DC@rubyforge.org>

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From noreply at rubyforge.org  Mon Feb  8 05:23:29 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon,  8 Feb 2010 05:23:29 -0500 (EST)
Subject: [BioCatalogue-developers] [1488]
 branches/integration-jan10/app/models: updated parser to allow for template
 parameters as well
Message-ID: <20100208102329.384731588074@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Mon Feb  8 07:08:46 2010
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 08 Feb 2010 12:08:46 +0000
Subject: [BioCatalogue-developers] Embrace Import
Message-ID: <4B6FFECE.7010004@ebi.ac.uk>

Hi Guys,

I have run the EMBRACE import locally there still is a considerable 
number of import failures(178 services).  These are mostly coming from 
the same provider, INB and they are mostly pointers or wrappers for 
Biomoby services. I have looked at the wsdls and it seems to me that 
they do no follow regular convention. Some do even validate as xml so 
they will fail as a consequence and others do not seem to follow wsdl 
convention.  I would like Franck to confirm or not confirm these 
observations. Additionally, I am not sure what action to take on these 
right now. It could be to write a custom parser for them. In any case we 
need to find a solution for these failures that that means the embrace 
import will not be complete and that has some huge implications.

Eric

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From jits at cs.man.ac.uk  Mon Feb  8 07:21:28 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 08 Feb 2010 12:21:28 +0000
Subject: [BioCatalogue-developers] service execution framework
In-Reply-To: <4B6FE3EF.7070702@ebi.ac.uk>
References: <4B6FE3EF.7070702@ebi.ac.uk>
Message-ID: <4B7001C8.4070509@cs.man.ac.uk>

Hi Eric,

The library I mentioned is: Savon - http://github.com/rubiii/savon

Note: I am on leave today and tomorrow.

Before you get on to service execution, please can you ensure all work
is finished for the test scripts and monitoring stuff. This includes a
decent enough UI that I can then tweak.

Also, look through the tasks list to see if there are any smallish tasks
that can be done for the next release. We want to be able to do the
small as well as the big things.

Cheers,
Jits



Eric Nzuobontane wrote:
> Hi Jits,
>
> Could you please send me some pointers on the service execution
> framework you mentioned in the last meeting?
>
> cheers,
>
> Eric
>


From jits at cs.man.ac.uk  Mon Feb  8 07:23:56 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 08 Feb 2010 12:23:56 +0000
Subject: [BioCatalogue-developers] Embrace Import
In-Reply-To: <4B6FFECE.7010004@ebi.ac.uk>
References: <4B6FFECE.7010004@ebi.ac.uk>
Message-ID: <4B70025C.1090304@cs.man.ac.uk>

Eric,

The last couple of errors are to do with REST Service submission.

When I'm back on Wednesday please can you remind me to look into this.
It might be a bug in my EMBRACE import script.

Cheers,
Jits


Eric Nzuobontane wrote:
> Hi Guys,
>
> I have run the EMBRACE import locally there still is a considerable
> number of import failures(178 services).  These are mostly coming from
> the same provider, INB and they are mostly pointers or wrappers for
> Biomoby services. I have looked at the wsdls and it seems to me that
> they do no follow regular convention. Some do even validate as xml so
> they will fail as a consequence and others do not seem to follow wsdl
> convention.  I would like Franck to confirm or not confirm these
> observations. Additionally, I am not sure what action to take on these
> right now. It could be to write a custom parser for them. In any case
> we need to find a solution for these failures that that means the
> embrace import will not be complete and that has some huge implications.
>
> Eric
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From ericnzuo at ebi.ac.uk  Mon Feb  8 07:34:10 2010
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 08 Feb 2010 12:34:10 +0000
Subject: [BioCatalogue-developers] service execution framework
In-Reply-To: <4B7001C8.4070509@cs.man.ac.uk>
References: <4B6FE3EF.7070702@ebi.ac.uk> <4B7001C8.4070509@cs.man.ac.uk>
Message-ID: <4B7004C2.2000400@ebi.ac.uk>

Hi Jits,

This was more to satisfy my curiosity rather than getting to actually 
work with it. I believe the priority should be getting all the embrace 
data and functionality into BioCatalogue and I do not think right now is 
the time to embark of new functionality.

I sent a mails earlier about issues with the embrace import. I am trying 
to make a few checks and to see of there are any quick fixes for this as 
this is a one-off import.

Eric


Jiten Bhagat wrote:
> Hi Eric,
>
> The library I mentioned is: Savon - http://github.com/rubiii/savon
>
> Note: I am on leave today and tomorrow.
>
> Before you get on to service execution, please can you ensure all work
> is finished for the test scripts and monitoring stuff. This includes a
> decent enough UI that I can then tweak.
>
> Also, look through the tasks list to see if there are any smallish tasks
> that can be done for the next release. We want to be able to do the
> small as well as the big things.
>
> Cheers,
> Jits
>
>
>
> Eric Nzuobontane wrote:
>   
>> Hi Jits,
>>
>> Could you please send me some pointers on the service execution
>> framework you mentioned in the last meeting?
>>
>> cheers,
>>
>> Eric
>>
>>     


From ytanoh at cs.man.ac.uk  Mon Feb  8 07:47:29 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Mon, 8 Feb 2010 12:47:29 +0000
Subject: [BioCatalogue-developers] Embrace Import
In-Reply-To: <4B6FFECE.7010004@ebi.ac.uk>
References: <4B6FFECE.7010004@ebi.ac.uk>
Message-ID: <d0ee827d1002080447t328cdc39pb2deefacdec499cb@mail.gmail.com>

Hi Eric,
they are all biomoby services not only from INB but aslo from MMB, UAM etc.
Some of these services can be found on the BioMoby wsdl list
(http://biomoby.org/cgi-bin/serviceList) with a different WSDL.
e.g:
<< http://biomoby.org/services/wsdl/mmb.pcb.ub.es/show3DFeature  (wsdl list)
                         vs
http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/show3DFeature
(embrace)


http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastn (Embrace)
                    vs
http://biomoby.org/services/wsdl/moby.ucalgary.ca/runNCBIBlastn (wsdl list) >>

Strangely the versions found on the list can be registered in the biocat.

How did embrace get them to work? did they write specific parsers ? I
think we need to get the answers from the Embrace team before we
decide what to do.

Franck





On 8 February 2010 12:08, Eric Nzuobontane <ericnzuo at ebi.ac.uk> wrote:
> Hi Guys,
>
> I have run the EMBRACE import locally there still is a considerable number
> of import failures(178 services). ?These are mostly coming from the same
> provider, INB and they are mostly pointers or wrappers for Biomoby services.
> I have looked at the wsdls and it seems to me that they do no follow regular
> convention. Some do even validate as xml so they will fail as a consequence
> and others do not seem to follow wsdl convention. ?I would like Franck to
> confirm or not confirm these observations. Additionally, I am not sure what
> action to take on these right now. It could be to write a custom parser for
> them. In any case we need to find a solution for these failures that that
> means the embrace import will not be complete and that has some huge
> implications.
>
> Eric
>
>
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastn'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastn'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/runEmbossTFscan_GFF_FromFasta'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/runEmbossTFscan_GFF_FromFasta'.
> Exception message: Fatal error: Extra content at the end of the document at
> :1...
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastp'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastp'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/runProStar_GFF_FromFasta'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/runProStar_GFF_FromFasta'.
> Exception message: Fatal error: Extra content at the end of the document at
> :1...
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/runSimpleTfbs'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/runSimpleTfbs'.
> Exception message: Fatal error: Extra content at the end of the document at
> :1...
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/showPDBFromFasta'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/showPDBFromFasta'.
> Exception message: Fatal error: Extra content at the end of the document at
> :1...
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/show3DFeature'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/show3DFeature'.
> Exception message: Fatal error: Extra content at the end of the document at
> :1...
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUTBlastx_2Seqs'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUTBlastx_2Seqs'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastp_2Seqs'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastp_2Seqs'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runBrownianMDFromPDBText'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runBrownianMDFromPDBText'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/getAnatComponentsFromGene'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/getAnatComponentsFromGene'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/runBindProteins'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/runBindProteins'.
> Exception message: Fatal error: Extra content at the end of the document at
> :1...
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runNormalModeAnalysisFromPDBText'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runNormalModeAnalysisFromPDBText'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/getGenesFromAnatComponent'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/getGenesFromAnatComponent'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/runEmbossCpGreport_GFF_FromFasta'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/runEmbossCpGreport_GFF_FromFasta'.
> Exception message: Fatal error: Extra content at the end of the document at
> :1...
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runDiscreteMDFromPDBText'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runDiscreteMDFromPDBText'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/getExpressionStatisticsFromGenes'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/getExpressionStatisticsFromGenes'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/getExpressionStatisticsFromStructures'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/getExpressionStatisticsFromStructures'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/parseExpressionStatistics'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/parseExpressionStatistics'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/parseExpressedGenes'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/parseExpressedGenes'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/parseAnatomicalStructures'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/parseAnatomicalStructures'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/parseExpressionLevel'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/parseExpressionLevel'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/parseExpressionPattern'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/parseExpressionPattern'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/runNonlinearPhysicalProperties'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/runNonlinearPhysicalProperties'.
> Exception message: Fatal error: Extra content at the end of the document at
> :1...
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/fromMGIToEMBL'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/fromMGIToEMBL'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBITBlastn_2Seqs'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBITBlastn_2Seqs'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/fromNucleotideCollectionToCleanNucleotideCollection'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/fromNucleotideCollectionToCleanNucleotideCollection'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/fromNucleotideSimplesToCleanNucleotideSimples'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/fromNucleotideSimplesToCleanNucleotideSimples'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/fromNucleotideSequenceCollectionToFASTA'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/www.cnb.uam.es/fromNucleotideSequenceCollectionToFASTA'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/optimizeStructureFromNAMD_Structure'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/mmb.pcb.ub.es/optimizeStructureFromNAMD_Structure'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastx_2Seqs'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastx_2Seqs'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUBlastx_2Seqs'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUBlastx_2Seqs'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runMDFromMD_TrajectoryXTC'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runMDFromMD_TrajectoryXTC'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/getNAMD_ConfFromNAMD_MD_Structure'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/getNAMD_ConfFromNAMD_MD_Structure'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runMDFromNAMD_MD_Structure'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runMDFromNAMD_MD_Structure'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runMDFromMD_TrajectoryDCD'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runMDFromMD_TrajectoryDCD'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runMDFromAMBER_MD_Structure'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runMDFromAMBER_MD_Structure'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runMDFromGROMACS_MD_Structure'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runMDFromGROMACS_MD_Structure'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSx3DEM?wsdl'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSx3DEM?wsdl'. Exception
> message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO?wsdl'. Error messages:
> Error occurred whilst processing the WSDL file. Error(s): There was a
> problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO?wsdl'. Exception
> message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSx3DEM_Reference?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSx3DEM_Reference?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSx3DEM_Fitting?wsdl'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSx3DEM_Fitting?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSx3DEM_EMDB?wsdl'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSx3DEM_EMDB?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_MGI_Reference?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_MGI_Reference?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/inb.bsc.es/runPSIBlastXML'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/inb.bsc.es/runPSIBlastXML'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_EMAP_Reference?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_EMAP_Reference?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_EMAGE_Features?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_EMAGE_Features?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastx'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastx'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_GXD_Features?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_GXD_Features?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBITBlastn'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBITBlastn'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_GENSAT_Features?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_GENSAT_Features?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_OMIM_Features?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_OMIM_Features?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/inb.bsc.es/runByoDyn'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/inb.bsc.es/runByoDyn'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_Symatlas_Features?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_Symatlas_Features?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/inb.bsc.es/runByoDynOED'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/inb.bsc.es/runByoDynOED'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_KEGG_Features?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_KEGG_Features?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/inb.bsc.es/runPrepareLigand'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/inb.bsc.es/runPrepareLigand'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_MTB_Features?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_MTB_Features?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_BAMS_Features?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://biocomp.cnb.csic.es:8092/axis2/services/WSxVO_BAMS_Features?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/optimizeStructureFromGROMACS_MD_Structure'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/optimizeStructureFromGROMACS_MD_Structure'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/optimizeStructureFromAMBER_MD_Structure'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/optimizeStructureFromAMBER_MD_Structure'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/optimizeStructureFromNAMD_MD_Structure'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/optimizeStructureFromNAMD_MD_Structure'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/solvateStructureFromNAMD_MD_Structure'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/solvateStructureFromNAMD_MD_Structure'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/solvateStructureFromAMBER_MD_Structure'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/solvateStructureFromAMBER_MD_Structure'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/solvateStructureWithLigandsFromAMBER_MD_Structure'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/solvateStructureWithLigandsFromAMBER_MD_Structure'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/solvateStructureWithLigandsFromPDBText'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/solvateStructureWithLigandsFromPDBText'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/cnio.es/sayHello'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/cnio.es/sayHello'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/solvateStructureFromGROMACS_MD_Structure'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/solvateStructureFromGROMACS_MD_Structure'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runLeapFromAMBER_MD_Structure'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/mmb.pcb.ub.es/runLeapFromAMBER_MD_Structure'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/cnio.es/runMBFromMSF'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/cnio.es/runMBFromMSF'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://api.bioinfo.no/wsdl/JasparDB.wsdl'. Error messages: Error occurred
> whilst processing the WSDL file. Error(s): There was a problem loading the
> WSDL file 'http://api.bioinfo.no/wsdl/JasparDB.wsdl'. Exception message:
> time's up!..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://api.bioinfo.no/wsdl/ELMdb.wsdl'. Error messages: Error occurred
> whilst processing the WSDL file. Error(s): There was a problem loading the
> WSDL file 'http://api.bioinfo.no/wsdl/ELMdb.wsdl'. Exception message: time's
> up!..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/cnio.es/runPrank'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/cnio.es/runPrank'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/cnio.es/runSLR'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/cnio.es/runSLR'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/cnio.es/runCExonic'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/cnio.es/runCExonic'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/cnio.es/runFirestar'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/cnio.es/runFirestar'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.cbs.dtu.dk/ws/NetCTL/NetCTL_1_2_ws0.wsdl'. Error messages: Error
> occurred whilst processing the WSDL file. Error(s): There was a problem
> parsing the WSDL file 'http://www.cbs.dtu.dk/ws/NetCTL/NetCTL_1_2_ws0.wsdl'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.cbs.dtu.dk/ws/NetChop/NetChop_3_1_ws0.wsdl'. Error messages:
> Error occurred whilst processing the WSDL file. Error(s): There was a
> problem parsing the WSDL file
> 'http://www.cbs.dtu.dk/ws/NetChop/NetChop_3_1_ws0.wsdl'. Exception message:
> undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.cbs.dtu.dk/ws/NetPhos/NetPhos_3_1b_ws0.wsdl'. Error messages:
> Error occurred whilst processing the WSDL file. Error(s): There was a
> problem parsing the WSDL file
> 'http://www.cbs.dtu.dk/ws/NetPhos/NetPhos_3_1b_ws0.wsdl'. Exception message:
> undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.cbs.dtu.dk/ws/NetOGlyc/NetOGlyc_3_1d_ws0.wsdl'. Error messages:
> Error occurred whilst processing the WSDL file. Error(s): There was a
> problem parsing the WSDL file
> 'http://www.cbs.dtu.dk/ws/NetOGlyc/NetOGlyc_3_1d_ws0.wsdl'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.cbs.dtu.dk/ws/NetGlycate/NetGlycate_1_0_ws0.wsdl'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.cbs.dtu.dk/ws/NetGlycate/NetGlycate_1_0_ws0.wsdl'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://sirisser.bccs.uib.no:8080/axis2/services/WorkflowDirectoryService2?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://sirisser.bccs.uib.no:8080/axis2/services/WorkflowDirectoryService2?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://sirisser.bccs.uib.no:8080/axis2/services/ProvenanceServicePT3?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://sirisser.bccs.uib.no:8080/axis2/services/ProvenanceServicePT3?wsdl'.
> Exception message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://mips.gsf.de/CronosWSService/CronosWS?wsdl'. Error messages: Error
> occurred whilst processing the WSDL file. Error(s): There was a problem
> parsing the WSDL file 'http://mips.gsf.de/CronosWSService/CronosWS?wsdl'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://utopia.cs.man.ac.uk/wsdl/prints.wsdl'. Error messages: Error
> occurred whilst processing the WSDL file. Error(s): There was a problem
> loading the WSDL file 'http://utopia.cs.man.ac.uk/wsdl/prints.wsdl'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_2a_ws0.wsdl'. Error messages:
> Error occurred whilst processing the WSDL file. Error(s): There was a
> problem parsing the WSDL file
> 'http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_2a_ws0.wsdl'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastn_2Seqs'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastn_2Seqs'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.cbs.dtu.dk/ws/TMHMM/TMHMM_2_0b.wsdl'. Error messages: Error
> occurred whilst processing the WSDL file. Error(s): There was a problem
> parsing the WSDL file 'http://www.cbs.dtu.dk/ws/TMHMM/TMHMM_2_0b.wsdl'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://fw.sbc.su.se/wsdl/proq.wsdl'. Error messages: Error occurred whilst
> processing the WSDL file. Error(s): There was a problem loading the WSDL
> file 'http://fw.sbc.su.se/wsdl/proq.wsdl'. Exception message: getaddrinfo:
> nodename nor servname provided, or not known..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/fromGenericSequenceToFasta'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/fromGenericSequenceToFasta'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBITBlastx_2Seqs'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBITBlastx_2Seqs'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/fromFastaToGenericSequence'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/fromFastaToGenericSequence'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://fw.sbc.su.se/wsdl/pfrag.wsdl'. Error messages: Error occurred whilst
> processing the WSDL file. Error(s): There was a problem loading the WSDL
> file 'http://fw.sbc.su.se/wsdl/pfrag.wsdl'. Exception message: getaddrinfo:
> nodename nor servname provided, or not known..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUTBlastn_2Seqs'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUTBlastn_2Seqs'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://genome.imim.es/webservices/WSDLs/runGeneIDGFF.wsdl'. Error messages:
> Error occurred whilst processing the WSDL file. Error(s): There was a
> problem parsing the WSDL file
> 'http://genome.imim.es/webservices/WSDLs/runGeneIDGFF.wsdl'. Exception
> message: undefined method `[]' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://fw.sbc.su.se/wsdl/shrimp.wsdl'. Error messages: Error occurred
> whilst processing the WSDL file. Error(s): There was a problem loading the
> WSDL file 'http://fw.sbc.su.se/wsdl/shrimp.wsdl'. Exception message:
> getaddrinfo: nodename nor servname provided, or not known..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.cbs.dtu.dk/ws/MaxAlign/MaxAlign_1_1_ws0.wsdl'. Error messages:
> Error occurred whilst processing the WSDL file. Error(s): There was a
> problem parsing the WSDL file
> 'http://www.cbs.dtu.dk/ws/MaxAlign/MaxAlign_1_1_ws0.wsdl'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUBlastp_2Seqs'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUBlastp_2Seqs'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://spank.ba.itb.cnr.it:8080/soaplab2/typed/services/itba.cluster1out?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://spank.ba.itb.cnr.it:8080/soaplab2/typed/services/itba.cluster1out?wsdl'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUBlastn_2Seqs'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUBlastn_2Seqs'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.cbs.dtu.dk/ws/GenomeAtlas/GenomeAtlas_3_0_ws1.wsdl'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.cbs.dtu.dk/ws/GenomeAtlas/GenomeAtlas_3_0_ws1.wsdl'. Exception
> message: undefined method `compact' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBITBlastx'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBITBlastx'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runBlat'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runBlat'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runClustalwFast'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runClustalwFast'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runClustalwFull'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runClustalwFull'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/optimizeStructureFromNAMD_Structure'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/optimizeStructureFromNAMD_Structure'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://api-v3-1.cathdb.info/static/wsdl/DataServices.wsdl'. Error messages:
> Error occurred whilst processing the WSDL file. Error(s): There was a
> problem loading the WSDL file
> 'http://api-v3-1.cathdb.info/static/wsdl/DataServices.wsdl'. Exception
> message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/bioinfo.cipf.es/displayDifferentialExpressionTest'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/bioinfo.cipf.es/displayDifferentialExpressionTest'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/bioinfo.cipf.es/displayFatiGO'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/bioinfo.cipf.es/displayFatiGO'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/bioinfo.cipf.es/displayFatiScan'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/bioinfo.cipf.es/displayFatiScan'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/bioinfo.cipf.es/buildPredictionModel'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/bioinfo.cipf.es/buildPredictionModel'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/bioinfo.cipf.es/runPrediction'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/bioinfo.cipf.es/runPrediction'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/bioinfo.cipf.es/getPlotFromPredictionModel'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/bioinfo.cipf.es/getPlotFromPredictionModel'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/bioinfo.cipf.es/getModelFromPredictionModel'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/bioinfo.cipf.es/getModelFromPredictionModel'.
> Exception message: 404 Not Found..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://rguha.ath.cx:8080/cdkws/services/Druglikeness?wsdl'. Error messages:
> Error occurred whilst processing the WSDL file. Error(s): There was a
> problem loading the WSDL file
> 'http://rguha.ath.cx:8080/cdkws/services/Druglikeness?wsdl'. Exception
> message: time's up!..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://gf1.ucs.indiana.edu:7880/axis/services/InChIGoogle?wsdl'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem loading the WSDL file
> 'http://gf1.ucs.indiana.edu:7880/axis/services/InChIGoogle?wsdl'. Exception
> message: Connection refused - connect(2)..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runFastaForAminoAcids'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runFastaForAminoAcids'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://rguha.ath.cx:8080/cdkws/services/Descriptors?wsdl'. Error messages:
> Error occurred whilst processing the WSDL file. Error(s): There was a
> problem loading the WSDL file
> 'http://rguha.ath.cx:8080/cdkws/services/Descriptors?wsdl'. Exception
> message: time's up!..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runFastaForNucleotides'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runFastaForNucleotides'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://rguha.ath.cx:8080/cdkws/services/Similarity?wsdl'. Error messages:
> Error occurred whilst processing the WSDL file. Error(s): There was a
> problem loading the WSDL file
> 'http://rguha.ath.cx:8080/cdkws/services/Similarity?wsdl'. Exception
> message: time's up!..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runFastx'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runFastx'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runFasty'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runFasty'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runHMMPfam'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runHMMPfam'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runHMMSearchAgainstDB'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runHMMSearchAgainstDB'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runHMMSearchAgainstSeqs'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runHMMSearchAgainstSeqs'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runNCut'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runNCut'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runISS'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runISS'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runMuscleFromSequences'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runMuscleFromSequences'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runFunCUT'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runFunCUT'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastAgainstDB'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastAgainstDB'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastnXML'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastnXML'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://kamet.ucs.indiana.edu:7680/axis/services/OSCAR3URLServer?wsdl'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem loading the WSDL file
> 'http://kamet.ucs.indiana.edu:7680/axis/services/OSCAR3URLServer?wsdl'.
> Exception message: time's up!..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastpXML'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastpXML'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastxXML'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIBlastxXML'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIFormatdb'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBIFormatdb'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runISSComplete'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runISSComplete'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBITBlastnXML'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBITBlastnXML'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runFASSFromMSF'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runFASSFromMSF'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBITBlastxXML'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runNCBITBlastxXML'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runFASSFromClustalw'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runFASSFromClustalw'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipDnadist'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipDnadist'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipDnaml'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipDnaml'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runFASS'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runFASS'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runMB'. Error messages:
> Error occurred whilst processing the WSDL file. Error(s): There was a
> problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runMB'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipDnamlk'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipDnamlk'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runSM'. Error messages:
> Error occurred whilst processing the WSDL file. Error(s): There was a
> problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runSM'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipDnapars'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipDnapars'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runSQUARE'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/cnio.es/runSQUARE'. Exception
> message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipDnapenny'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipDnapenny'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipFitch'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipFitch'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipKitsch'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipKitsch'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipNeighbor'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipNeighbor'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipProtdist'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipProtdist'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipProtpars'.
> Error messages: Error occurred whilst processing the WSDL file. Error(s):
> There was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runPhylipProtpars'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runTFastx'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runTFastx'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runTFasty'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runTFasty'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUBlastn'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUBlastn'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUBlastp'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUBlastp'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUBlastx'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUBlastx'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUTBlastn'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUTBlastn'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUTBlastx'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB/inb.bsc.es/runWUTBlastx'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to populate SoapService object from WSDL URL
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/cnio.es/runS3det'. Error
> messages: Error occurred whilst processing the WSDL file. Error(s): There
> was a problem parsing the WSDL file
> 'http://www.inab.org/cgi-bin/getMOBYWSDL/INB-dev/cnio.es/runS3det'.
> Exception message: undefined method `each' for nil:NilClass..
> ERROR: creation/updation of this service failed!
> ERROR: failed to carry out submit_service of RestService object with
> endpoint URL '' (ie: db has not been populated with the RestService and
> associated objects). Check the relevant Rails log file for more info.
> ERROR: creation/updation of this service failed!
> ERROR: failed to carry out submit_service of RestService object with
> endpoint URL '' (ie: db has not been populated with the RestService and
> associated objects). Check the relevant Rails log file for more info.
> ERROR: creation/updation of this service failed!
> Total annotations failed to create = 0
> Total annotations failed to update = 0
> Total services failed to create = 178
>
> _______________________________________________
> BioCatalogue-developers mailing list
> 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 Feb  9 07:04:49 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  9 Feb 2010 07:04:49 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2912] Test Status Activity Events
Message-ID: <20100209120449.F11D13C8046@rubyforge.org>

Task #2912 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Test Status Activity Events
Complete: 0%
Status: Open

Description: Create an event when there is a change of status of a test. This can be used in the activity updates box to indicate service monitoring changes

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2912&group_id=6901&group_project_id=12540

From ytanoh at cs.man.ac.uk  Tue Feb  9 07:45:17 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Tue, 9 Feb 2010 12:45:17 +0000
Subject: [BioCatalogue-developers] roadmap 2010
Message-ID: <d0ee827d1002090445x6f8ca1e9we22f84ec0a9f732a@mail.gmail.com>

Hi guys,

I've made a new roadmap for 2010 :
http://www.biocatalogue.org/wiki/doku.php?id=public_staging:roadmap
please comment and edit before i post it on the main list

Franck

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

From jerzyo at genesilico.pl  Tue Feb  9 10:54:27 2010
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Tue, 09 Feb 2010 16:54:27 +0100
Subject: [BioCatalogue-developers] roadmap 2010
In-Reply-To: <d0ee827d1002090445x6f8ca1e9we22f84ec0a9f732a@mail.gmail.com>
References: <d0ee827d1002090445x6f8ca1e9we22f84ec0a9f732a@mail.gmail.com>
Message-ID: <4B718533.8030708@genesilico.pl>

In myexperiment part I would add linking to (or displaying parts of) 
workflows from MyExperiment that contain a service/operation in BioCatalogue

George

Franck Tanoh wrote:
> Hi guys,
>
> I've made a new roadmap for 2010 :
> http://www.biocatalogue.org/wiki/doku.php?id=public_staging:roadmap
> please comment and edit before i post it on the main list
>
> Franck
>
>   


From noreply at rubyforge.org  Wed Feb 10 04:43:31 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 04:43:31 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2913] Help text about cookies
	required for logging in
Message-ID: <20100210094334.8083218582DF@rubyforge.org>

Task #2913 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Help text about cookies required for logging in
Complete: 0%
Status: Open

Description: Via Pieter Neerincx:

I was trying yesterday from a machine, which had cookies disabled. I know many sites which require a login also require session cookies, so I knew what to look for, but for those who are less familiar with the tech behind websites it would be nice if BioCatalogue will show a warning that it cannot set a session cookie when you try to login...

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2913&group_id=6901&group_project_id=12540

From jits at cs.man.ac.uk  Wed Feb 10 04:58:38 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 10 Feb 2010 09:58:38 +0000
Subject: [BioCatalogue-developers] roadmap 2010
In-Reply-To: <d0ee827d1002090445x6f8ca1e9we22f84ec0a9f732a@mail.gmail.com>
References: <d0ee827d1002090445x6f8ca1e9we22f84ec0a9f732a@mail.gmail.com>
Message-ID: <4B72834E.8040600@cs.man.ac.uk>

Franck,

I've made some updates based on what I think are priorities.

I have also added George's thing.

Also, where has the previous stuff from 2008/2009 gone? Would be good to
have it at the bottom, or link to it on a different page as a way of
showing people what we've done so far.

Jits


Franck Tanoh wrote:
> Hi guys,
>
> I've made a new roadmap for 2010 :
> http://www.biocatalogue.org/wiki/doku.php?id=public_staging:roadmap
> please comment and edit before i post it on the main list
>
> Franck
>
>   


From jits at cs.man.ac.uk  Wed Feb 10 05:21:01 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 10 Feb 2010 10:21:01 +0000
Subject: [BioCatalogue-developers] roadmap 2010
In-Reply-To: <4B72834E.8040600@cs.man.ac.uk>
References: <d0ee827d1002090445x6f8ca1e9we22f84ec0a9f732a@mail.gmail.com>
	<4B72834E.8040600@cs.man.ac.uk>
Message-ID: <4B72888D.8000605@cs.man.ac.uk>

Franck,

Please could you also remind the list about my new wiki homepage design -
http://www.biocatalogue.org/wiki/doku.php?id=public_staging:homepage

I'd like to get this live soon as well.

Cheers,
Jits


Jiten Bhagat wrote:
> Franck,
>
> I've made some updates based on what I think are priorities.
>
> I have also added George's thing.
>
> Also, where has the previous stuff from 2008/2009 gone? Would be good to
> have it at the bottom, or link to it on a different page as a way of
> showing people what we've done so far.
>
> Jits
>
>
> Franck Tanoh wrote:
>   
>> Hi guys,
>>
>> I've made a new roadmap for 2010 :
>> http://www.biocatalogue.org/wiki/doku.php?id=public_staging:roadmap
>> please comment and edit before i post it on the main list
>>
>> Franck
>>
>>   
>>     
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From ytanoh at cs.man.ac.uk  Wed Feb 10 05:47:14 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 10 Feb 2010 10:47:14 +0000
Subject: [BioCatalogue-developers] roadmap 2010
In-Reply-To: <4B72834E.8040600@cs.man.ac.uk>
References: <d0ee827d1002090445x6f8ca1e9we22f84ec0a9f732a@mail.gmail.com>
	<4B72834E.8040600@cs.man.ac.uk>
Message-ID: <d0ee827d1002100247t45f97752v5969ed382f675d7b@mail.gmail.com>

Hi guys,

Jits - cheers for the updates

>I have also added George's thing.
Cool. Thanks George for pointing it out.

> Also, where has the previous stuff from 2008/2009 gone?
I've not touched the public site so they are still there.

>Would be good to have it at the bottom, or link to it on a different page as a way of
> showing people what we've done so far.
Good idea... will do once Carole and Rodrigo are ok with the new roadmap.

Eric, anything else to add or edit?

Franck


On 10 February 2010 09:58, Jiten Bhagat <jits at cs.man.ac.uk> wrote:
> Franck,
>
> I've made some updates based on what I think are priorities.
>
> I have also added George's thing.
>
> Also, where has the previous stuff from 2008/2009 gone? Would be good to
> have it at the bottom, or link to it on a different page as a way of
> showing people what we've done so far.
>
> Jits
>
>
> Franck Tanoh wrote:
>> Hi guys,
>>
>> I've made a new roadmap for 2010 :
>> http://www.biocatalogue.org/wiki/doku.php?id=public_staging:roadmap
>> please comment and edit before i post it on the main list
>>
>> Franck
>>
>>
>
>



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

From noreply at rubyforge.org  Wed Feb 10 06:35:24 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 06:35:24 -0500 (EST)
Subject: [BioCatalogue-developers] [1489]
 branches/integration-jan10/script/biocatalogue: REST API work: set up a
 test suite for testing the REST API.
Message-ID: <20100210113524.8E7A318582F1@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 06:35:51 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 06:35:51 -0500 (EST)
Subject: [BioCatalogue-developers] [1490]
 branches/integration-jan10/script/biocatalogue/api/run_tests.rb: Removed
 irrelevant comment.
Message-ID: <20100210113551.2D52C18582F1@rubyforge.org>

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From ytanoh at cs.man.ac.uk  Wed Feb 10 07:06:37 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 10 Feb 2010 12:06:37 +0000
Subject: [BioCatalogue-developers] screen scraping
Message-ID: <d0ee827d1002100406h6b285202j405a26f6987db6de@mail.gmail.com>

Hi guys,

I'm writing some Perl scripts to extract web service info from web
page such as http://xml.ddbj.nig.ac.jp/index.html,
http://www.ebi.ac.uk/Tools/webservices/,
http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchlit_help.html
etc. and send it to the corresponding service in biocat. Extracting
the info looks straight forward so far but how to populate the biocat
with the info? I think i can use the same process as you guys did for
Feta...

Please help!

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

From noreply at rubyforge.org  Wed Feb 10 07:16:13 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 07:16:13 -0500 (EST)
Subject: [BioCatalogue-developers] [1491] branches/integration-jan10: REST
	API work:
Message-ID: <20100210121613.F408918582EF@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 07:53:35 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 07:53:35 -0500 (EST)
Subject: [BioCatalogue-developers] [1492]
 branches/integration-jan10/script/biocatalogue/api/tests: REST API work:
 refactored the tests and moved configuration of these tests into a separate
 config file .
Message-ID: <20100210125335.F30BB18582F3@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 08:00:42 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 08:00:42 -0500 (EST)
Subject: [BioCatalogue-developers] [1493]
 branches/integration-jan10/script/biocatalogue/api/tests: REST API work:
 added tests for individual Service, SoapService and RestService resources.
Message-ID: <20100210130042.C973918582F5@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 08:04:43 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 08:04:43 -0500 (EST)
Subject: [BioCatalogue-developers] [1494]
 branches/integration-jan10/script/biocatalogue/api/tests/
 xml_schema_validations.rb: REST API work: added test for root.
Message-ID: <20100210130443.DEFA318582F7@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 08:11:59 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 08:11:59 -0500 (EST)
Subject: [BioCatalogue-developers] [1495]
 branches/integration-jan10/script/biocatalogue/api/tests/test_helper .rb:
 REST API work: fix for activity logs so that test calls are not logged!
Message-ID: <20100210131209.F2AC915B802B@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 08:47:15 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 08:47:15 -0500 (EST)
Subject: [BioCatalogue-developers] [1496]
 branches/integration-jan10/app/controllers: Disabled certain actions .
Message-ID: <20100210134715.DA4B218582E9@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 09:05:09 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 09:05:09 -0500 (EST)
Subject: [BioCatalogue-developers] [1497]
 branches/integration-jan10/app/controllers: Various fixes for request mime
 type handling and activity logging.
Message-ID: <20100210140509.7489615B8029@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 09:49:37 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 09:49:37 -0500 (EST)
Subject: [BioCatalogue-developers] [1498] branches/integration-jan10: REST
 API work: 'flattened' the <versions > section in /service/{id} to greatly
 simplify things.
Message-ID: <20100210144937.8917F15B8029@rubyforge.org>

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From jits at cs.man.ac.uk  Wed Feb 10 09:56:10 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 10 Feb 2010 14:56:10 +0000
Subject: [BioCatalogue-developers] screen scraping
In-Reply-To: <d0ee827d1002100406h6b285202j405a26f6987db6de@mail.gmail.com>
References: <d0ee827d1002100406h6b285202j405a26f6987db6de@mail.gmail.com>
Message-ID: <4B72C90A.2030304@cs.man.ac.uk>

Hi Franck,

There is no easy way right now for a Perl script to easily interact with
the BioCat application without some kind of write API.

For now maybe you can output to a CSV file following the annotations
data model and that way we can easily import these?

For Feta I wrote a custom import script that ran over some Feta XML
files and imported all possible data from these.

Cheers,
Jits


Franck Tanoh wrote:
> Hi guys,
>
> I'm writing some Perl scripts to extract web service info from web
> page such as http://xml.ddbj.nig.ac.jp/index.html,
> http://www.ebi.ac.uk/Tools/webservices/,
> http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchlit_help.html
> etc. and send it to the corresponding service in biocat. Extracting
> the info looks straight forward so far but how to populate the biocat
> with the info? I think i can use the same process as you guys did for
> Feta...
>
> Please help!
>
> Cheers,
> Franck
>   


From jerzyo at genesilico.pl  Wed Feb 10 10:03:29 2010
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Wed, 10 Feb 2010 16:03:29 +0100
Subject: [BioCatalogue-developers] screen scraping
In-Reply-To: <d0ee827d1002100406h6b285202j405a26f6987db6de@mail.gmail.com>
References: <d0ee827d1002100406h6b285202j405a26f6987db6de@mail.gmail.com>
Message-ID: <4B72CAC1.9040104@genesilico.pl>

For ddbj I would go down to examples and options like:
http://xml.ddbj.nig.ac.jp/wabi/Method?&lang=en&serviceName=Blast&methodName=searchSimple&mode=methodDetail
Because it makes users life much easier.

For EBI, you should be able to get the structurized data. I guess Eric 
na make an SQL script to make it all

For NCBI I suggest parsing parameters description and usage examples

George




Franck Tanoh wrote:
> Hi guys,
>
> I'm writing some Perl scripts to extract web service info from web
> page such as http://xml.ddbj.nig.ac.jp/index.html,
> http://www.ebi.ac.uk/Tools/webservices/,
> http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchlit_help.html
> etc. and send it to the corresponding service in biocat. Extracting
> the info looks straight forward so far but how to populate the biocat
> with the info? I think i can use the same process as you guys did for
> Feta...
>
> Please help!
>
> Cheers,
> Franck
>   


From noreply at rubyforge.org  Wed Feb 10 10:25:06 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 10:25:06 -0500 (EST)
Subject: [BioCatalogue-developers] [1499]
 branches/integration-jan10/script/biocatalogue/api/tests/
 xml_schema_validations.rb: REST API work: added more tests.
Message-ID: <20100210152506.3549F18582EC@rubyforge.org>

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From ytanoh at cs.man.ac.uk  Wed Feb 10 10:33:27 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 10 Feb 2010 15:33:27 +0000
Subject: [BioCatalogue-developers] screen scraping
In-Reply-To: <4B72C90A.2030304@cs.man.ac.uk>
References: <d0ee827d1002100406h6b285202j405a26f6987db6de@mail.gmail.com>
	<4B72C90A.2030304@cs.man.ac.uk>
Message-ID: <d0ee827d1002100733k7fb8024arf74135acbbb74c37@mail.gmail.com>

Hi Jits,

> For now maybe you can output to a CSV file following the annotations
> data model and that way we can easily import these?
I can give it a go. Can you point me to the data model, please?

> There is no easy way right now for a Perl script to easily interact with
> the BioCat application without some kind of write API.
Will I be able to do it through the API we're releasing?

Cheers,
Franck

On 10 February 2010 14:56, Jiten Bhagat <jits at cs.man.ac.uk> wrote:
> Hi Franck,
>
> There is no easy way right now for a Perl script to easily interact with
> the BioCat application without some kind of write API.
>
> For now maybe you can output to a CSV file following the annotations
> data model and that way we can easily import these?
>
> For Feta I wrote a custom import script that ran over some Feta XML
> files and imported all possible data from these.
>
> Cheers,
> Jits
>
>
> Franck Tanoh wrote:
>> Hi guys,
>>
>> I'm writing some Perl scripts to extract web service info from web
>> page such as http://xml.ddbj.nig.ac.jp/index.html,
>> http://www.ebi.ac.uk/Tools/webservices/,
>> http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchlit_help.html
>> etc. and send it to the corresponding service in biocat. Extracting
>> the info looks straight forward so far but how to populate the biocat
>> with the info? I think i can use the same process as you guys did for
>> Feta...
>>
>> Please help!
>>
>> Cheers,
>> Franck
>>
>
>



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

From ytanoh at cs.man.ac.uk  Wed Feb 10 10:36:47 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 10 Feb 2010 15:36:47 +0000
Subject: [BioCatalogue-developers] screen scraping
In-Reply-To: <4B72CAC1.9040104@genesilico.pl>
References: <d0ee827d1002100406h6b285202j405a26f6987db6de@mail.gmail.com>
	<4B72CAC1.9040104@genesilico.pl>
Message-ID: <d0ee827d1002100736t6c3f6b5cy596c9e8b13454f80@mail.gmail.com>

Hi George,

> For ddbj I would go down to examples and options like:
> http://xml.ddbj.nig.ac.jp/wabi/Method?&lang=en&serviceName=Blast&methodName=searchSimple&mode=methodDetail
> Because it makes users life much easier.
Absolutely, that's one of the reasons why I want to use scripts
instead of spending hours and hours copying and pasting ...

> For EBI, you should be able to get the structurized data. I guess Eric na
> make an SQL script to make it all
Eric, is that possible?

Cheers,
Franck

On 10 February 2010 15:03, Jerzy Orlowski <jerzyo at genesilico.pl> wrote:
> For ddbj I would go down to examples and options like:
> http://xml.ddbj.nig.ac.jp/wabi/Method?&lang=en&serviceName=Blast&methodName=searchSimple&mode=methodDetail
> Because it makes users life much easier.
>
> For EBI, you should be able to get the structurized data. I guess Eric na
> make an SQL script to make it all
>
> For NCBI I suggest parsing parameters description and usage examples
>
> George
>
>
>
>
> Franck Tanoh wrote:
>>
>> Hi guys,
>>
>> I'm writing some Perl scripts to extract web service info from web
>> page such as http://xml.ddbj.nig.ac.jp/index.html,
>> http://www.ebi.ac.uk/Tools/webservices/,
>> http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchlit_help.html
>> etc. and send it to the corresponding service in biocat. Extracting
>> the info looks straight forward so far but how to populate the biocat
>> with the info? I think i can use the same process as you guys did for
>> Feta...
>>
>> Please help!
>>
>> Cheers,
>> Franck
>>
>
> _______________________________________________
> BioCatalogue-developers mailing list
> 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  Wed Feb 10 10:39:20 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 10:39:20 -0500 (EST)
Subject: [BioCatalogue-developers] [1500] branches/integration-jan10: REST
 API work: added tests for / categories and /categories/ {id} and fixed a
 small bug in the schema as a result.
Message-ID: <20100210153920.EB0B715B8029@rubyforge.org>

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From jits at cs.man.ac.uk  Wed Feb 10 10:46:10 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 10 Feb 2010 15:46:10 +0000
Subject: [BioCatalogue-developers] screen scraping
In-Reply-To: <d0ee827d1002100733k7fb8024arf74135acbbb74c37@mail.gmail.com>
References: <d0ee827d1002100406h6b285202j405a26f6987db6de@mail.gmail.com>	
	<4B72C90A.2030304@cs.man.ac.uk>
	<d0ee827d1002100733k7fb8024arf74135acbbb74c37@mail.gmail.com>
Message-ID: <4B72D4C2.9070301@cs.man.ac.uk>

Franck,

Franck Tanoh wrote:
> Hi Jits,
>
>   
>> For now maybe you can output to a CSV file following the annotations
>> data model and that way we can easily import these?
>>     
> I can give it a go. Can you point me to the data model, please?
>   

Actually, this is tricky, because you have to reference the exact IDs of
the objects.

So for now, put this into a spreadsheet or output to a CSV with your own
custom columns (eg: wsdl_location, input_port_name,
annotation_attribute, annotation_value etc etc), making sure that each
row can be uniquely identified.

>   
>> There is no easy way right now for a Perl script to easily interact with
>> the BioCat application without some kind of write API.
>>     
> Will I be able to do it through the API we're releasing?
>   

No, the first release of the API will just be a read API.

Jits

> Cheers,
> Franck
>
> On 10 February 2010 14:56, Jiten Bhagat <jits at cs.man.ac.uk> wrote:
>   
>> Hi Franck,
>>
>> There is no easy way right now for a Perl script to easily interact with
>> the BioCat application without some kind of write API.
>>
>> For now maybe you can output to a CSV file following the annotations
>> data model and that way we can easily import these?
>>
>> For Feta I wrote a custom import script that ran over some Feta XML
>> files and imported all possible data from these.
>>
>> Cheers,
>> Jits
>>
>>
>> Franck Tanoh wrote:
>>     
>>> Hi guys,
>>>
>>> I'm writing some Perl scripts to extract web service info from web
>>> page such as http://xml.ddbj.nig.ac.jp/index.html,
>>> http://www.ebi.ac.uk/Tools/webservices/,
>>> http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchlit_help.html
>>> etc. and send it to the corresponding service in biocat. Extracting
>>> the info looks straight forward so far but how to populate the biocat
>>> with the info? I think i can use the same process as you guys did for
>>> Feta...
>>>
>>> Please help!
>>>
>>> Cheers,
>>> Franck
>>>
>>>       
>>     
>
>
>
>   


From noreply at rubyforge.org  Wed Feb 10 10:50:55 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 10:50:55 -0500 (EST)
Subject: [BioCatalogue-developers] [1501] branches/integration-jan10: REST
 API work: more tests and fixes ( centred around /services/{id})
Message-ID: <20100210155055.EC51218582DC@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 11:13:46 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 11:13:46 -0500 (EST)
Subject: [BioCatalogue-developers] [1502]
 branches/integration-jan10/script/biocatalogue/api/tests: REST API work:
 added tests for /tags and /tags/{id}
Message-ID: <20100210161347.1267318582FA@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 11:23:43 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 11:23:43 -0500 (EST)
Subject: [BioCatalogue-developers] [1503]
 branches/integration-jan10/script/biocatalogue/api/tests: REST API work:
 added tests for /service_providers and /service_providers/ {id}
Message-ID: <20100210162343.1FB5B18582E5@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 12:13:39 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 12:13:39 -0500 (EST)
Subject: [BioCatalogue-developers] [1504] branches/integration-jan10/app:
 REST API work: security work to disable certain actions when called via the
 API (ie: via non-HTML or non-JS calls).
Message-ID: <20100210171340.0B8B418582E3@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 12:26:19 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 12:26:19 -0500 (EST)
Subject: [BioCatalogue-developers] [1505] branches/integration-jan10: -
 added support to describe a rest service using rest representations
Message-ID: <20100210172619.C75F018582D7@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 13:30:06 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 13:30:06 -0500 (EST)
Subject: [BioCatalogue-developers] [1506] branches/integration-jan10: REST
 API work: implemented /users and / users/{id}.
Message-ID: <20100210183006.A0B3A15B8028@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 13:31:37 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 13:31:37 -0500 (EST)
Subject: [BioCatalogue-developers] [1507]
 branches/integration-jan10/script/biocatalogue/api/tests/
 xml_schema_validations.rb: REST API work: more tests.
Message-ID: <20100210183137.7456E18582BF@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 13:48:30 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 13:48:30 -0500 (EST)
Subject: [BioCatalogue-developers] [1508]
 branches/integration-jan10/app/views/users/api/_related_links.xml. builder:
 REST API work: minor textual change.
Message-ID: <20100210184830.EEDA618582D5@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 10 14:12:01 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 10 Feb 2010 14:12:01 -0500 (EST)
Subject: [BioCatalogue-developers] [1509] branches/integration-jan10: REST
 API work: implemented / registries and /registry.
Message-ID: <20100210191201.D1D6318582F3@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 11 05:28:54 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 11 Feb 2010 05:28:54 -0500 (EST)
Subject: [BioCatalogue-developers] [1510]
 branches/integration-jan10/app/controllers/rest_methods_controller. rb: bug
 fix: when a RestMethod object was deleted,
 the parameters and representations associated with it were deleted as well
 regardless of whether they were being used or not .
Message-ID: <20100211102854.C59F3158806E@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 11 07:57:12 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 11 Feb 2010 07:57:12 -0500 (EST)
Subject: [BioCatalogue-developers] [1511]
 branches/integration-jan10/app/views/tags/index.xml.builder: REST API work:
 bugfix for the pagination links for /tags
Message-ID: <20100211125712.5B95B18582D3@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 11 08:07:38 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 11 Feb 2010 08:07:38 -0500 (EST)
Subject: [BioCatalogue-developers] [1512]
 branches/integration-jan10/app/controllers/tags_controller.rb: Bugfix for
 /tags HTML page.
Message-ID: <20100211130738.F15761588079@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 11 08:34:39 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 11 Feb 2010 08:34:39 -0500 (EST)
Subject: [BioCatalogue-developers] [1513] branches/integration-jan10: Work
	on the search query suggestions:
Message-ID: <20100211133439.932D31588033@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 11 09:57:57 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 11 Feb 2010 09:57:57 -0500 (EST)
Subject: [BioCatalogue-developers] [1514] branches/integration-jan10:
 Various work for the search query suggestions auto complete:
Message-ID: <20100211145758.1D3AE185830B@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 11 10:38:54 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 11 Feb 2010 10:38:54 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2914] Move lib/country_codes.rb
	into a plugin
Message-ID: <20100211153854.88DD018582F8@rubyforge.org>

Task #2914 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Move lib/country_codes.rb into a plugin
Complete: 0%
Status: Open

Description: Make a completely reusable plugin out of the country_codes AND flag icons.

Use: http://en.wikipedia.org/wiki/ISO_3166-1_alpha-2

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2914&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Feb 11 10:47:13 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 11 Feb 2010 10:47:13 -0500 (EST)
Subject: [BioCatalogue-developers] [1515] branches/integration-jan10: -
 updated url_for_web_interface() in the application controller
Message-ID: <20100211154714.01BA41858308@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 11 10:55:57 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 11 Feb 2010 10:55:57 -0500 (EST)
Subject: [BioCatalogue-developers] [1516] branches/integration-jan10/app: -
	minor naming changes
Message-ID: <20100211155557.CD73B1858306@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 11 13:41:47 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 11 Feb 2010 13:41:47 -0500 (EST)
Subject: [BioCatalogue-developers] [1517] branches/integration-jan10: REST
 API work: added <iso3166CountryCode > and <flag> elements to all <location>
 elements.
Message-ID: <20100211184147.D427D18582DF@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 11 13:53:09 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 11 Feb 2010 13:53:09 -0500 (EST)
Subject: [BioCatalogue-developers] [1518] branches/integration-jan10: REST
 API work: changed the monitoring status symbol and small symbol elements to
 be ResourceLink elements .
Message-ID: <20100211185309.8544118582E0@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 12 07:26:23 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 12 Feb 2010 07:26:23 -0500 (EST)
Subject: [BioCatalogue-developers] [1519] branches/integration-jan10: REST
 API and tags work: the get_tags method and the / tags index now allow for
 both limit AND pagination to be set.
Message-ID: <20100212122625.3959C18582D6@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 12 07:28:48 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 12 Feb 2010 07:28:48 -0500 (EST)
Subject: [BioCatalogue-developers] [1520]
 branches/integration-jan10/app/views/tags/index.html.erb: Minor textual
 update
Message-ID: <20100212122848.4821818582E2@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 12 07:31:56 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 12 Feb 2010 07:31:56 -0500 (EST)
Subject: [BioCatalogue-developers] [1521]
 branches/integration-jan10/app/helpers/application_helper.rb: Fix for flag
 icons helper
Message-ID: <20100212123156.C5F2118582E2@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 12 08:01:27 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 12 Feb 2010 08:01:27 -0500 (EST)
Subject: [BioCatalogue-developers] [1522] branches/integration-jan10: -
 updated the authorisation to take into account rest service components
Message-ID: <20100212130127.9F23218582D6@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 12 08:46:22 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 12 Feb 2010 08:46:22 -0500 (EST)
Subject: [BioCatalogue-developers] [1523] branches/integration-jan10: allow
 failure (red) status for individual tests
Message-ID: <20100212134622.BF90418582E9@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 12 09:44:34 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 12 Feb 2010 09:44:34 -0500 (EST)
Subject: [BioCatalogue-developers] [1524]
	branches/integration-jan10/app/controllers: REST SUPPORT WORK
Message-ID: <20100212144434.3014518582D6@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 12 09:50:47 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 12 Feb 2010 09:50:47 -0500 (EST)
Subject: [BioCatalogue-developers] [1525]
	branches/integration-jan10/app/controllers: REST SUPPORT WORK
Message-ID: <20100212145047.259751588033@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 12 10:33:17 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 12 Feb 2010 10:33:17 -0500 (EST)
Subject: [BioCatalogue-developers] [1526] branches/integration-jan10/app:
	REST SUPPORT WORK
Message-ID: <20100212153317.38A3718582C3@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 12 11:23:09 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 12 Feb 2010 11:23:09 -0500 (EST)
Subject: [BioCatalogue-developers] [1527] branches/integration-jan10: REST
	API work:
Message-ID: <20100212162310.051B518582CC@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 12 11:46:14 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 12 Feb 2010 11:46:14 -0500 (EST)
Subject: [BioCatalogue-developers] [1528]
 branches/integration-jan10/script/biocatalogue/embrace_import.rb: Fix for
 EMRBACE import script
Message-ID: <20100212164614.5C40E18582D6@rubyforge.org>

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From jerzyo at genesilico.pl  Sun Feb 14 05:33:02 2010
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Sun, 14 Feb 2010 11:33:02 +0100
Subject: [BioCatalogue-developers] Link to Filequirks
Message-ID: <4B77D15E.1060903@genesilico.pl>

Hi

Is it possible for you to make a link to FileQuirks 
(filequirks.genesilico.pl) from Search By Data or help pages? That is my 
program I took the algorithm and regular expressions from. I am linking 
to BioCatalogue as usage example.

George

From jits at cs.man.ac.uk  Sun Feb 14 11:08:52 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Sun, 14 Feb 2010 16:08:52 +0000
Subject: [BioCatalogue-developers] Link to Filequirks
In-Reply-To: <4B77D15E.1060903@genesilico.pl>
References: <4B77D15E.1060903@genesilico.pl>
Message-ID: <4B782014.50109@cs.man.ac.uk>

Hi George,

I can do this. But can you first confirm this with the main BioCatalogue
mailing list?

We need agreement from both sides - Manchester and the EBI in order to
do something like this. I don't envisage a problem though :-)

Cheers,
Jits


Jerzy Orlowski wrote:
> Hi
>
> Is it possible for you to make a link to FileQuirks
> (filequirks.genesilico.pl) from Search By Data or help pages? That is
> my program I took the algorithm and regular expressions from. I am
> linking to BioCatalogue as usage example.
>
> George
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From noreply at rubyforge.org  Sun Feb 14 11:19:36 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 14 Feb 2010 11:19:36 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2915] error_to_home and other such
	should return appropriate HTTP codes
Message-ID: <20100214161936.ACCE418582D6@rubyforge.org>

Task #2915 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: error_to_home and other such should return appropriate HTTP codes
Complete: 0%
Status: Open

Description: Methods like error_to_home etc should return appropriate HTTP status codes. Right now there's just a redirect, and no way of telling that a genuine error has occurred.

Need to rethink this whole thing. Maybe beef up the 404 etc error pages and have those served up.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2915&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Sun Feb 14 13:36:23 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 14 Feb 2010 13:36:23 -0500 (EST)
Subject: [BioCatalogue-developers] [1529] branches/integration-jan10/app:
 REST API work: moved back to the convention that the <description> field in
 / soap_services/{id} and /rest_services/{id} is the "official" description
 that comes from some description doc.
Message-ID: <20100214183623.1F05F18582CC@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 14 14:27:06 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 14 Feb 2010 14:27:06 -0500 (EST)
Subject: [BioCatalogue-developers] [1530] branches/integration-jan10: REST
 API work: fix for the ordering of related links in /services/{id}
Message-ID: <20100214192706.5C82C18582C7@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 14 14:53:55 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 14 Feb 2010 14:53:55 -0500 (EST)
Subject: [BioCatalogue-developers] [1531] branches/integration-jan10: REST
 API work: implemented / soap_operations/{id} and linked these with
 /soap_services/{id}.
Message-ID: <20100214195355.D306718582C7@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 14 16:29:28 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 14 Feb 2010 16:29:28 -0500 (EST)
Subject: [BioCatalogue-developers] [1532] branches/integration-jan10: REST
 API work: implemented /soap_inputs/ {id} and /soap_outputs/{id} and linked
 them to /soap_operations/{id}
Message-ID: <20100214212928.A7EAE18582CC@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 14 18:20:15 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 14 Feb 2010 18:20:15 -0500 (EST)
Subject: [BioCatalogue-developers] [1533] branches/integration-jan10: REST
 API work: introduced the notion of <ancestors> in order to be able to
 easily traverse up the graph/ tree of the data model (eg: get from
 SoapInput to SoapService easily).
Message-ID: <20100214232015.F3F5D1588033@rubyforge.org>

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From noreply at rubyforge.org  Mon Feb 15 01:14:37 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 15 Feb 2010 01:14:37 -0500 (EST)
Subject: [BioCatalogue-developers] [1534]
 branches/integration-jan10/vendor/embrace_scripts: fixes to the harness
 script
Message-ID: <20100215061437.D0BBE1588033@rubyforge.org>

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From noreply at rubyforge.org  Mon Feb 15 01:22:28 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 15 Feb 2010 01:22:28 -0500 (EST)
Subject: [BioCatalogue-developers] [1535] branches/integration-jan10/app:
 create an activity log when service test changes status
Message-ID: <20100215062229.0904B18582DF@rubyforge.org>

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From noreply at rubyforge.org  Mon Feb 15 06:23:28 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 15 Feb 2010 06:23:28 -0500 (EST)
Subject: [BioCatalogue-developers] [1536]
 branches/integration-jan10/app/controllers: Further fixes for checker
 methods.
Message-ID: <20100215112329.04E1718582AC@rubyforge.org>

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From ytanoh at cs.man.ac.uk  Mon Feb 15 07:48:15 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Mon, 15 Feb 2010 12:48:15 +0000
Subject: [BioCatalogue-developers] Link to Filequirks
In-Reply-To: <4B782014.50109@cs.man.ac.uk>
References: <4B77D15E.1060903@genesilico.pl> <4B782014.50109@cs.man.ac.uk>
Message-ID: <d0ee827d1002150448g7f741f59ubeeb38fd13485c47@mail.gmail.com>

Franck
I think we can add a link on the help page here:
http://www.biocatalogue.org/wiki/doku.php?id=public:help:biocatalogue:discovering_web_services
without getting into the politics.
Is something like: <<The ?Search by data? depends on example inputs
and outputs of service operations in BioCatalogue. It is based on the
FileQuirks algorithm:  http://filequirks.genesilico.pl/>>  OK with
you?

cheers,
Franck

On 14 February 2010 16:08, Jiten Bhagat <jits at cs.man.ac.uk> wrote:
> Hi George,
>
> I can do this. But can you first confirm this with the main BioCatalogue
> mailing list?
>
> We need agreement from both sides - Manchester and the EBI in order to
> do something like this. I don't envisage a problem though :-)
>
> Cheers,
> Jits
>
>
> Jerzy Orlowski wrote:
>> Hi
>>
>> Is it possible for you to make a link to FileQuirks
>> (filequirks.genesilico.pl) from Search By Data or help pages? That is
>> my program I took the algorithm and regular expressions from. I am
>> linking to BioCatalogue as usage example.
>>
>> George
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>



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

From jerzyo at genesilico.pl  Mon Feb 15 08:38:47 2010
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Mon, 15 Feb 2010 14:38:47 +0100
Subject: [BioCatalogue-developers] Link to Filequirks
In-Reply-To: <d0ee827d1002150448g7f741f59ubeeb38fd13485c47@mail.gmail.com>
References: <4B77D15E.1060903@genesilico.pl> <4B782014.50109@cs.man.ac.uk>
	<d0ee827d1002150448g7f741f59ubeeb38fd13485c47@mail.gmail.com>
Message-ID: <4B794E67.8030701@genesilico.pl>

That's OK

Franck Tanoh wrote:
> Franck
> I think we can add a link on the help page here:
> http://www.biocatalogue.org/wiki/doku.php?id=public:help:biocatalogue:discovering_web_services
> without getting into the politics.
> Is something like: <<The ?Search by data? depends on example inputs
> and outputs of service operations in BioCatalogue. It is based on the
> FileQuirks algorithm:  http://filequirks.genesilico.pl/>>  OK with
> you?
>
> cheers,
> Franck
>
> On 14 February 2010 16:08, Jiten Bhagat <jits at cs.man.ac.uk> wrote:
>   
>> Hi George,
>>
>> I can do this. But can you first confirm this with the main BioCatalogue
>> mailing list?
>>
>> We need agreement from both sides - Manchester and the EBI in order to
>> do something like this. I don't envisage a problem though :-)
>>
>> Cheers,
>> Jits
>>
>>
>> Jerzy Orlowski wrote:
>>     
>>> Hi
>>>
>>> Is it possible for you to make a link to FileQuirks
>>> (filequirks.genesilico.pl) from Search By Data or help pages? That is
>>> my program I took the algorithm and regular expressions from. I am
>>> linking to BioCatalogue as usage example.
>>>
>>> George
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>       
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>
>>     
>
>
>
>   


From jits at cs.man.ac.uk  Mon Feb 15 10:22:36 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 15 Feb 2010 15:22:36 +0000
Subject: [BioCatalogue-developers] REST service support
Message-ID: <4B7966BC.7030004@cs.man.ac.uk>

Hi Mannie,

I've been playing around with the REST service work you've been doing.
Nice work. Good that you've taken all the design work and feedback on
board :-)

A couple of issues:
- The help texts etc really need to explain things much more clearly,
and should have popup/tooltip help too.
- It doesn't seem to handle URLs like this very well:
http://www.myexperiment.org/workflows.xml?id={workflow_id}
- Related to the previous point, when adding endpoints, it's not clear
whether it's expecting "templatised" URLs or actual example URLs (ie:
http://.../{id} or http://.../23)

Cheers,
Jits



From noreply at rubyforge.org  Mon Feb 15 10:33:04 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 15 Feb 2010 10:33:04 -0500 (EST)
Subject: [BioCatalogue-developers] [1537]
 branches/integration-jan10/vendor/embrace_scripts/src/
 script_listing_reader.py: rename reader of the listings file
Message-ID: <20100215153304.68C0D167830E@rubyforge.org>

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From ytanoh at cs.man.ac.uk  Mon Feb 15 10:54:03 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Mon, 15 Feb 2010 15:54:03 +0000
Subject: [BioCatalogue-developers] REST service support
In-Reply-To: <4B7966BC.7030004@cs.man.ac.uk>
References: <4B7966BC.7030004@cs.man.ac.uk>
Message-ID: <d0ee827d1002150754v68c9ef22ta679fbf184539223@mail.gmail.com>

> I've been playing around with the REST service work you've been doing.
> Nice work.
Can I play with it too? Can it handle real bio REST service?

Franck

On 15 February 2010 15:22, Jiten Bhagat <jits at cs.man.ac.uk> wrote:
> Hi Mannie,
>
> I've been playing around with the REST service work you've been doing.
> Nice work. Good that you've taken all the design work and feedback on
> board :-)
>
> A couple of issues:
> - The help texts etc really need to explain things much more clearly,
> and should have popup/tooltip help too.
> - It doesn't seem to handle URLs like this very well:
> http://www.myexperiment.org/workflows.xml?id={workflow_id}
> - Related to the previous point, when adding endpoints, it's not clear
> whether it's expecting "templatised" URLs or actual example URLs (ie:
> http://.../{id} or http://.../23)
>
> Cheers,
> Jits
>
>
> _______________________________________________
> BioCatalogue-developers mailing list
> 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  Mon Feb 15 11:03:59 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 15 Feb 2010 16:03:59 +0000
Subject: [BioCatalogue-developers] REST service support
In-Reply-To: <d0ee827d1002150754v68c9ef22ta679fbf184539223@mail.gmail.com>
References: <4B7966BC.7030004@cs.man.ac.uk>
	<d0ee827d1002150754v68c9ef22ta679fbf184539223@mail.gmail.com>
Message-ID: <4B79706F.9000802@cs.man.ac.uk>

Franck Tanoh wrote:
>> I've been playing around with the REST service work you've been doing.
>> Nice work.
>>     
> Can I play with it too? Can it handle real bio REST service?
>   

Ofcourse you can... try it out on http://sandbox.biocatalogue.org and
give us all the feedback you can! :-)

Not sure about real bio REST services, but it sounds like an experiment
you can do ;-)

Cheers,
Jits


> Franck
>
> On 15 February 2010 15:22, Jiten Bhagat <jits at cs.man.ac.uk> wrote:
>   
>> Hi Mannie,
>>
>> I've been playing around with the REST service work you've been doing.
>> Nice work. Good that you've taken all the design work and feedback on
>> board :-)
>>
>> A couple of issues:
>> - The help texts etc really need to explain things much more clearly,
>> and should have popup/tooltip help too.
>> - It doesn't seem to handle URLs like this very well:
>> http://www.myexperiment.org/workflows.xml?id={workflow_id}
>> - Related to the previous point, when adding endpoints, it's not clear
>> whether it's expecting "templatised" URLs or actual example URLs (ie:
>> http://.../{id} or http://.../23)
>>
>> Cheers,
>> Jits
>>
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>
>>     
>
>
>
>   


From noreply at rubyforge.org  Mon Feb 15 11:10:59 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 15 Feb 2010 11:10:59 -0500 (EST)
Subject: [BioCatalogue-developers] [1538] branches/integration-jan10: REST
 API work: flattened the <statistics > section in all collection resources,
 so that it is cleaner and easier to extend and understand.
Message-ID: <20100215161059.892F518582DC@rubyforge.org>

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From noreply at rubyforge.org  Mon Feb 15 12:17:27 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 15 Feb 2010 12:17:27 -0500 (EST)
Subject: [BioCatalogue-developers] [1539] branches/integration-jan10: REST
 API work: more changes to < statistics>:
Message-ID: <20100215171727.6CE2B18582E7@rubyforge.org>

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From noreply at rubyforge.org  Mon Feb 15 12:19:47 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 15 Feb 2010 12:19:47 -0500 (EST)
Subject: [BioCatalogue-developers] [1540]
 branches/integration-jan10/public/2009/xml/rest/schema-v1.xsd: REST API
 work: fix to XSD for previous changes.
Message-ID: <20100215171947.8738F18582EE@rubyforge.org>

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From jerzyo at genesilico.pl  Mon Feb 15 12:45:06 2010
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Mon, 15 Feb 2010 18:45:06 +0100
Subject: [BioCatalogue-developers] MyExperiment Input data
In-Reply-To: <d0ee827d1002040623q3a25f17aweb3f2de10b84e3d8@mail.gmail.com>
References: <4B6A7DC3.6090102@genesilico.pl>	
	<d0ee827d1002040218o588e17b7re3797fc07be3076b@mail.gmail.com>	
	<4B6AA7A4.8020200@genesilico.pl>
	<d0ee827d1002040623q3a25f17aweb3f2de10b84e3d8@mail.gmail.com>
Message-ID: <4B798822.1010405@genesilico.pl>

OK, we could use a test server or something like this, write a script to 
import all the inputs (and operations/services) then tag all the 
services to be deleted then remove them from import script and add them 
on live site.

I can use my script to import the inputs, but Jits, we need you to 
import services and operations if they are not in biocat. Can you modify 
the script?

George

Franck Tanoh wrote:
> Hum, might as well do everything manually... How about we use the
> script first then manually check the services the script will flag?
> At least that will hopefully reduce the number of services to be curated.
>
> Franck
>
> On 4 February 2010 10:55, Jerzy Orlowski <jerzyo at genesilico.pl> wrote:
>   
>> Sure.
>>
>> However, it needs to be checked manually before:
>> 1. Some sevices might be not from life sciences
>> 2. Some services might be not in biocatalogue (and needed to be created)
>> 3. Some services might be dead
>> Once these 3 issues are solved, we can use the script
>>
>> George
>>
>> Franck Tanoh wrote:
>>     
>>> Yep, good stuff. We now need to think of a better way to export them
>>> into biocat. Probably a generic script we can use again and again.
>>> Can your Feta import script be customized for that?
>>>
>>> Franck
>>>
>>> On 4 February 2010 07:56, Jerzy Orlowski <jerzyo at genesilico.pl> wrote:
>>>
>>>       
>>>> Hi
>>>>
>>>> Franck, Is there anything interesting in the inputs I parsed from
>>>> MyExperiment?
>>>>
>>>> George
>>>> _______________________________________________
>>>> BioCatalogue-developers mailing list
>>>> BioCatalogue-developers at rubyforge.org
>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>>
>>>>
>>>>         
>>>
>>>
>>>       
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>
>>     
>
>
>
>   


From jits at cs.man.ac.uk  Tue Feb 16 04:58:23 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 16 Feb 2010 09:58:23 +0000
Subject: [BioCatalogue-developers] MyExperiment Input data
In-Reply-To: <4B798822.1010405@genesilico.pl>
References: <4B6A7DC3.6090102@genesilico.pl>		<d0ee827d1002040218o588e17b7re3797fc07be3076b@mail.gmail.com>		<4B6AA7A4.8020200@genesilico.pl>	<d0ee827d1002040623q3a25f17aweb3f2de10b84e3d8@mail.gmail.com>
	<4B798822.1010405@genesilico.pl>
Message-ID: <4B7A6C3F.5050707@cs.man.ac.uk>

Jerzy Orlowski wrote:
> OK, we could use a test server or something like this, write a script
> to import all the inputs (and operations/services) then tag all the
> services to be deleted then remove them from import script and add
> them on live site.
>
> I can use my script to import the inputs, but Jits, we need you to
> import services and operations if they are not in biocat. Can you
> modify the script?

I can, but not in the next 2 weeks - we are very busy preparing for a
release, and for the last half of next week I am away in London for a
developer conference.

Can we pick this up after please?

Jits

>
> George
>
> Franck Tanoh wrote:
>> Hum, might as well do everything manually... How about we use the
>> script first then manually check the services the script will flag?
>> At least that will hopefully reduce the number of services to be
>> curated.
>>
>> Franck
>>
>> On 4 February 2010 10:55, Jerzy Orlowski <jerzyo at genesilico.pl> wrote:
>>  
>>> Sure.
>>>
>>> However, it needs to be checked manually before:
>>> 1. Some sevices might be not from life sciences
>>> 2. Some services might be not in biocatalogue (and needed to be
>>> created)
>>> 3. Some services might be dead
>>> Once these 3 issues are solved, we can use the script
>>>
>>> George
>>>
>>> Franck Tanoh wrote:
>>>    
>>>> Yep, good stuff. We now need to think of a better way to export them
>>>> into biocat. Probably a generic script we can use again and again.
>>>> Can your Feta import script be customized for that?
>>>>
>>>> Franck
>>>>
>>>> On 4 February 2010 07:56, Jerzy Orlowski <jerzyo at genesilico.pl> wrote:
>>>>
>>>>      
>>>>> Hi
>>>>>
>>>>> Franck, Is there anything interesting in the inputs I parsed from
>>>>> MyExperiment?
>>>>>
>>>>> George
>>>>> _______________________________________________
>>>>> BioCatalogue-developers mailing list
>>>>> BioCatalogue-developers at rubyforge.org
>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>>>
>>>>>
>>>>>         
>>>>
>>>>
>>>>       
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>
>>>     
>>
>>
>>
>>   
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From noreply at rubyforge.org  Tue Feb 16 06:35:29 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 16 Feb 2010 06:35:29 -0500 (EST)
Subject: [BioCatalogue-developers] [1541]
 branches/integration-jan10/vendor/embrace_scripts/src: generate a config
 file that can be used offline to run scripts
Message-ID: <20100216113529.480D418582F9@rubyforge.org>

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From mannie.tags at googlemail.com  Tue Feb 16 07:21:34 2010
From: mannie.tags at googlemail.com (Mannie Tagarira)
Date: Tue, 16 Feb 2010 12:21:34 +0000
Subject: [BioCatalogue-developers] REST service support
In-Reply-To: <4B79706F.9000802@cs.man.ac.uk>
References: <4B7966BC.7030004@cs.man.ac.uk>
	<d0ee827d1002150754v68c9ef22ta679fbf184539223@mail.gmail.com>
	<4B79706F.9000802@cs.man.ac.uk>
Message-ID: <C27E3260-529A-45AD-9E67-D6A1BCE2926A@gmail.com>

Hi Franck,

I noticed you have added a REST Service.  Would you care to provide some feedback :)

Thanks,
Mannie



On 15 Feb 2010, at 16:03, Jiten Bhagat wrote:

> Franck Tanoh wrote:
>>> I've been playing around with the REST service work you've been doing.
>>> Nice work.
>>> 
>> Can I play with it too? Can it handle real bio REST service?
>> 
> 
> Ofcourse you can... try it out on http://sandbox.biocatalogue.org and
> give us all the feedback you can! :-)
> 
> Not sure about real bio REST services, but it sounds like an experiment
> you can do ;-)
> 
> Cheers,
> Jits
> 
> 
>> Franck
>> 
>> On 15 February 2010 15:22, Jiten Bhagat <jits at cs.man.ac.uk> wrote:
>> 
>>> Hi Mannie,
>>> 
>>> I've been playing around with the REST service work you've been doing.
>>> Nice work. Good that you've taken all the design work and feedback on
>>> board :-)
>>> 
>>> A couple of issues:
>>> - The help texts etc really need to explain things much more clearly,
>>> and should have popup/tooltip help too.
>>> - It doesn't seem to handle URLs like this very well:
>>> http://www.myexperiment.org/workflows.xml?id={workflow_id}
>>> - Related to the previous point, when adding endpoints, it's not clear
>>> whether it's expecting "templatised" URLs or actual example URLs (ie:
>>> http://.../{id} or http://.../23)
>>> 
>>> Cheers,
>>> Jits
>>> 
>>> 
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>> 
>>> 
>> 
>> 
>> 
>> 
> 


From mannie.tags at googlemail.com  Tue Feb 16 07:20:25 2010
From: mannie.tags at googlemail.com (Mannie Tagarira)
Date: Tue, 16 Feb 2010 12:20:25 +0000
Subject: [BioCatalogue-developers] REST service support
In-Reply-To: <4B7966BC.7030004@cs.man.ac.uk>
References: <4B7966BC.7030004@cs.man.ac.uk>
Message-ID: <AC5832E3-AE47-4BCB-8327-3E19E6A4A0BA@gmail.com>

Hi Jits,

On 15 Feb 2010, at 15:22, Jiten Bhagat wrote:

> Hi Mannie,
> 
> I've been playing around with the REST service work you've been doing.
> Nice work. Good that you've taken all the design work and feedback on
> board :-)

Thanks.

> A couple of issues:
> - The help texts etc really need to explain things much more clearly,
> and should have popup/tooltip help too.

This is at the top of my list.  I wanted to get the core functionality out of the way before I started work on help text.  I wanted to dedicate some proper time for that.  I will update the existing text to make it much clearer and to take into account the work that I have just added.  I will include tooltips as well :)

> - It doesn't seem to handle URLs like this very well:
> http://www.myexperiment.org/workflows.xml?id={workflow_id}

Ok, I will make it like it :)

> - Related to the previous point, when adding endpoints, it's not clear
> whether it's expecting "templatised" URLs or actual example URLs (ie:
> http://.../{id} or http://.../23)
> 

I have updated the parser to handle both of the examples you have given above :)  So, a user can enter: http://.../{db}/{id} OR http://.../myDatabase/{id} OR http://.../myDB/3 and it will try to parse it.

> Cheers,
> Jits

Thanks,
Mannie


From noreply at rubyforge.org  Tue Feb 16 08:52:16 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 16 Feb 2010 08:52:16 -0500 (EST)
Subject: [BioCatalogue-developers] [1542] branches/integration-jan10: REST
	SUPPORT WORK
Message-ID: <20100216135216.A1627158806F@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 16 09:36:19 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 16 Feb 2010 09:36:19 -0500 (EST)
Subject: [BioCatalogue-developers] [1543]
 branches/integration-jan10/vendor/embrace_scripts: fixes to test running
 scripts
Message-ID: <20100216143619.547F918582DD@rubyforge.org>

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From ytanoh at cs.man.ac.uk  Tue Feb 16 09:40:52 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Tue, 16 Feb 2010 14:40:52 +0000
Subject: [BioCatalogue-developers] annotation best practice
Message-ID: <d0ee827d1002160640u2886a81by1fbf5352a7275b63@mail.gmail.com>

Hi guys,

I've identified some areas in the BioCatalogue where we can add some
annotation best practice notes. We may add them as tooltips or descriptive
text.
The list below follows the pattern: *annotation predicate: *tooltips text
If you're OK with that it can go into the next release.

<<
*Category: *
Assign one or more categories to the service based on its function(s).
*
Documentation url: *
Use one or several URLs to point to the service documentation.

*Service description: *
Define the purpose of the service. Clearly describe what the service does by
giving clear and simple details of what the service is meant to do.

*Contact info: *
State the contact details of the provider of the service or the support
team. This could be an e-mail address or a feedback form.
*
Operation description: *
Clearly describe what the operation does.

*Input description: *
Clearly describe the input and provide example values in the ?Example Data?
field.

*Output description:*
Clearly describe the output and provide example values in the ?Example Data?
field.

*Service tag: *
Tag this service

*Operation tag: *
Tag this operation

*Input tag: *
Tag this input

*Output tag*:
Tag this output
>>

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 noreply at rubyforge.org  Tue Feb 16 10:24:19 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 16 Feb 2010 10:24:19 -0500 (EST)
Subject: [BioCatalogue-developers] [1544]
 branches/integration-jan10/app/views: Error emails will now include the
 information about what request. format Rails parsed out.
Message-ID: <20100216152419.2AE7718582EF@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 16 10:26:46 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 16 Feb 2010 10:26:46 -0500 (EST)
Subject: [BioCatalogue-developers] [1545]
 branches/integration-jan10/vendor/embrace_scripts/src/biocat_harness .py:
Message-ID: <20100216152647.0300A18582F7@rubyforge.org>

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From ytanoh at cs.man.ac.uk  Tue Feb 16 11:18:40 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Tue, 16 Feb 2010 16:18:40 +0000
Subject: [BioCatalogue-developers] REST service support
In-Reply-To: <C27E3260-529A-45AD-9E67-D6A1BCE2926A@gmail.com>
References: <4B7966BC.7030004@cs.man.ac.uk>
	<d0ee827d1002150754v68c9ef22ta679fbf184539223@mail.gmail.com>
	<4B79706F.9000802@cs.man.ac.uk>
	<C27E3260-529A-45AD-9E67-D6A1BCE2926A@gmail.com>
Message-ID: <d0ee827d1002160818w1e666f2ax5c6507317b9c2f59@mail.gmail.com>

Hi Mannie,
It was really painful to add a new endpoint. I couldn't make sense of the
documentation. The example in the documentation didn't look like the one I
was submitted so got confused.
Not sure what you mean by 'input/output representation'.
An 'id' appears as input when i added the following endpoint:
http://xml.nig.ac.jp/rest/Invoke?service=DDBJ&method=countBasePair&accession=AB000100<http://xml.nig.ac.jp/rest/Invoke?service=DDBJ&amp;method=countBasePair&amp;accession=AB000100>
i deleted it at the end.
For the service i submitted
http://sandbox.biocatalogue.org/services/2159-ddbj_182677#endpoints  I want
to be able to annotate each of what you named 'example endpoint'. They all
have different descriptions even though they have technically the same
endpoint. Basically, you can see them as configured endpoint for specific
tasks. These configured endpoints have their own inputs. But right now all
the input are grouped together. No sure what is for what.

I like the fact that when you get it right it strips out all the inputs from
the endpoint. Overall it looks good, you just need to make the interface
more user friendly with plenty of help text and possibly a wiki help page
for more info.

Cheers,
Franck


On 16 February 2010 12:21, Mannie Tagarira <mannie.tags at googlemail.com>wrote:

> Hi Franck,
>
> I noticed you have added a REST Service.  Would you care to provide some
> feedback :)
>
> Thanks,
> Mannie
>
>
>
> On 15 Feb 2010, at 16:03, Jiten Bhagat wrote:
>
> > Franck Tanoh wrote:
> >>> I've been playing around with the REST service work you've been doing.
> >>> Nice work.
> >>>
> >> Can I play with it too? Can it handle real bio REST service?
> >>
> >
> > Ofcourse you can... try it out on http://sandbox.biocatalogue.org and
> > give us all the feedback you can! :-)
> >
> > Not sure about real bio REST services, but it sounds like an experiment
> > you can do ;-)
> >
> > Cheers,
> > Jits
> >
> >
> >> Franck
> >>
> >> On 15 February 2010 15:22, Jiten Bhagat <jits at cs.man.ac.uk> wrote:
> >>
> >>> Hi Mannie,
> >>>
> >>> I've been playing around with the REST service work you've been doing.
> >>> Nice work. Good that you've taken all the design work and feedback on
> >>> board :-)
> >>>
> >>> A couple of issues:
> >>> - The help texts etc really need to explain things much more clearly,
> >>> and should have popup/tooltip help too.
> >>> - It doesn't seem to handle URLs like this very well:
> >>> http://www.myexperiment.org/workflows.xml?id={workflow_id}<http://www.myexperiment.org/workflows.xml?id=%7Bworkflow_id%7D>
> >>> - Related to the previous point, when adding endpoints, it's not clear
> >>> whether it's expecting "templatised" URLs or actual example URLs (ie:
> >>> http://.../{id} or http://.../23)
> >>>
> >>> Cheers,
> >>> Jits
> >>>
> >>>
> >>> _______________________________________________
> >>> BioCatalogue-developers mailing list
> >>> 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
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From noreply at rubyforge.org  Tue Feb 16 11:39:41 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 16 Feb 2010 11:39:41 -0500 (EST)
Subject: [BioCatalogue-developers] [1546] branches/integration-jan10/app:
	REST SUPPORT
Message-ID: <20100216163942.0482C18582F6@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 16 12:15:37 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 16 Feb 2010 12:15:37 -0500 (EST)
Subject: [BioCatalogue-developers] [1547] branches/integration-jan10: REST
 API work: added <hostedVersion> to <serviceDeployment>.
Message-ID: <20100216171537.9C97F158806F@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 16 12:26:21 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 16 Feb 2010 12:26:21 -0500 (EST)
Subject: [BioCatalogue-developers] [1548]
	branches/integration-jan10/app/controllers: REST SUPPORT
Message-ID: <20100216172622.0DDC118582CE@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 17 05:11:32 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 17 Feb 2010 05:11:32 -0500 (EST)
Subject: [BioCatalogue-developers] [1549]
 branches/integration-jan10/app/controllers: - added "return true" to the
 authorise method of these controllers
Message-ID: <20100217101132.A731118582C2@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 17 05:41:23 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 17 Feb 2010 05:41:23 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2916] Look to making the HTML
	pages more Linked Data compliant
Message-ID: <20100217104124.4B8E718582CB@rubyforge.org>

Task #2916 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Look to making the HTML pages more Linked Data compliant
Complete: 0%
Status: Open

Description: 2 sub tasks:

1. Use the 303 redirect way, via extensions way 

eg: URIs like "http://www.biocatalogue.org/services/23" should become noon-information resource URIs and when a request is made to it a response should be given back redirecting to the appropriate URL, eg: http://www.biocatalogue.org/services/23.html).

2. In the various documents that are outputted, ensure that a link to the non-information resource URI is there. For XML this is done. For HTML, look to using a <link> tag with foaf:primaryTopic through RDFa [1].

An email thread with Sean:

---
Jits

I started a thread on public-lod:

http://lists.w3.org/Archives/Public/public-lod/2010Feb/0118.html

It looks like a possible initial solution would be to use a <link> element with an appropriate attribute (possibly foaf:primaryTopic). 
---

---
On 17 Feb 2010, at 10:20, Jiten Bhagat wrote:

> Sean Bechhofer wrote:
>>
>> On 17 Feb 2010, at 10:01, Jiten Bhagat wrote:
>>
>>> Thanks Sean, some useful responses there. I'll go with the
>>> foaf:primaryTopic <link> for now.
>>
>> The RDFa solution might also be worth considering -- it would provide
>> an route for migration in the future if you wanted to provide richer
>> information in the HTML (and is W3C Rec [1]). Happy to chat about this
>> if you want.
>
> Good point. I would prefer to do it the RDFa way as I can see a need for
> the future. I need to first check to ensure that we are generating XHTML
> compliant pages. Then I should be able to add the foaf:primarryTopic as
> starters.

Cool. It would be nice for us to be producing some RDFa pages.

> I'll run things past you when I have something to show :-)


Great.

    Sean 
---

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2916&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Wed Feb 17 07:56:27 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 17 Feb 2010 07:56:27 -0500 (EST)
Subject: [BioCatalogue-developers] [1550]
 branches/integration-jan10/lib/bio_catalogue/has_submitter.rb: Updated the
 submitter_name method to follow a similar pattern to the BioCatalogue
 ::Util.display_name method.
Message-ID: <20100217125627.7A01B18582CB@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 17 09:21:31 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 17 Feb 2010 09:21:31 -0500 (EST)
Subject: [BioCatalogue-developers] [1551] branches/integration-jan10: REST
 API work: submitters are now just ResourceLinks.
Message-ID: <20100217142131.26C291588062@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 17 09:25:01 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 17 Feb 2010 09:25:01 -0500 (EST)
Subject: [BioCatalogue-developers] [1552] branches/integration-jan10: REST
 API work: removed <specifiedName> from <service> core elements since this
 doesn't make sense in the API;
 the specified name is always the one from the SoapService or RestService
 version of the service .
Message-ID: <20100217142502.1481418582CC@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Wed Feb 17 09:43:26 2010
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 17 Feb 2010 14:43:26 +0000
Subject: [BioCatalogue-developers] annotation best practice
In-Reply-To: <d0ee827d1002160640u2886a81by1fbf5352a7275b63@mail.gmail.com>
References: <d0ee827d1002160640u2886a81by1fbf5352a7275b63@mail.gmail.com>
Message-ID: <4B7C008E.6010104@ebi.ac.uk>


Hi Franck,

I agree with most of what you have suggested for annotation help. 
Additionally, I think what we need to do is identify a well annotated 
service which some of these help messages can have pointers to. This 
could be one annotated by you but would be better if it one one that is 
annotated by the provider. 

The other thing I would suggest is that we should try to guide the user 
to give us quality data like informative tags. So instead of saying 'Tag 
this service' we could say ' provide a keyword or keywords that best 
describe(s)/identify(ies) this service. Example:  a good tag for service 
doing multiple sequence alignment is - multiple sequence alignment- .

Eric


>
> I've identified some areas in the BioCatalogue where we can add some 
> annotation best practice notes. We may add them as tooltips or 
> descriptive text.
> The list below follows the pattern: *annotation predicate: *tooltips text
> If you're OK with that it can go into the next release.
>
> <<
> *Category: *
> Assign one or more categories to the service based on its function(s).
> *
> Documentation url: *
> Use one or several URLs to point to the service documentation.
>
> *Service description: *
> Define the purpose of the service. Clearly describe what the service 
> does by giving clear and simple details of what the service is meant 
> to do.
>
> *Contact info: *
> State the contact details of the provider of the service or the 
> support team. This could be an e-mail address or a feedback form.
> *
> Operation description: *
> Clearly describe what the operation does.
>
> *Input description: * 
> Clearly describe the input and provide example values in the ?Example 
> Data? field.  
>
> *Output description:*
> Clearly describe the output and provide example values in the ?Example 
> Data? field.
>
> *Service tag: *
> Tag this service
>
> *Operation tag: *
> Tag this operation
>
> *Input tag: *
> Tag this input
>
> *Output tag*:
> Tag this output
> >>
>
> 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 ytanoh at cs.man.ac.uk  Wed Feb 17 10:11:43 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 17 Feb 2010 15:11:43 +0000
Subject: [BioCatalogue-developers] annotation best practice
In-Reply-To: <4B7C008E.6010104@ebi.ac.uk>
References: <d0ee827d1002160640u2886a81by1fbf5352a7275b63@mail.gmail.com>
	<4B7C008E.6010104@ebi.ac.uk>
Message-ID: <d0ee827d1002170711g58de76ddv68ad7c83a1cb9da6@mail.gmail.com>

Eric,

I agree with your comments and will edit the document accordingly.
The following service is a good example but practically it is not possible
to point to a service description, tag etc..
http://www.biocatalogue.org/services/2-efetchpmcservice_906306

Franck


On 17 February 2010 14:43, Eric Nzuobontane <ericnzuo at ebi.ac.uk> wrote:

>
> Hi Franck,
>
> I agree with most of what you have suggested for annotation help.
> Additionally, I think what we need to do is identify a well annotated
> service which some of these help messages can have pointers to. This could
> be one annotated by you but would be better if it one one that is annotated
> by the provider.
> The other thing I would suggest is that we should try to guide the user to
> give us quality data like informative tags. So instead of saying 'Tag this
> service' we could say ' provide a keyword or keywords that best
> describe(s)/identify(ies) this service. Example:  a good tag for service
> doing multiple sequence alignment is - multiple sequence alignment- .
>
> Eric
>
>
>
>> I've identified some areas in the BioCatalogue where we can add some
>> annotation best practice notes. We may add them as tooltips or descriptive
>> text.
>> The list below follows the pattern: *annotation predicate: *tooltips text
>> If you're OK with that it can go into the next release.
>>
>> <<
>> *Category: *
>> Assign one or more categories to the service based on its function(s).
>> *
>> Documentation url: *
>> Use one or several URLs to point to the service documentation.
>>
>> *Service description: *
>> Define the purpose of the service. Clearly describe what the service does
>> by giving clear and simple details of what the service is meant to do.
>>
>> *Contact info: *
>> State the contact details of the provider of the service or the support
>> team. This could be an e-mail address or a feedback form.
>> *
>> Operation description: *
>> Clearly describe what the operation does.
>>
>> *Input description: * Clearly describe the input and provide example
>> values in the ?Example Data? field.
>> *Output description:*
>> Clearly describe the output and provide example values in the ?Example
>> Data? field.
>>
>> *Service tag: *
>> Tag this service
>>
>> *Operation tag: *
>> Tag this operation
>>
>> *Input tag: *
>> Tag this input
>>
>> *Output tag*:
>> Tag this output
>> >>
>>
>> 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
>>
>>
>
>


-- 
"Science knows no country, because knowledge belongs to humanity, and is the
torch which illuminates the world." - Louis Pasteur
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From noreply at rubyforge.org  Wed Feb 17 10:30:38 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 17 Feb 2010 10:30:38 -0500 (EST)
Subject: [BioCatalogue-developers] [1553] branches/integration-jan10/app:
	REST SUPPORT
Message-ID: <20100217153038.3ED7118582D6@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Wed Feb 17 10:35:33 2010
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 17 Feb 2010 15:35:33 +0000
Subject: [BioCatalogue-developers] annotation best practice
In-Reply-To: <d0ee827d1002170711g58de76ddv68ad7c83a1cb9da6@mail.gmail.com>
References: <d0ee827d1002160640u2886a81by1fbf5352a7275b63@mail.gmail.com>	
	<4B7C008E.6010104@ebi.ac.uk>
	<d0ee827d1002170711g58de76ddv68ad7c83a1cb9da6@mail.gmail.com>
Message-ID: <4B7C0CC5.1070100@ebi.ac.uk>


>
> I agree with your comments and will edit the document accordingly.
> The following service is a good example but practically it is not 
> possible to point to a service description, tag etc..
> http://www.biocatalogue.org/services/2-efetchpmcservice_906306
I think it may not matter much whether the url points directly to the 
specific item being annotated. It  is more in the realm of  - if you 
want to look at an example of a well annotated service, here is where to 
look- kind of thing. Personally what I do in such circumstances is to 
have that example in one window and the thing I am working on in 
another,  then flip between the windows as may be necessary.


>
> Franck
>
>
> On 17 February 2010 14:43, Eric Nzuobontane <ericnzuo at ebi.ac.uk 
> <mailto:ericnzuo at ebi.ac.uk>> wrote:
>
>
>     Hi Franck,
>
>     I agree with most of what you have suggested for annotation help.
>     Additionally, I think what we need to do is identify a well
>     annotated service which some of these help messages can have
>     pointers to. This could be one annotated by you but would be
>     better if it one one that is annotated by the provider.
>     The other thing I would suggest is that we should try to guide the
>     user to give us quality data like informative tags. So instead of
>     saying 'Tag this service' we could say ' provide a keyword or
>     keywords that best describe(s)/identify(ies) this service.
>     Example:  a good tag for service doing multiple sequence alignment
>     is - multiple sequence alignment- .
>
>     Eric
>
>
>
>         I've identified some areas in the BioCatalogue where we can
>         add some annotation best practice notes. We may add them as
>         tooltips or descriptive text.
>         The list below follows the pattern: *annotation predicate:
>         *tooltips text
>         If you're OK with that it can go into the next release.
>
>         <<
>         *Category: *
>         Assign one or more categories to the service based on its
>         function(s).
>         *
>         Documentation url: *
>         Use one or several URLs to point to the service documentation.
>
>         *Service description: *
>         Define the purpose of the service. Clearly describe what the
>         service does by giving clear and simple details of what the
>         service is meant to do.
>
>         *Contact info: *
>         State the contact details of the provider of the service or
>         the support team. This could be an e-mail address or a
>         feedback form.
>         *
>         Operation description: *
>         Clearly describe what the operation does.
>
>         *Input description: * Clearly describe the input and provide
>         example values in the ?Example Data? field.  
>         *Output description:*
>         Clearly describe the output and provide example values in the
>         ?Example Data? field.
>
>         *Service tag: *
>         Tag this service
>
>         *Operation tag: *
>         Tag this operation
>
>         *Input tag: *
>         Tag this input
>
>         *Output tag*:
>         Tag this output
>         >>
>
>         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  Wed Feb 17 12:26:46 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 17 Feb 2010 12:26:46 -0500 (EST)
Subject: [BioCatalogue-developers] [1554] branches/integration-jan10: REST
	API work:
Message-ID: <20100217172646.A017218582CB@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 17 19:08:41 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 17 Feb 2010 19:08:41 -0500 (EST)
Subject: [BioCatalogue-developers] [1555]
 branches/integration-jan10/app/views/tags/api/_related_links.xml. builder:
 Minor textual change
Message-ID: <20100218000841.13F8C18582EF@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 18 04:14:34 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 18 Feb 2010 04:14:34 -0500 (EST)
Subject: [BioCatalogue-developers] [1556]
 branches/integration-jan10/lib/bio_catalogue/wsdl_parser.rb: adapt INB moby
 wsdl to expected structure
Message-ID: <20100218091434.4E23618582E4@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Thu Feb 18 05:11:19 2010
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 18 Feb 2010 10:11:19 +0000
Subject: [BioCatalogue-developers] annotation best practice
In-Reply-To: <d0ee827d1002170711g58de76ddv68ad7c83a1cb9da6@mail.gmail.com>
References: <d0ee827d1002160640u2886a81by1fbf5352a7275b63@mail.gmail.com>	
	<4B7C008E.6010104@ebi.ac.uk>
	<d0ee827d1002170711g58de76ddv68ad7c83a1cb9da6@mail.gmail.com>
Message-ID: <4B7D1247.9010007@ebi.ac.uk>

Hi Franck,

I was reading through the help documentation we have on the wiki, 
especially in relation to the annotations. Most of the needed material 
seems to be there just that I wanted to add a few screen shots but when 
I looked at the example of a well annotated service you pointed to me, I 
found the sample data part a bit scary. Just wondering whether this is 
an appropriate example to show to new members who are the people that 
will most likely need help with annotation...

Eric



Franck Tanoh wrote:
> Eric,
>
> I agree with your comments and will edit the document accordingly.
> The following service is a good example but practically it is not 
> possible to point to a service description, tag etc..
> http://www.biocatalogue.org/services/2-efetchpmcservice_906306
>
> Franck
>
>
> On 17 February 2010 14:43, Eric Nzuobontane <ericnzuo at ebi.ac.uk 
> <mailto:ericnzuo at ebi.ac.uk>> wrote:
>
>
>     Hi Franck,
>
>     I agree with most of what you have suggested for annotation help.
>     Additionally, I think what we need to do is identify a well
>     annotated service which some of these help messages can have
>     pointers to. This could be one annotated by you but would be
>     better if it one one that is annotated by the provider.
>     The other thing I would suggest is that we should try to guide the
>     user to give us quality data like informative tags. So instead of
>     saying 'Tag this service' we could say ' provide a keyword or
>     keywords that best describe(s)/identify(ies) this service.
>     Example:  a good tag for service doing multiple sequence alignment
>     is - multiple sequence alignment- .
>
>     Eric
>
>
>
>         I've identified some areas in the BioCatalogue where we can
>         add some annotation best practice notes. We may add them as
>         tooltips or descriptive text.
>         The list below follows the pattern: *annotation predicate:
>         *tooltips text
>         If you're OK with that it can go into the next release.
>
>         <<
>         *Category: *
>         Assign one or more categories to the service based on its
>         function(s).
>         *
>         Documentation url: *
>         Use one or several URLs to point to the service documentation.
>
>         *Service description: *
>         Define the purpose of the service. Clearly describe what the
>         service does by giving clear and simple details of what the
>         service is meant to do.
>
>         *Contact info: *
>         State the contact details of the provider of the service or
>         the support team. This could be an e-mail address or a
>         feedback form.
>         *
>         Operation description: *
>         Clearly describe what the operation does.
>
>         *Input description: * Clearly describe the input and provide
>         example values in the ?Example Data? field.  
>         *Output description:*
>         Clearly describe the output and provide example values in the
>         ?Example Data? field.
>
>         *Service tag: *
>         Tag this service
>
>         *Operation tag: *
>         Tag this operation
>
>         *Input tag: *
>         Tag this input
>
>         *Output tag*:
>         Tag this output
>         >>
>
>         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 ytanoh at cs.man.ac.uk  Thu Feb 18 06:56:51 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Thu, 18 Feb 2010 11:56:51 +0000
Subject: [BioCatalogue-developers] annotation best practice
In-Reply-To: <4B7D1247.9010007@ebi.ac.uk>
References: <d0ee827d1002160640u2886a81by1fbf5352a7275b63@mail.gmail.com>
	<4B7C008E.6010104@ebi.ac.uk>
	<d0ee827d1002170711g58de76ddv68ad7c83a1cb9da6@mail.gmail.com>
	<4B7D1247.9010007@ebi.ac.uk>
Message-ID: <d0ee827d1002180356n6f8f77b7qdb85d6c3f6305c8b@mail.gmail.com>

Hi Eric,
The reasons why I selected that service was because it's got only 1
operation (meaning less scrolling) and was not annotated by me.
i understand your concern.
This service might be a another good example:
http://www.biocatalogue.org/services/20-gibenv_401120  but it was annotated
by me (it shouldn't matter).

Franck

On 18 February 2010 10:11, Eric Nzuobontane <ericnzuo at ebi.ac.uk> wrote:

> Hi Franck,
>
> I was reading through the help documentation we have on the wiki,
> especially in relation to the annotations. Most of the needed material seems
> to be there just that I wanted to add a few screen shots but when I looked
> at the example of a well annotated service you pointed to me, I found the
> sample data part a bit scary. Just wondering whether this is an appropriate
> example to show to new members who are the people that will most likely need
> help with annotation...
>
> Eric
>
>
>
> Franck Tanoh wrote:
>
>> Eric,
>>
>> I agree with your comments and will edit the document accordingly.
>> The following service is a good example but practically it is not possible
>> to point to a service description, tag etc..
>> http://www.biocatalogue.org/services/2-efetchpmcservice_906306
>>
>> Franck
>>
>>
>> On 17 February 2010 14:43, Eric Nzuobontane <ericnzuo at ebi.ac.uk <mailto:
>> ericnzuo at ebi.ac.uk>> wrote:
>>
>>
>>    Hi Franck,
>>
>>    I agree with most of what you have suggested for annotation help.
>>    Additionally, I think what we need to do is identify a well
>>    annotated service which some of these help messages can have
>>    pointers to. This could be one annotated by you but would be
>>    better if it one one that is annotated by the provider.
>>    The other thing I would suggest is that we should try to guide the
>>    user to give us quality data like informative tags. So instead of
>>    saying 'Tag this service' we could say ' provide a keyword or
>>    keywords that best describe(s)/identify(ies) this service.
>>    Example:  a good tag for service doing multiple sequence alignment
>>    is - multiple sequence alignment- .
>>
>>    Eric
>>
>>
>>
>>        I've identified some areas in the BioCatalogue where we can
>>        add some annotation best practice notes. We may add them as
>>        tooltips or descriptive text.
>>        The list below follows the pattern: *annotation predicate:
>>        *tooltips text
>>        If you're OK with that it can go into the next release.
>>
>>        <<
>>        *Category: *
>>        Assign one or more categories to the service based on its
>>        function(s).
>>        *
>>        Documentation url: *
>>        Use one or several URLs to point to the service documentation.
>>
>>        *Service description: *
>>        Define the purpose of the service. Clearly describe what the
>>        service does by giving clear and simple details of what the
>>        service is meant to do.
>>
>>        *Contact info: *
>>        State the contact details of the provider of the service or
>>        the support team. This could be an e-mail address or a
>>        feedback form.
>>        *
>>        Operation description: *
>>        Clearly describe what the operation does.
>>
>>        *Input description: * Clearly describe the input and provide
>>        example values in the ?Example Data? field.          *Output
>> description:*
>>        Clearly describe the output and provide example values in the
>>        ?Example Data? field.
>>
>>        *Service tag: *
>>        Tag this service
>>
>>        *Operation tag: *
>>        Tag this operation
>>
>>        *Input tag: *
>>        Tag this input
>>
>>        *Output tag*:
>>        Tag this output
>>        >>
>>
>>        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
>>
>
>


-- 
"Science knows no country, because knowledge belongs to humanity, and is the
torch which illuminates the world." - Louis Pasteur
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From noreply at rubyforge.org  Thu Feb 18 12:02:01 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 18 Feb 2010 12:02:01 -0500 (EST)
Subject: [BioCatalogue-developers] [1557] branches/integration-jan10: REST
	SUPPORT
Message-ID: <20100218170201.34B7218582C9@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 18 12:14:56 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 18 Feb 2010 12:14:56 -0500 (EST)
Subject: [BioCatalogue-developers] [1558] branches/integration-jan10: REST
 API work: initial (unfinished!) work on XML and JSON endpoints.
Message-ID: <20100218171456.E97103C803E@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 18 13:01:04 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 18 Feb 2010 13:01:04 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2917] Add meta keywords and meta
	descriptions to web pages
Message-ID: <20100218180104.EA9DF185828D@rubyforge.org>

Task #2917 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Add meta keywords and meta descriptions to web pages
Complete: 0%
Status: Open

Description: For better SEO!!

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2917&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Feb 18 13:37:46 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 18 Feb 2010 13:37:46 -0500 (EST)
Subject: [BioCatalogue-developers] [1559]
 branches/integration-jan10/vendor/plugins/annotations: Updated the
 Annotations plugin to latest (which fixes a bug).
Message-ID: <20100218183746.E59E31858289@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 18 13:44:23 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 18 Feb 2010 13:44:23 -0500 (EST)
Subject: [BioCatalogue-developers] [1560] branches/integration-jan10: REST
 API work: implemented all JSON endpoint for annotations sub collections
 (eg: / services/{id}/annotations).
Message-ID: <20100218184424.1067D1858282@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 19 11:11:23 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 19 Feb 2010 11:11:23 -0500 (EST)
Subject: [BioCatalogue-developers] [1561] branches/integration-jan10/app:
 create an activity log entry when service test status changes
Message-ID: <20100219161123.64F6B18582E4@rubyforge.org>

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From noreply at rubyforge.org  Sat Feb 20 11:58:49 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 20 Feb 2010 11:58:49 -0500 (EST)
Subject: [BioCatalogue-developers] [1562]
 branches/integration-jan10/app/helpers/api_helper.rb: REST API work: bugfix
 for a regression bug from previous refactorings.
Message-ID: <20100220165850.10E6718582D5@rubyforge.org>

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From jits at cs.man.ac.uk  Sat Feb 20 13:27:20 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Sat, 20 Feb 2010 18:27:20 +0000
Subject: [BioCatalogue-developers] [1561]
 branches/integration-jan10/app: create an activity log entry when service
 test status changes
In-Reply-To: <20100219161123.64F6B18582E4@rubyforge.org>
References: <20100219161123.64F6B18582E4@rubyforge.org>
Message-ID: <4B802988.8030209@cs.man.ac.uk>

Hi Eric,

Just wanted to quickly check something regarding this status change
recording work. As we agreed, there were two steps to do:

1. move logic to model
2. add submitter_type, submitter_id to test_results table

I assume step 2 is still in consideration / progress / to be done? This
is quite important in ensuring we can record the :culprit in the
ActivityLog entry. Though we could assume the submitter from the
ServiceTest type? What will our policy be on this?

Feel free to discuss this with me further.

Cheers,
Jits


noreply at rubyforge.org wrote:
>
> Revision
>     1561
> Author
>     ebontane
> Date
>     2010-02-19 11:11:23 -0500 (Fri, 19 Feb 2010)
>
>
>       Log Message
>
> create an activity log entry when service test status changes
>
>
>       Modified Paths
>
>     * branches/integration-jan10/app/controllers/application_controller.rb
>       <#branchesintegrationjan10appcontrollersapplication_controllerrb>
>     * branches/integration-jan10/app/models/service_test.rb
>       <#branchesintegrationjan10appmodelsservice_testrb>
>     * branches/integration-jan10/app/models/test_result.rb
>       <#branchesintegrationjan10appmodelstest_resultrb>
>
>
>       Diff
>
>
>         Modified:
>         branches/integration-jan10/app/controllers/application_controller.rb
>         (1560 => 1561)
>
>
> --- branches/integration-jan10/app/controllers/application_controller.rb	2010-02-18 18:44:22 UTC (rev 1560)
> +++ branches/integration-jan10/app/controllers/application_controller.rb	2010-02-19 16:11:23 UTC (rev 1561)
> @@ -442,16 +442,6 @@
>                               :activity_loggable => @annotation))
>          end
>        end
> -      
> -      if c=="test_results"
> -        if a == "create"
> -          if @test_result.service_test.status_change?
> -            ActivityLog.create(@log_event_core_data.merge(:action => "status_change",
> -                                :culprit => current_user, :data =>{:result_id => @test_result.id},
> -                                :activity_loggable => @test_result.service_test))
> -          end
> -        end
> -      end
>  
>      end
>    end
>
>
>         Modified:
>         branches/integration-jan10/app/models/service_test.rb (1560 =>
>         1561)
>
>
> --- branches/integration-jan10/app/models/service_test.rb	2010-02-18 18:44:22 UTC (rev 1560)
> +++ branches/integration-jan10/app/models/service_test.rb	2010-02-19 16:11:23 UTC (rev 1561)
> @@ -42,7 +42,7 @@
>      BioCatalogue::Monitoring::ServiceTestStatus.new(self)
>    end
>    
> -  def status_change?
> +  def status_changed?
>      results = self.test_results.last(2)
>      case results.length
>        when 0
> @@ -50,7 +50,9 @@
>        when 1
>          return true
>        when 2
> -        if results[0].result == results[1].result
> +        stat1 = BioCatalogue::Monitoring::TestResultStatus.new(results[0])
> +        stat2 = BioCatalogue::Monitoring::TestResultStatus.new(results[1])
> +        if stat1.label == stat2.label
>            return false
>          end
>          return true
>
>
>         Modified: branches/integration-jan10/app/models/test_result.rb
>         (1560 => 1561)
>
>
> --- branches/integration-jan10/app/models/test_result.rb	2010-02-18 18:44:22 UTC (rev 1560)
> +++ branches/integration-jan10/app/models/test_result.rb	2010-02-19 16:11:23 UTC (rev 1561)
> @@ -9,6 +9,8 @@
>    
>    before_create :valid_result_range
>    
> +  after_create :update_status
> +  
>    belongs_to :service_test
>    
>    validates_presence_of :result,
> @@ -50,4 +52,24 @@
>      BioCatalogue::Monitoring::TestResultStatus.new(self)
>    end
>    
> +  # previous result id is set to nil for new_with_unknown_status
> +  def update_status
> +    if self.service_test.status_changed?
> +      results = self.service_test.test_results.last(2)
> +      unless results.empty?
> +        case results.length
> +          when 1
> +            previous = TestResult.new_with_unknown_status
> +          when 2
> +            previous = results[0]    
> +        end
> +        if USE_EVENT_LOG
> +          ActivityLog.create(:action => "status_change",
> +                           :data =>{:current_result_id => self.id, :previous_result_id =>previous.id },
> +                           :activity_loggable => self.service_test)
> +        end
> +      end
> +    end
> +  end
> +  
>  end
> ------------------------------------------------------------------------
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From jits at cs.man.ac.uk  Sat Feb 20 13:39:04 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Sat, 20 Feb 2010 18:39:04 +0000
Subject: [BioCatalogue-developers] BioCatalogue data model
In-Reply-To: <4B7E72F9.3010301@cs.man.ac.uk>
References: <4B7E72F9.3010301@cs.man.ac.uk>
Message-ID: <4B802C48.2040102@cs.man.ac.uk>

Hi Sergey,

Some good questions!

See my comments inline below...

Sergejs Aleksejevs wrote:
> Hi Jits,
>
> This is quite an important topic, because it actually touches on what
> various elements in the API output (and so in BioCatalogue data model)
> actually mean (and how these are best presented to the user). I'm sure
> I'm now going through a similar process as you did when you created
> the data model, so everything should have explanations :-) .

Great. I'll be interested in your perceptions of the data model!

>
> My current understanding is as follows --
>
>     * Service may have several deployments; each deployment hosts only
>       one version.
>

Correct.

>     * In the HTML user interface most services have only one
>       deployment and the only version - which is why all the data is
>       collected and presented as one Service (alternatively, there
>       would be a choice of various deployments to view or something
>       like that?).
>

Correct.

Yes, in the future you can imagine:
- SOAP vs REST version shown side by side.
- Multiple deployments (aka mirrors) shown in a list. Each with their
own annotations on cost, usage conditions and their own monitoring data.

>     * A service version (e.g. <soap_service>, <rest_service> in the
>       API terms) only makes sense within the "parent" deployment.
>

Not necessarily. In many cases someone won't care about the deployment
when just trying to find out what a service does. So when they first
view info about a service instance (aka service version) it doesn't need
to be in the context of where it is deployed. Then when they want to
*use* the service they will need to see info on the deployment so they
can get the base endpoint, monitoring data, and also get the annotations.

> Most likely I'm missing something, but if the above is correct, I
> don't understand why:
>
>     *  the /services/{id} endpoint has separate top level elements for
>       <deployments> and <versions> - i.e. why the only version within
>       the deployment is not listed as an inline element within the
>       relevant deployment?
>

Please see my previous comment and my comments below.

Look at the relationship between Services, ServiceDeployments and
ServiceVersions as a triangle...
- Services have many deployments and versions.
- Deployments host one particular version and belong to a service.
- Versions can be run on one or more deployments and belong to a service.

>     * <soap_service> / <rest_service> instances within <versions> in
>       /services/{id} (or in the dedicated /soap_services/{id}) don't
>       have a reference to the deployment where they are hosted? Does
>       this mean that from the users point of view the physical
>       deployments are less important than the data about the actual
>       versions?
>

Thanks for reminding me about this! I need to add the associated
ServiceDeployments in.

> Maybe there is some design document or a wiki page that I could read
> about this?

Not yet, but there will be a wiki page on our upcoming "For Developers"
wiki section about the data model and other things.

Thanks for the input here, I'll be sure to use clarify this on the wiki
page.

Cheers,
Jits

>
> Thank you,
> Sergey


From jits at cs.man.ac.uk  Sat Feb 20 13:49:53 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Sat, 20 Feb 2010 18:49:53 +0000
Subject: [BioCatalogue-developers] BioCatalogue data model
In-Reply-To: <4B802E42.5030300@cs.man.ac.uk>
References: <4B7E72F9.3010301@cs.man.ac.uk> <4B802C48.2040102@cs.man.ac.uk>
	<4B802E42.5030300@cs.man.ac.uk>
Message-ID: <4B802ED1.1080103@cs.man.ac.uk>

Great. I look forward to seeing how this works out.

This is also hugely relevant to the Taverna next gen workbench work.

Jits


Sergejs Aleksejevs wrote:
> Hi Jits,
>
> Thank you - that answers most of my questions!
>
> I'm still not too sure what's the best way to represent services /
> deployments / versions in the service preview within the plugin. I'll
> take some time to think about the options - given the new information
> that I now have - and then will discuss them with you.
>
> Thank you,
> Sergey
>
>
> Jiten Bhagat wrote:
>> Hi Sergey,
>>
>> Some good questions!
>>
>> See my comments inline below...
>>
>> Sergejs Aleksejevs wrote:
>>   
>>> Hi Jits,
>>>
>>> This is quite an important topic, because it actually touches on what
>>> various elements in the API output (and so in BioCatalogue data model)
>>> actually mean (and how these are best presented to the user). I'm sure
>>> I'm now going through a similar process as you did when you created
>>> the data model, so everything should have explanations :-) .
>>>     
>>
>> Great. I'll be interested in your perceptions of the data model!
>>
>>   
>>> My current understanding is as follows --
>>>
>>>     * Service may have several deployments; each deployment hosts only
>>>       one version.
>>>
>>>     
>>
>> Correct.
>>
>>   
>>>     * In the HTML user interface most services have only one
>>>       deployment and the only version - which is why all the data is
>>>       collected and presented as one Service (alternatively, there
>>>       would be a choice of various deployments to view or something
>>>       like that?).
>>>
>>>     
>>
>> Correct.
>>
>> Yes, in the future you can imagine:
>> - SOAP vs REST version shown side by side.
>> - Multiple deployments (aka mirrors) shown in a list. Each with their
>> own annotations on cost, usage conditions and their own monitoring data.
>>
>>   
>>>     * A service version (e.g. <soap_service>, <rest_service> in the
>>>       API terms) only makes sense within the "parent" deployment.
>>>
>>>     
>>
>> Not necessarily. In many cases someone won't care about the deployment
>> when just trying to find out what a service does. So when they first
>> view info about a service instance (aka service version) it doesn't need
>> to be in the context of where it is deployed. Then when they want to
>> *use* the service they will need to see info on the deployment so they
>> can get the base endpoint, monitoring data, and also get the annotations.
>>
>>   
>>> Most likely I'm missing something, but if the above is correct, I
>>> don't understand why:
>>>
>>>     *  the /services/{id} endpoint has separate top level elements for
>>>       <deployments> and <versions> - i.e. why the only version within
>>>       the deployment is not listed as an inline element within the
>>>       relevant deployment?
>>>
>>>     
>>
>> Please see my previous comment and my comments below.
>>
>> Look at the relationship between Services, ServiceDeployments and
>> ServiceVersions as a triangle...
>> - Services have many deployments and versions.
>> - Deployments host one particular version and belong to a service.
>> - Versions can be run on one or more deployments and belong to a service.
>>
>>   
>>>     * <soap_service> / <rest_service> instances within <versions> in
>>>       /services/{id} (or in the dedicated /soap_services/{id}) don't
>>>       have a reference to the deployment where they are hosted? Does
>>>       this mean that from the users point of view the physical
>>>       deployments are less important than the data about the actual
>>>       versions?
>>>
>>>     
>>
>> Thanks for reminding me about this! I need to add the associated
>> ServiceDeployments in.
>>
>>   
>>> Maybe there is some design document or a wiki page that I could read
>>> about this?
>>>     
>>
>> Not yet, but there will be a wiki page on our upcoming "For Developers"
>> wiki section about the data model and other things.
>>
>> Thanks for the input here, I'll be sure to use clarify this on the wiki
>> page.
>>
>> Cheers,
>> Jits
>>
>>   
>>> Thank you,
>>> Sergey
>>>     
>>
>>   
>


From noreply at rubyforge.org  Sat Feb 20 13:55:17 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 20 Feb 2010 13:55:17 -0500 (EST)
Subject: [BioCatalogue-developers] [1563]
 branches/integration-jan10/app/controllers/
 service_deployments_controller.rb: Minor bug fix.
Message-ID: <20100220185517.9FB6F18582E0@rubyforge.org>

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From alekses6 at cs.man.ac.uk  Sat Feb 20 13:47:30 2010
From: alekses6 at cs.man.ac.uk (Sergejs Aleksejevs)
Date: Sat, 20 Feb 2010 18:47:30 +0000
Subject: [BioCatalogue-developers] BioCatalogue data model
In-Reply-To: <4B802C48.2040102@cs.man.ac.uk>
References: <4B7E72F9.3010301@cs.man.ac.uk> <4B802C48.2040102@cs.man.ac.uk>
Message-ID: <4B802E42.5030300@cs.man.ac.uk>

Hi Jits,

Thank you - that answers most of my questions!

I'm still not too sure what's the best way to represent services / 
deployments / versions in the service preview within the plugin. I'll 
take some time to think about the options - given the new information 
that I now have - and then will discuss them with you.

Thank you,
Sergey


Jiten Bhagat wrote:
> Hi Sergey,
>
> Some good questions!
>
> See my comments inline below...
>
> Sergejs Aleksejevs wrote:
>   
>> Hi Jits,
>>
>> This is quite an important topic, because it actually touches on what
>> various elements in the API output (and so in BioCatalogue data model)
>> actually mean (and how these are best presented to the user). I'm sure
>> I'm now going through a similar process as you did when you created
>> the data model, so everything should have explanations :-) .
>>     
>
> Great. I'll be interested in your perceptions of the data model!
>
>   
>> My current understanding is as follows --
>>
>>     * Service may have several deployments; each deployment hosts only
>>       one version.
>>
>>     
>
> Correct.
>
>   
>>     * In the HTML user interface most services have only one
>>       deployment and the only version - which is why all the data is
>>       collected and presented as one Service (alternatively, there
>>       would be a choice of various deployments to view or something
>>       like that?).
>>
>>     
>
> Correct.
>
> Yes, in the future you can imagine:
> - SOAP vs REST version shown side by side.
> - Multiple deployments (aka mirrors) shown in a list. Each with their
> own annotations on cost, usage conditions and their own monitoring data.
>
>   
>>     * A service version (e.g. <soap_service>, <rest_service> in the
>>       API terms) only makes sense within the "parent" deployment.
>>
>>     
>
> Not necessarily. In many cases someone won't care about the deployment
> when just trying to find out what a service does. So when they first
> view info about a service instance (aka service version) it doesn't need
> to be in the context of where it is deployed. Then when they want to
> *use* the service they will need to see info on the deployment so they
> can get the base endpoint, monitoring data, and also get the annotations.
>
>   
>> Most likely I'm missing something, but if the above is correct, I
>> don't understand why:
>>
>>     *  the /services/{id} endpoint has separate top level elements for
>>       <deployments> and <versions> - i.e. why the only version within
>>       the deployment is not listed as an inline element within the
>>       relevant deployment?
>>
>>     
>
> Please see my previous comment and my comments below.
>
> Look at the relationship between Services, ServiceDeployments and
> ServiceVersions as a triangle...
> - Services have many deployments and versions.
> - Deployments host one particular version and belong to a service.
> - Versions can be run on one or more deployments and belong to a service.
>
>   
>>     * <soap_service> / <rest_service> instances within <versions> in
>>       /services/{id} (or in the dedicated /soap_services/{id}) don't
>>       have a reference to the deployment where they are hosted? Does
>>       this mean that from the users point of view the physical
>>       deployments are less important than the data about the actual
>>       versions?
>>
>>     
>
> Thanks for reminding me about this! I need to add the associated
> ServiceDeployments in.
>
>   
>> Maybe there is some design document or a wiki page that I could read
>> about this?
>>     
>
> Not yet, but there will be a wiki page on our upcoming "For Developers"
> wiki section about the data model and other things.
>
> Thanks for the input here, I'll be sure to use clarify this on the wiki
> page.
>
> Cheers,
> Jits
>
>   
>> Thank you,
>> Sergey
>>     
>
>   

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From noreply at rubyforge.org  Sat Feb 20 16:08:10 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 20 Feb 2010 16:08:10 -0500 (EST)
Subject: [BioCatalogue-developers] [1564]
 branches/integration-jan10/app/controllers/application_controller.rb :
 Minor refactorings
Message-ID: <20100220210810.AAA4F18582CA@rubyforge.org>

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From noreply at rubyforge.org  Sat Feb 20 17:38:19 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 20 Feb 2010 17:38:19 -0500 (EST)
Subject: [BioCatalogue-developers] [1565] branches/integration-jan10/app:
 REST API work: initial implementation of Linked Data compliance for API
 endpoints ( using the 303 redirect mechanism).
Message-ID: <20100220223819.9B6A318582E3@rubyforge.org>

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From noreply at rubyforge.org  Sat Feb 20 17:48:48 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 20 Feb 2010 17:48:48 -0500 (EST)
Subject: [BioCatalogue-developers] [1566]
 branches/integration-jan10/app/metal/linked_data_handler.rb: More comments
 to explain the LinkedDataHandler.
Message-ID: <20100220224848.C052718582DC@rubyforge.org>

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From noreply at rubyforge.org  Sat Feb 20 18:17:50 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 20 Feb 2010 18:17:50 -0500 (EST)
Subject: [BioCatalogue-developers] [1567] branches/integration-jan10: REST
 API work: fix for the root endpoint .
Message-ID: <20100220231750.AB78918582C1@rubyforge.org>

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From noreply at rubyforge.org  Sat Feb 20 19:44:29 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 20 Feb 2010 19:44:29 -0500 (EST)
Subject: [BioCatalogue-developers] [1568] branches/integration-jan10: REST
 API work : implemented all the necessary {resource_type}/{id}/services
 endpoints, as 302 redirects to the filtered services index.
Message-ID: <20100221004429.D0E6418582DC@rubyforge.org>

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From noreply at rubyforge.org  Sat Feb 20 20:02:03 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sat, 20 Feb 2010 20:02:03 -0500 (EST)
Subject: [BioCatalogue-developers] [1569] branches/integration-jan10: REST
 API work: added <displayName> to < tag> to provide a more human friendly
 label.
Message-ID: <20100221010203.965CB18582E3@rubyforge.org>

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From jits at cs.man.ac.uk  Sun Feb 21 13:06:33 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Sun, 21 Feb 2010 18:06:33 +0000
Subject: [BioCatalogue-developers] Prep for next release
Message-ID: <4B817629.3030303@cs.man.ac.uk>

Hi guys,

We need to prep for the release this week.

Before we release to the test server we need to:
1. Disable the REST services support work in the UI + routes *
2. Merge into trunk

Can you think of any other tasks?

Cheer,
Jits

* Mannie: so disable all the Restxxx routes EXCEPT for RestService.
Ensure that the user experience is the same as how it was before (ie:
can create a basic REST service). Then once the release is out you can
finish off the work in trunk.

From noreply at rubyforge.org  Sun Feb 21 14:45:49 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 14:45:49 -0500 (EST)
Subject: [BioCatalogue-developers] [1570]
 branches/integration-jan10/app/metal/linked_data_handler.rb: Updates to the
 Linked Data Handler
Message-ID: <20100221194549.4AF1918582D2@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 14:47:00 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 14:47:00 -0500 (EST)
Subject: [BioCatalogue-developers] [1571]
 branches/integration-jan10/app/metal/linked_data_handler.rb: Minor typo
 spelling
Message-ID: <20100221194700.71D6218582D2@rubyforge.org>

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From jits at cs.man.ac.uk  Sun Feb 21 14:58:48 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Sun, 21 Feb 2010 19:58:48 +0000
Subject: [BioCatalogue-developers] Making the BioCatalogue API Linked Data
	Compliant
Message-ID: <4B819078.5020707@cs.man.ac.uk>

Hi all,

There were some discussions a little while back about making
myExperiment and BioCatalogue "Linked Data compliant".

I'll point you to this wiki page for more info -
http://wiki.myexperiment.org/index.php/LinkedData

We agreed that we would try the "extensions" way (described further down).

For BioCatalogue we agreed that, to start with, I would make the API
endpoints (XML and JSON) all Linked Data compliant (see example below).

I have just implemented this. It took me a good few hours to get right
so might be helpful for other Ruby on Rails projects -
http://gist.github.com/309966

Note that I have implemented the redirect handler using a new Rails
feature called "Metal" [1], which is only available in Rails 2.3.x. This
bypasses the whole Rails stack and gives the best possible performance.

This code:
- only does the 303 redirects for HTTP GET requests.
- only acts on non HTML and non JS endpoints  (so the web interface is
not yet Linked Data compliant).
- has a couple of caveats. Taken from the comments in the code:

# Caveats with this implementation:
# - Doesn't handle well situations where *multiple* HTTP Accept content
types are specified (it will always pick the first one and handle that).
#   In "proper" scenarios it should be able to select the most
appropriate one based on what the system can provide.
# - To check that a specific representation has been accessed, it will
check the path info (this doesn't include the host name nor the query
parameters)
#   for a dot ('.'). If this is the case it won't do a redirect.

An example of what happens now...

[jits at dev8:~]$ curl -i -H "Accept: application/xml"
"http://localhost:3000/services"

HTTP/1.1 303 See Other
Connection: close
Date: Sun, 21 Feb 2010 19:38:55 GMT
Location: http://localhost:3000/services.xml
Content-Type: text/plain
Content-Length: 0

Is this what we are after?

Any further suggestions/feedback welcome.

Jits


From noreply at rubyforge.org  Sun Feb 21 15:04:10 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 15:04:10 -0500 (EST)
Subject: [BioCatalogue-developers] [1572] branches/integration-jan10: Work
	on Annotations:
Message-ID: <20100221200411.3087A18582DF@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 16:27:53 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 16:27:53 -0500 (EST)
Subject: [BioCatalogue-developers] [1573]
 branches/integration-jan10/script/biocatalogue/api/tests/
 xml_schema_validations.rb: REST API work: added more tests.
Message-ID: <20100221212753.75D1318582E7@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 16:38:48 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 16:38:48 -0500 (EST)
Subject: [BioCatalogue-developers] [1574]
 branches/integration-jan10/app/models/annotation.rb: REST API work: changed
 the JSON output for the Annotation model to wrap each annotation' s output
 in an outer "annotation" hash.
Message-ID: <20100221213848.CC22B18582C2@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 16:43:05 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 16:43:05 -0500 (EST)
Subject: [BioCatalogue-developers] [1575] branches/integration-jan10: REST
 API work: implemented the JSON endpoints for annotation_attributes.
Message-ID: <20100221214305.48E7318582C2@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 17:00:43 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 17:00:43 -0500 (EST)
Subject: [BioCatalogue-developers] [1576]
 branches/integration-jan10/app/views/categories/index.xml.builder: Fixed
 typo
Message-ID: <20100221220043.CF8B318582DF@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 17:11:44 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 17:11:44 -0500 (EST)
Subject: [BioCatalogue-developers] [1577] branches/integration-jan10: REST
 API work: implemented the annotation_attributes index and show endpoints
 for XML.
Message-ID: <20100221221144.E745218582D8@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 17:17:01 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 17:17:01 -0500 (EST)
Subject: [BioCatalogue-developers] [1578]
 branches/integration-jan10/app/controllers/annotations_controller.rb : REST
 API work: implemented /annotations JSON endpoint (paged).
Message-ID: <20100221221701.CAA0218582C7@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 17:19:57 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 17:19:57 -0500 (EST)
Subject: [BioCatalogue-developers] [1579]
 branches/integration-jan10/app/views/annotation_attributes: Grrrr,
 fixed more typos!
Message-ID: <20100221221957.B4CCD18582D8@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 17:56:56 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 17:56:56 -0500 (EST)
Subject: [BioCatalogue-developers] [1580] branches/integration-jan10: REST
 API work: implemented a basic / annotations XML endpoint and also the
 /annotations/{id} XML endpoint.
Message-ID: <20100221225656.880C318582D5@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 19:16:56 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 19:16:56 -0500 (EST)
Subject: [BioCatalogue-developers] [1581] branches/integration-jan10:
 Refactoring of all backend service specific filtering logic into a separate
 BioCatalogue ::Filtering::Services module.
Message-ID: <20100222001656.8EA4A18582C2@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 19:44:16 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 19:44:16 -0500 (EST)
Subject: [BioCatalogue-developers] [1582] branches/integration-jan10/app:
 Made the include/ exclude filters URL generator methods more generic so
 they can be used with more than just services .
Message-ID: <20100222004416.B7D0718582D5@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 20:20:55 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 20:20:55 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2919] Possibly reimplement the
	service filtering method for conditions
Message-ID: <20100222012055.342D918582D2@rubyforge.org>

Task #2919 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Possibly reimplement the service filtering method for conditions 
Complete: 0%
Status: Open

Description: A new way of doing it was done for BioCatalogue::Filtering::Annotations::generate_conditions_and_joins_from_filters

Possibly reimplement the services one to do it this way.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2919&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Sun Feb 21 21:13:00 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 21:13:00 -0500 (EST)
Subject: [BioCatalogue-developers] [1583] branches/integration-jan10: Intial
 implementation of Annotations filtering!!
Message-ID: <20100222021300.86B1218582C2@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 21:35:40 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 21:35:40 -0500 (EST)
Subject: [BioCatalogue-developers] [1584] branches/integration-jan10: REST
 API work: implemented the filtered XML /annotations endpoint.
Message-ID: <20100222023541.094F31588033@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 21:58:04 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 21:58:04 -0500 (EST)
Subject: [BioCatalogue-developers] [1585] branches/integration-jan10: REST
 API work: implemented all / {resource_type}/{id}/annotations XML endpoints.
Message-ID: <20100222025804.2C08E18582DC@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 22:14:53 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 22:14:53 -0500 (EST)
Subject: [BioCatalogue-developers] [1586]
 branches/integration-jan10/lib/bio_catalogue/filtering: Commented out some
 debug logging, to prevent logfile size proliferation.
Message-ID: <20100222031453.A6E3D1588033@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 22:15:27 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 22:15:27 -0500 (EST)
Subject: [BioCatalogue-developers] [1587]
 branches/integration-jan10/lib/bio_catalogue/filtering/annotations. rb:
 Bugfix - fixed a typo in code.
Message-ID: <20100222031527.7614018582DC@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 22:19:25 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 22:19:25 -0500 (EST)
Subject: [BioCatalogue-developers] [1588]
 branches/integration-jan10/lib/bio_catalogue/filtering/annotations. rb:
 Another bugfix
Message-ID: <20100222031925.B15C6185828D@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 21 22:24:51 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 21 Feb 2010 22:24:51 -0500 (EST)
Subject: [BioCatalogue-developers] [1589] branches/integration-jan10: REST
 API work: added more tests and did some bugfixes.
Message-ID: <20100222032451.AA65C18582D7@rubyforge.org>

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From jerzyo at genesilico.pl  Mon Feb 22 04:42:30 2010
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Mon, 22 Feb 2010 10:42:30 +0100
Subject: [BioCatalogue-developers] annotation best practice
In-Reply-To: <d0ee827d1002160640u2886a81by1fbf5352a7275b63@mail.gmail.com>
References: <d0ee827d1002160640u2886a81by1fbf5352a7275b63@mail.gmail.com>
Message-ID: <4B825186.1040107@genesilico.pl>

I think annotating everything is too much.
Tips should also point to what is more important to provide like:

1st place:
    - service description
    - operation description
2nd place
    - input port description
    - example input
3rd place
   - ...
   - ...

Franck Tanoh wrote:
> Hi guys,
>
> I've identified some areas in the BioCatalogue where we can add some 
> annotation best practice notes. We may add them as tooltips or 
> descriptive text.
> The list below follows the pattern: *annotation predicate: *tooltips text
> If you're OK with that it can go into the next release.
>
> <<
> *Category: *
> Assign one or more categories to the service based on its function(s).
> *
> Documentation url: *
> Use one or several URLs to point to the service documentation.
>
> *Service description: *
> Define the purpose of the service. Clearly describe what the service 
> does by giving clear and simple details of what the service is meant 
> to do.
>
> *Contact info: *
> State the contact details of the provider of the service or the 
> support team. This could be an e-mail address or a feedback form.
> *
> Operation description: *
> Clearly describe what the operation does.
>
> *Input description: * 
> Clearly describe the input and provide example values in the ?Example 
> Data? field.  
>
> *Output description:*
> Clearly describe the output and provide example values in the ?Example 
> Data? field.
>
> *Service tag: *
> Tag this service
>
> *Operation tag: *
> Tag this operation
>
> *Input tag: *
> Tag this input
>
> *Output tag*:
> Tag this output
> >>
>
> 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  Mon Feb 22 05:56:35 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 22 Feb 2010 05:56:35 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2920] myExp Integration: use
	George's SPARQL query
Message-ID: <20100222105635.5669018582E3@rubyforge.org>

Task #2920 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: myExp Integration: use George's SPARQL query
Complete: 0%
Status: Open

Description: We can mine useful info from myExperiment...


http://rdf.myexperiment.org/sparql

I am working on a version that will go with xmlsplitters

George

-----------------
#get all stringconstant input of wsdl processors
PREFIX mecomp: <http://rdf.myexperiment.org/ontologies/components/>
PREFIX mebase: <http://rdf.myexperiment.org/ontologies/base/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
select distinct ?output_processor_type, ?output_service, ?output_uri, ?output_port,   ?input_processor_value where{
 ?link rdf:type mecomp:Link .
 ?link mecomp:from-output ?output .
 ?output mecomp:for-component ?input_processor .
 ?input_processor mecomp:processor-type ?input_processor_type .
 ?input_processor mecomp:processor-value ?input_processor_value .
 ?link mecomp:to-input ?input .
 ?input mecomp:for-component ?output_processor .
 ?output_processor mecomp:processor-type ?output_processor_type .
 ?output_processor mecomp:processor-uri ?output_uri .
 ?output_processor mecomp:service-name ?output_service .
 ?input dcterms:title ?output_port .
 FILTER(REGEX(?input_processor_type,'stringconstant')) .
 FILTER(REGEX(?output_processor_type,'wsdl')) .
}

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

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2920&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Feb 22 06:06:58 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 22 Feb 2010 06:06:58 -0500 (EST)
Subject: [BioCatalogue-developers] [1590] branches/integration-jan10: PREP
	FOR NEXT RELEASE
Message-ID: <20100222110658.2B1241588033@rubyforge.org>

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From noreply at rubyforge.org  Mon Feb 22 06:30:47 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 22 Feb 2010 06:30:47 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2921] Import myExperiment example
	data into the BioCatalogue
Message-ID: <20100222113047.E331718582E3@rubyforge.org>

Task #2921 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Import myExperiment example data into the BioCatalogue 
Complete: 0%
Status: Open

Description: Find a way to automatically import all example data provide by the SPARQL query from George: 

Here's the SPARQL query just put it on

http://rdf.myexperiment.org/sparql

I am working on a version that will go with xmlsplitters

George

-----------------
#get all stringconstant input of wsdl processors
PREFIX mecomp: <http://rdf.myexperiment.org/ontologies/components/>
PREFIX mebase: <http://rdf.myexperiment.org/ontologies/base/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
select distinct ?output_processor_type, ?output_service, ?output_uri, ?output_port,   ?input_processor_value where{
 ?link rdf:type mecomp:Link .
 ?link mecomp:from-output ?output .
 ?output mecomp:for-component ?input_processor .
 ?input_processor mecomp:processor-type ?input_processor_type .
 ?input_processor mecomp:processor-value ?input_processor_value .
 ?link mecomp:to-input ?input .
 ?input mecomp:for-component ?output_processor .
 ?output_processor mecomp:processor-type ?output_processor_type .
 ?output_processor mecomp:processor-uri ?output_uri .
 ?output_processor mecomp:service-name ?output_service .
 ?input dcterms:title ?output_port .
 FILTER(REGEX(?input_processor_type,'stringconstant')) .
 FILTER(REGEX(?output_processor_type,'wsdl')) .
}

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2921&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Feb 22 06:58:56 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 22 Feb 2010 06:58:56 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2920] myExp Integration: use
	George's SPARQL query
Message-ID: <20100222115857.155E618582E7@rubyforge.org>

Task #2920 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: myExp Integration: use George's SPARQL query
Complete: 0%
Status: Deleted

Description: We can mine useful info from myExperiment...


http://rdf.myexperiment.org/sparql

I am working on a version that will go with xmlsplitters

George

-----------------
#get all stringconstant input of wsdl processors
PREFIX mecomp: <http://rdf.myexperiment.org/ontologies/components/>
PREFIX mebase: <http://rdf.myexperiment.org/ontologies/base/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
select distinct ?output_processor_type, ?output_service, ?output_uri, ?output_port,   ?input_processor_value where{
 ?link rdf:type mecomp:Link .
 ?link mecomp:from-output ?output .
 ?output mecomp:for-component ?input_processor .
 ?input_processor mecomp:processor-type ?input_processor_type .
 ?input_processor mecomp:processor-value ?input_processor_value .
 ?link mecomp:to-input ?input .
 ?input mecomp:for-component ?output_processor .
 ?output_processor mecomp:processor-type ?output_processor_type .
 ?output_processor mecomp:processor-uri ?output_uri .
 ?output_processor mecomp:service-name ?output_service .
 ?input dcterms:title ?output_port .
 FILTER(REGEX(?input_processor_type,'stringconstant')) .
 FILTER(REGEX(?output_processor_type,'wsdl')) .
}

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

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2920&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Feb 22 07:00:56 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 22 Feb 2010 07:00:56 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2920] myExp Integration: use
	George's SPARQL query
Message-ID: <20100222120056.49A3D18582E5@rubyforge.org>

Task #2920 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: myExp Integration: use George's SPARQL query
Complete: 0%
Status: Deleted

Description: We can mine useful info from myExperiment...


http://rdf.myexperiment.org/sparql

I am working on a version that will go with xmlsplitters

George

-----------------
#get all stringconstant input of wsdl processors
PREFIX mecomp: <http://rdf.myexperiment.org/ontologies/components/>
PREFIX mebase: <http://rdf.myexperiment.org/ontologies/base/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
select distinct ?output_processor_type, ?output_service, ?output_uri, ?output_port,   ?input_processor_value where{
 ?link rdf:type mecomp:Link .
 ?link mecomp:from-output ?output .
 ?output mecomp:for-component ?input_processor .
 ?input_processor mecomp:processor-type ?input_processor_type .
 ?input_processor mecomp:processor-value ?input_processor_value .
 ?link mecomp:to-input ?input .
 ?input mecomp:for-component ?output_processor .
 ?output_processor mecomp:processor-type ?output_processor_type .
 ?output_processor mecomp:processor-uri ?output_uri .
 ?output_processor mecomp:service-name ?output_service .
 ?input dcterms:title ?output_port .
 FILTER(REGEX(?input_processor_type,'stringconstant')) .
 FILTER(REGEX(?output_processor_type,'wsdl')) .
}

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

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2920&group_id=6901&group_project_id=12540

From ericnzuo at ebi.ac.uk  Mon Feb 22 08:11:11 2010
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 22 Feb 2010 13:11:11 +0000
Subject: [BioCatalogue-developers] redirecting http://wiki.biocatalogue.org
	to http://www.biocatalogue.org/wiki
Message-ID: <4B82826F.5010207@ebi.ac.uk>

Hi Jits,

This request has not fallen through the cracks. The domain admin has 
promised to give me credentials to enable me to do this myself. She is 
not here now but I will follow this up again & hopefully will able to do 
that soon afterwards,

Eric


From jits at cs.man.ac.uk  Mon Feb 22 08:34:47 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 22 Feb 2010 13:34:47 +0000
Subject: [BioCatalogue-developers] redirecting
 http://wiki.biocatalogue.org to http://www.biocatalogue.org/wiki
In-Reply-To: <4B82826F.5010207@ebi.ac.uk>
References: <4B82826F.5010207@ebi.ac.uk>
Message-ID: <4B8287F7.6040501@cs.man.ac.uk>

Thanks Eric!

Turns out it now works, and has been for a couple of weeks now :-)

Cheers,
Jits


Eric Nzuobontane wrote:
> Hi Jits,
>
> This request has not fallen through the cracks. The domain admin has
> promised to give me credentials to enable me to do this myself. She is
> not here now but I will follow this up again & hopefully will able to
> do that soon afterwards,
>
> Eric
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From ericnzuo at ebi.ac.uk  Mon Feb 22 08:47:29 2010
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 22 Feb 2010 13:47:29 +0000
Subject: [BioCatalogue-developers] redirecting
 http://wiki.biocatalogue.org to http://www.biocatalogue.org/wiki
In-Reply-To: <4B82826F.5010207@ebi.ac.uk>
References: <4B82826F.5010207@ebi.ac.uk>
Message-ID: <4B828AF1.8010102@ebi.ac.uk>

Eric Nzuobontane wrote:
OK, I did not realise that.  I did send a few reminders but I was not 
informed that it was done. Anyway, if I get the credentials I may be 
able to handle future requests myself.

Eric
> Hi Jits,
>
> This request has not fallen through the cracks. The domain admin has 
> promised to give me credentials to enable me to do this myself. She is 
> not here now but I will follow this up again & hopefully will able to 
> do that soon afterwards,
>
> Eric
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From noreply at rubyforge.org  Mon Feb 22 12:35:31 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 22 Feb 2010 12:35:31 -0500 (EST)
Subject: [BioCatalogue-developers] [1591] branches/integration-jan10/app:
 REST API work: initial work on the Monitoring data API
Message-ID: <20100222173531.5A4C1158806E@rubyforge.org>

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From noreply at rubyforge.org  Mon Feb 22 13:40:17 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 22 Feb 2010 13:40:17 -0500 (EST)
Subject: [BioCatalogue-developers] [1592] branches/integration-jan10: REST
 API work: initial implementation of the XML endpoint for
 /annotations/filters
Message-ID: <20100222184018.ACAD218582D3@rubyforge.org>

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From jits at cs.man.ac.uk  Mon Feb 22 13:58:15 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 22 Feb 2010 18:58:15 +0000
Subject: [BioCatalogue-developers] Can't upload test script
Message-ID: <4B82D3C7.8060308@cs.man.ac.uk>

Hi Eric,

I can't seem to upload a test script. I'm trying to upload an arbitrary
Ruby script. It keeps coming back with the error "There was a problem
submitting this test! Please check that you provided all fields and that
file is of right type." with no indication of what the error(s) was!

I think we should move the test script upload form into a separate page
and have better error handling when it fails. Right now it redirects
back to the service page and doesn't even take you back to the right tab.

Jits

From noreply at rubyforge.org  Mon Feb 22 14:13:22 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 22 Feb 2010 14:13:22 -0500 (EST)
Subject: [BioCatalogue-developers] [1593]
 branches/integration-jan10/app/controllers/test_scripts_controller. rb:
 Added better error handling to make life slightly easier.
Message-ID: <20100222191322.BE75918582F1@rubyforge.org>

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From jits at cs.man.ac.uk  Mon Feb 22 14:20:52 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 22 Feb 2010 19:20:52 +0000
Subject: [BioCatalogue-developers] Can't upload test script
In-Reply-To: <4B82D3C7.8060308@cs.man.ac.uk>
References: <4B82D3C7.8060308@cs.man.ac.uk>
Message-ID: <4B82D914.6010606@cs.man.ac.uk>

After adding better logging, I get the following...

---
dev8.4646  19:04:44  ERROR    Failed to upload Test Script. Exception:
Validation failed: Service tests is invalid, Service tests is invalid
dev8.4646  19:04:44  ERROR   
/usr/lib/ruby/gems/1.8/gems/activerecord-2.3.2/lib/active_record/validations.rb:1021:in
`save_without_dirty!'
dev8.4646 
/usr/lib/ruby/gems/1.8/gems/activerecord-2.3.2/lib/active_record/dirty.rb:87:in
`save_without_transactions!'
dev8.4646 
/usr/lib/ruby/gems/1.8/gems/activerecord-2.3.2/lib/active_record/transactions.rb:200:in
`save!'
dev8.4646 
/usr/lib/ruby/gems/1.8/gems/activerecord-2.3.2/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in
`transaction'
dev8.4646 
/usr/lib/ruby/gems/1.8/gems/activerecord-2.3.2/lib/active_record/transactions.rb:182:in
`transaction'
---

Can you please move ALL the creation logic into the TestScript model?

Just use an after_create callback in the TestScript model to create the
new ServiceTest. If the creation of this ServiceTest fails you can
always return false in this after_create callback and then the whole
create process will rollback automatically. Make sure to add to the
TestScript#errors collection any new errors that are encountered!

Then in the controller you just need to do things the Rails way by
calling "if obj.save..." and then the errors collection is available in
the UI for rendering of all the validation errors.

And don't save the top level Service!! This updates the updated_at
timestamp on it and kicks into motion all the callbacks for the Service
model. Instead just set :service_id for the new ServiceTest object to
the service ID.

This really begs the question of how the EMBRACE import script is
importing the existing scripts. Does it manually replicate all this logic?

With the current way, the validation errors just get lost.

Jits


Jiten Bhagat wrote:
> Hi Eric,
>
> I can't seem to upload a test script. I'm trying to upload an arbitrary
> Ruby script. It keeps coming back with the error "There was a problem
> submitting this test! Please check that you provided all fields and that
> file is of right type." with no indication of what the error(s) was!
>
> I think we should move the test script upload form into a separate page
> and have better error handling when it fails. Right now it redirects
> back to the service page and doesn't even take you back to the right tab.
>
> Jits
>
>   


From ericnzuo at ebi.ac.uk  Tue Feb 23 04:33:07 2010
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Tue, 23 Feb 2010 09:33:07 +0000
Subject: [BioCatalogue-developers] Can't upload test script
In-Reply-To: <4B82D914.6010606@cs.man.ac.uk>
References: <4B82D3C7.8060308@cs.man.ac.uk> <4B82D914.6010606@cs.man.ac.uk>
Message-ID: <4B83A0D3.8070307@ebi.ac.uk>

Jiten Bhagat wrote:
> After adding better logging, I get the following...
>
> ---
> dev8.4646  19:04:44  ERROR    Failed to upload Test Script. Exception:
> Validation failed: Service tests is invalid, Service tests is invalid
> dev8.4646  19:04:44  ERROR   
> /usr/lib/ruby/gems/1.8/gems/activerecord-2.3.2/lib/active_record/validations.rb:1021:in
> `save_without_dirty!'
> dev8.4646 
> /usr/lib/ruby/gems/1.8/gems/activerecord-2.3.2/lib/active_record/dirty.rb:87:in
> `save_without_transactions!'
> dev8.4646 
> /usr/lib/ruby/gems/1.8/gems/activerecord-2.3.2/lib/active_record/transactions.rb:200:in
> `save!'
> dev8.4646 
> /usr/lib/ruby/gems/1.8/gems/activerecord-2.3.2/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in
> `transaction'
> dev8.4646 
> /usr/lib/ruby/gems/1.8/gems/activerecord-2.3.2/lib/active_record/transactions.rb:182:in
> `transaction'
> ---
>
> Can you please move ALL the creation logic into the TestScript model?
>
> Just use an after_create callback in the TestScript model to create the
> new ServiceTest. If the creation of this ServiceTest fails you can
> always return false in this after_create callback and then the whole
> create process will rollback automatically. Make sure to add to the
> TestScript#errors collection any new errors that are encountered!
>   
Yes, I can and I did initially. But the problem was that meant the test 
script would be created first and an after create would create the 
service test.
However, I needed the service id in the after create and I am not sure 
how you pass that to the model. Maybe creating the service test and the 
test script in an after create would work.

> Then in the controller you just need to do things the Rails way by
> calling "if obj.save..." and then the errors collection is available in
> the UI for rendering of all the validation errors.
>
> And don't save the top level Service!! This updates the updated_at
> timestamp on it and kicks into motion all the callbacks for the Service
> model. Instead just set :service_id for the new ServiceTest object to
> the service ID.
>   
Ok, but I thought that one would want to know when the state of the 
service changed and adding a new test changes state.
> This really begs the question of how the EMBRACE import script is
> importing the existing scripts. Does it manually replicate all this logic?
>
>   
of creating the relationship?
> With the current way, the validation errors just get lost.
>   
I add to the errors object.

Eric




>
> Jiten Bhagat wrote:
>   
>> Hi Eric,
>>
>> I can't seem to upload a test script. I'm trying to upload an arbitrary
>> Ruby script. It keeps coming back with the error "There was a problem
>> submitting this test! Please check that you provided all fields and that
>> file is of right type." with no indication of what the error(s) was!
>>
>> I think we should move the test script upload form into a separate page
>> and have better error handling when it fails. Right now it redirects
>> back to the service page and doesn't even take you back to the right tab.
>>
>> Jits
>>
>>   
>>     


From jits at cs.man.ac.uk  Tue Feb 23 05:43:47 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 23 Feb 2010 10:43:47 +0000
Subject: [BioCatalogue-developers] Can't upload test script
In-Reply-To: <4B83A0D3.8070307@ebi.ac.uk>
References: <4B82D3C7.8060308@cs.man.ac.uk> <4B82D914.6010606@cs.man.ac.uk>
	<4B83A0D3.8070307@ebi.ac.uk>
Message-ID: <4B83B163.1080900@cs.man.ac.uk>

Hi Eric,

Eric Nzuobontane wrote:
> Jiten Bhagat wrote:
>> [...]
>>
>> Can you please move ALL the creation logic into the TestScript model?
>>
>> Just use an after_create callback in the TestScript model to create the
>> new ServiceTest. If the creation of this ServiceTest fails you can
>> always return false in this after_create callback and then the whole
>> create process will rollback automatically. Make sure to add to the
>> TestScript#errors collection any new errors that are encountered!
>>   
> Yes, I can and I did initially. But the problem was that meant the
> test script would be created first and an after create would create
> the service test.
> However, I needed the service id in the after create and I am not sure
> how you pass that to the model. Maybe creating the service test and
> the test script in an after create would work.

Ah ha! Okay, in that case you could have a similar approach to how we do
SoapService#submit_service, ie: do lots of stuff within a transaction
and return back the result + errors. (The error handling for
SoapService#submit does need to be improved because no useful errors are
provided to the end user! Though that is a much more complex logic
involved than here).

Another approach is to create a virtual field...

def service_id=(val)
  @service_id = val
end

... and use this in the after_create.

I would think that a TestScript should at least have the ID of the
associated SoapService / RestService it tests?

We should always take a step back in situations like this; it seems to
me that the rule here is that *every time* a new TestScript is created
(anywhere in the system) an associated ServiceTest should be created
too. Is the case? Can you ever think of a need to only just create a
TestScript without creating a ServiceTest? Maybe in cases where a
TestScript needs to be created and an *existing* ServiceTest needs to be
updated? In that case the logic of creating/updating ServiceTests should
sit separately (like in the controller).

>
>> Then in the controller you just need to do things the Rails way by
>> calling "if obj.save..." and then the errors collection is available in
>> the UI for rendering of all the validation errors.
>>
>> And don't save the top level Service!! This updates the updated_at
>> timestamp on it and kicks into motion all the callbacks for the Service
>> model. Instead just set :service_id for the new ServiceTest object to
>> the service ID.
>>   
> Ok, but I thought that one would want to know when the state of the
> service changed and adding a new test changes state.

When new Annotations are added for any part of the Service, do we update
the associated Service object?

I know that in an ideal scenario we should! But in this case its just
not a reliable method.

Rails 2.3.3 has a new ActiveRecord::Base#touch method which allows to do
just this, in a more perf appropriate way. We're still on 2.3.2 though.

>> This really begs the question of how the EMBRACE import script is
>> importing the existing scripts. Does it manually replicate all this
>> logic?
>>
>>   
> of creating the relationship?

Yes, the whole process of creating the TestScript, ServiceTest and
updating the Service.

>> With the current way, the validation errors just get lost.
>>   
> I add to the errors object.

Okay. I struggled yesterday to understand where this happens... all I
could get was: "Validation failed: Service tests is invalid, Service
tests is invalid"

Jits

>
> Eric
>
>
>
>
>>
>> Jiten Bhagat wrote:
>>  
>>> Hi Eric,
>>>
>>> I can't seem to upload a test script. I'm trying to upload an arbitrary
>>> Ruby script. It keeps coming back with the error "There was a problem
>>> submitting this test! Please check that you provided all fields and
>>> that
>>> file is of right type." with no indication of what the error(s) was!
>>>
>>> I think we should move the test script upload form into a separate page
>>> and have better error handling when it fails. Right now it redirects
>>> back to the service page and doesn't even take you back to the right
>>> tab.
>>>
>>> Jits
>>>
>>>       
>


From ytanoh at cs.man.ac.uk  Tue Feb 23 07:23:13 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Tue, 23 Feb 2010 12:23:13 +0000
Subject: [BioCatalogue-developers] bye bye beta?
Message-ID: <d0ee827d1002230423h530e1ddr78285cb18bbe4f9a@mail.gmail.com>

Hi guys,
Are we getting rid of 'beta' in the logo for this release?  Last time I
spoke to Carole she was fine with that. I think we have a task on rubyforge
for that.

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 jits at cs.man.ac.uk  Tue Feb 23 08:19:52 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 23 Feb 2010 13:19:52 +0000
Subject: [BioCatalogue-developers] bye bye beta?
In-Reply-To: <d0ee827d1002230423h530e1ddr78285cb18bbe4f9a@mail.gmail.com>
References: <d0ee827d1002230423h530e1ddr78285cb18bbe4f9a@mail.gmail.com>
Message-ID: <4B83D5F8.7010108@cs.man.ac.uk>

Can we wait until the next release?

I know it doesn't really mean much, but this release will be a BIG one
and there might be some issues cropping up later that we hadn't
envisioned (or just bugs!), so it I don't want us to claim that we are a
fully production ready system just yet!

Jits


Franck Tanoh wrote:
> Hi guys,
> Are we getting rid of 'beta' in the logo for this release?  Last time
> I spoke to Carole she was fine with that. I think we have a task on
> rubyforge for that.
>
> cheers,
> 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  Tue Feb 23 08:45:23 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 23 Feb 2010 08:45:23 -0500 (EST)
Subject: [BioCatalogue-developers] [1594] branches/integration-jan10: PREP
	FOR NEXT RELEASE
Message-ID: <20100223134526.49545159807F@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 23 09:23:11 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 23 Feb 2010 09:23:11 -0500 (EST)
Subject: [BioCatalogue-developers] [1595]
 branches/integration-jan10/lib/bio_catalogue/monitoring/status.rb: Minor
 textual changes
Message-ID: <20100223142312.05D1218582C7@rubyforge.org>

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From ytanoh at cs.man.ac.uk  Tue Feb 23 09:30:18 2010
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Tue, 23 Feb 2010 14:30:18 +0000
Subject: [BioCatalogue-developers] bye bye beta?
In-Reply-To: <4B83D5F8.7010108@cs.man.ac.uk>
References: <d0ee827d1002230423h530e1ddr78285cb18bbe4f9a@mail.gmail.com>
	<4B83D5F8.7010108@cs.man.ac.uk>
Message-ID: <d0ee827d1002230630k180f4347n89d66b215864edbe@mail.gmail.com>

>Can we wait until the next release?
It came to light because of the NAR paper. If it doesn't harm it then we can
wait... George may know better

Is this new release going first on the test site before going live?

Franck

On 23 February 2010 13:19, Jiten Bhagat <jits at cs.man.ac.uk> wrote:

> Can we wait until the next release?
>
> I know it doesn't really mean much, but this release will be a BIG one
> and there might be some issues cropping up later that we hadn't
> envisioned (or just bugs!), so it I don't want us to claim that we are a
> fully production ready system just yet!
>
> Jits
>
>
> Franck Tanoh wrote:
> > Hi guys,
> > Are we getting rid of 'beta' in the logo for this release?  Last time
> > I spoke to Carole she was fine with that. I think we have a task on
> > rubyforge for that.
> >
> > cheers,
> > 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
> >
>
>


-- 
"Science knows no country, because knowledge belongs to humanity, and is the
torch which illuminates the world." - Louis Pasteur
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From jits at cs.man.ac.uk  Tue Feb 23 09:34:49 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 23 Feb 2010 14:34:49 +0000
Subject: [BioCatalogue-developers] bye bye beta?
In-Reply-To: <d0ee827d1002230630k180f4347n89d66b215864edbe@mail.gmail.com>
References: <d0ee827d1002230423h530e1ddr78285cb18bbe4f9a@mail.gmail.com>	
	<4B83D5F8.7010108@cs.man.ac.uk>
	<d0ee827d1002230630k180f4347n89d66b215864edbe@mail.gmail.com>
Message-ID: <4B83E789.2000905@cs.man.ac.uk>

Franck Tanoh wrote:
> >Can we wait until the next release?
> It came to light because of the NAR paper. If it doesn't harm it then
> we can wait... George may know better

Ah ok. It would be great if you could find out.

>
> Is this new release going first on the test site before going live?

Definitely! We're working on tying some lose ends right now. So the
release will be delayed a bit.

Jits

>
> Franck
>
> On 23 February 2010 13:19, Jiten Bhagat <jits at cs.man.ac.uk
> <mailto:jits at cs.man.ac.uk>> wrote:
>
>     Can we wait until the next release?
>
>     I know it doesn't really mean much, but this release will be a BIG one
>     and there might be some issues cropping up later that we hadn't
>     envisioned (or just bugs!), so it I don't want us to claim that we
>     are a
>     fully production ready system just yet!
>
>     Jits
>
>
>     Franck Tanoh wrote:
>     > Hi guys,
>     > Are we getting rid of 'beta' in the logo for this release?  Last
>     time
>     > I spoke to Carole she was fine with that. I think we have a task on
>     > rubyforge for that.
>     >
>     > cheers,
>     > 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 Feb 23 10:05:00 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 23 Feb 2010 10:05:00 -0500 (EST)
Subject: [BioCatalogue-developers] [1596] branches/integration-jan10/app:
 REST API work: initial implementation of /test_results/{id} (XML).
Message-ID: <20100223150500.3CFBC18582C2@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 23 10:11:15 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 23 Feb 2010 10:11:15 -0500 (EST)
Subject: [BioCatalogue-developers] [1597] branches/integration-jan10: REST
 API work: added <filters> link to < related> for <annotations>.
Message-ID: <20100223151115.545301598081@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 23 10:35:25 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 23 Feb 2010 10:35:25 -0500 (EST)
Subject: [BioCatalogue-developers] [1598] branches/integration-jan10/app:
 REST API work: initial implementation of /test_results (XML) with the
 ability to filter by a specific Service Test.
Message-ID: <20100223153526.01D841598096@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 23 11:05:41 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 23 Feb 2010 11:05:41 -0500 (EST)
Subject: [BioCatalogue-developers] [1599]
 branches/integration-jan10/app/views: REST API work: bugfixes for certain
 outputs.
Message-ID: <20100223160541.B058F167830F@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 23 11:21:03 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 23 Feb 2010 11:21:03 -0500 (EST)
Subject: [BioCatalogue-developers] [1600] branches/integration-jan10:
 changes to test script creation process,
 especially in relation to associated service test
Message-ID: <20100223162103.BCAC818582CA@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 23 11:46:38 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 23 Feb 2010 11:46:38 -0500 (EST)
Subject: [BioCatalogue-developers] [1601] branches/integration-jan10: REST
 API work: implemented / annotation_attributes/{id}/annotations endpoint
 (both XML and JSON).
Message-ID: <20100223164638.634A11598086@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 23 13:07:36 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 23 Feb 2010 13:07:36 -0500 (EST)
Subject: [BioCatalogue-developers] [1602]
 branches/integration-jan10/lib/bio_catalogue/monitoring/status.rb: give
 more information on the services which failed for overall status
Message-ID: <20100223180736.E633418582C2@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 23 14:18:08 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 23 Feb 2010 14:18:08 -0500 (EST)
Subject: [BioCatalogue-developers] [1603]
 branches/integration-jan10/lib/bio_catalogue/monitoring/status.rb: service
 status message give info about failed tests.
Message-ID: <20100223191808.9E8991598098@rubyforge.org>

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From noreply at rubyforge.org  Tue Feb 23 14:24:55 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 23 Feb 2010 14:24:55 -0500 (EST)
Subject: [BioCatalogue-developers] [1604]
 branches/integration-jan10/script/biocatalogue/
 embrace_test_scripts_import.rb: remove db config values
Message-ID: <20100223192455.EC9011598086@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 24 06:14:44 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 24 Feb 2010 06:14:44 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2923] Implemented descriptions
	pages for annotation attributes
Message-ID: <20100224111445.00E4A185828E@rubyforge.org>

Task #2923 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Implemented descriptions pages for annotation attributes
Complete: 0%
Status: Open

Description: So things like:

http://biocatalogue.org/attribute/description

... have a page and are not just empty URLs.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2923&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Wed Feb 24 06:23:01 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 24 Feb 2010 06:23:01 -0500 (EST)
Subject: [BioCatalogue-developers] [1605] branches/integration-jan10: REST
	API work:
Message-ID: <20100224112301.93F961598081@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 24 06:26:05 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 24 Feb 2010 06:26:05 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2923] Implement descriptions pages
	for annotation attributes
Message-ID: <20100224112605.9EAD618582D3@rubyforge.org>

Task #2923 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Implement descriptions pages for annotation attributes
Complete: 0%
Status: Open

Description: So things like:

http://biocatalogue.org/attribute/description

... have a page and are not just empty URLs.

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2923&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Wed Feb 24 06:32:29 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 24 Feb 2010 06:32:29 -0500 (EST)
Subject: [BioCatalogue-developers] [1606]
 branches/integration-jan10/app/models: bugfix,
 missing require test_id during service_test creation
Message-ID: <20100224113229.E842518582D5@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 24 10:53:39 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 24 Feb 2010 10:53:39 -0500 (EST)
Subject: [BioCatalogue-developers] [1607]
 branches/integration-jan10/public/2009/xml/rest/schema-v1.xsd: REST API
 work: schema for <testResults> and <testResult>.
Message-ID: <20100224155339.9F67418582DC@rubyforge.org>

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From jerzyo at genesilico.pl  Wed Feb 24 12:37:02 2010
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Wed, 24 Feb 2010 18:37:02 +0100
Subject: [BioCatalogue-developers] bye bye beta?
In-Reply-To: <4B83E789.2000905@cs.man.ac.uk>
References: <d0ee827d1002230423h530e1ddr78285cb18bbe4f9a@mail.gmail.com>		<4B83D5F8.7010108@cs.man.ac.uk>	<d0ee827d1002230630k180f4347n89d66b215864edbe@mail.gmail.com>
	<4B83E789.2000905@cs.man.ac.uk>
Message-ID: <4B8563BE.6010103@genesilico.pl>

When is the big release if it's 2 weeks from now, it's OK.
Is it the one with embrace finally moved?
If so than I suggest waiting.


George


Jiten Bhagat wrote:
> Franck Tanoh wrote:
>   
>>> Can we wait until the next release?
>>>       
>> It came to light because of the NAR paper. If it doesn't harm it then
>> we can wait... George may know better
>>     
>
> Ah ok. It would be great if you could find out.
>
>   
>> Is this new release going first on the test site before going live?
>>     
>
> Definitely! We're working on tying some lose ends right now. So the
> release will be delayed a bit.
>
> Jits
>
>   
>> Franck
>>
>> On 23 February 2010 13:19, Jiten Bhagat <jits at cs.man.ac.uk
>> <mailto:jits at cs.man.ac.uk>> wrote:
>>
>>     Can we wait until the next release?
>>
>>     I know it doesn't really mean much, but this release will be a BIG one
>>     and there might be some issues cropping up later that we hadn't
>>     envisioned (or just bugs!), so it I don't want us to claim that we
>>     are a
>>     fully production ready system just yet!
>>
>>     Jits
>>
>>
>>     Franck Tanoh wrote:
>>     > Hi guys,
>>     > Are we getting rid of 'beta' in the logo for this release?  Last
>>     time
>>     > I spoke to Carole she was fine with that. I think we have a task on
>>     > rubyforge for that.
>>     >
>>     > cheers,
>>     > 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
>>     
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>
>
>
>   


From noreply at rubyforge.org  Wed Feb 24 14:48:43 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 24 Feb 2010 14:48:43 -0500 (EST)
Subject: [BioCatalogue-developers] [1608] branches/integration-jan10: using
 better auth for test scripts and more appropriate rendering on success &
 failure
Message-ID: <20100224194843.B72E118582D2@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 24 15:11:05 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 24 Feb 2010 15:11:05 -0500 (EST)
Subject: [BioCatalogue-developers] [1609]
 branches/integration-jan10/app/controllers/test_scripts_controller. rb: add
 layout to partial rendering on test script submit error
Message-ID: <20100224201105.C144D18582EC@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 24 15:14:45 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 24 Feb 2010 15:14:45 -0500 (EST)
Subject: [BioCatalogue-developers] [1610]
 branches/integration-jan10/app/controllers/test_scripts_controller. rb:
 change of flash message
Message-ID: <20100224201445.1F58118582D8@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 24 17:51:24 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 24 Feb 2010 17:51:24 -0500 (EST)
Subject: [BioCatalogue-developers] [1611]
 branches/integration-jan10/app/models/test_script.rb: better validation
 error messages
Message-ID: <20100224225124.DD76118582E3@rubyforge.org>

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From noreply at rubyforge.org  Wed Feb 24 19:22:31 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Wed, 24 Feb 2010 19:22:31 -0500 (EST)
Subject: [BioCatalogue-developers] [1612]
 branches/integration-jan10/script/biocatalogue/
 embrace_test_scripts_import.rb: add debug messages
Message-ID: <20100225002231.2B20B18582E7@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 06:26:25 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 06:26:25 -0500 (EST)
Subject: [BioCatalogue-developers] [1613]
 branches/integration-jan10/public/2009/xml/rest/schema-v1.xsd: REST API
 work: schema for <serviceTest>.
Message-ID: <20100225112626.08AAF1588033@rubyforge.org>

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From jits at cs.man.ac.uk  Thu Feb 25 06:29:33 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Thu, 25 Feb 2010 11:29:33 +0000
Subject: [BioCatalogue-developers] bye bye beta?
In-Reply-To: <4B8563BE.6010103@genesilico.pl>
References: <d0ee827d1002230423h530e1ddr78285cb18bbe4f9a@mail.gmail.com>		<4B83D5F8.7010108@cs.man.ac.uk>	<d0ee827d1002230630k180f4347n89d66b215864edbe@mail.gmail.com>	<4B83E789.2000905@cs.man.ac.uk>
	<4B8563BE.6010103@genesilico.pl>
Message-ID: <4B865F1D.4080208@cs.man.ac.uk>

Hi George,

Jerzy Orlowski wrote:
> When is the big release if it's 2 weeks from now, it's OK.
> Is it the one with embrace finally moved?

Yes.

> If so than I suggest waiting.

Okay. I'll wait to remove the beta until the *next* release, which
should be in about 2 weeks.

Jits

>
>
> George
>
>
> Jiten Bhagat wrote:
>> Franck Tanoh wrote:
>>  
>>>> Can we wait until the next release?
>>>>       
>>> It came to light because of the NAR paper. If it doesn't harm it then
>>> we can wait... George may know better
>>>     
>>
>> Ah ok. It would be great if you could find out.
>>
>>  
>>> Is this new release going first on the test site before going live?
>>>     
>>
>> Definitely! We're working on tying some lose ends right now. So the
>> release will be delayed a bit.
>>
>> Jits
>>
>>  
>>> Franck
>>>
>>> On 23 February 2010 13:19, Jiten Bhagat <jits at cs.man.ac.uk
>>> <mailto:jits at cs.man.ac.uk>> wrote:
>>>
>>>     Can we wait until the next release?
>>>
>>>     I know it doesn't really mean much, but this release will be a
>>> BIG one
>>>     and there might be some issues cropping up later that we hadn't
>>>     envisioned (or just bugs!), so it I don't want us to claim that we
>>>     are a
>>>     fully production ready system just yet!
>>>
>>>     Jits
>>>
>>>
>>>     Franck Tanoh wrote:
>>>     > Hi guys,
>>>     > Are we getting rid of 'beta' in the logo for this release?  Last
>>>     time
>>>     > I spoke to Carole she was fine with that. I think we have a
>>> task on
>>>     > rubyforge for that.
>>>     >
>>>     > cheers,
>>>     > 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
>>>     
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>
>>
>>
>>   
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From noreply at rubyforge.org  Thu Feb 25 06:59:20 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 06:59:20 -0500 (EST)
Subject: [BioCatalogue-developers] [1614]
 branches/integration-jan10/app/metal/linked_data_handler.rb: Fix to Linked
 Data handler - now we deal with XML, JSON and ATOM requests explcitly.
Message-ID: <20100225115920.AEEA318582F3@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 07:04:01 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 07:04:01 -0500 (EST)
Subject: [BioCatalogue-developers] [1615]
 branches/integration-jan10/app/metal/linked_data_handler.rb: Update to
 comments.
Message-ID: <20100225120401.EFF3718582F3@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 07:25:54 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 07:25:54 -0500 (EST)
Subject: [BioCatalogue-developers] [1616]
 branches/integration-jan10/public/2009/xml/rest/schema-v1.xsd: REST API
 work: schema for <monitoring> section of <service>.
Message-ID: <20100225122555.1A4CD18582F3@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 07:36:10 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 07:36:10 -0500 (EST)
Subject: [BioCatalogue-developers] [1617]
 branches/integration-jan10/script/biocatalogue/api/tests/
 xml_schema_validations.rb: REST API work: more tests.
Message-ID: <20100225123610.94DB018582F4@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 07:36:38 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 07:36:38 -0500 (EST)
Subject: [BioCatalogue-developers] [1618]
 branches/integration-jan10/script/biocatalogue/api/tests/config.yml. pre:
 REST API work: updated tests config.
Message-ID: <20100225123638.DB9AB18582F3@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 07:57:02 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 07:57:02 -0500 (EST)
Subject: [BioCatalogue-developers] [1619] branches/integration-jan10: REST
	API work: various fixes.
Message-ID: <20100225125702.4768E18582EA@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 07:57:46 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 07:57:46 -0500 (EST)
Subject: [BioCatalogue-developers] [1620]
 branches/integration-jan10/script/biocatalogue/api/tests/
 xml_schema_validations.rb: REST API work: added a test for /annotations/
 filters.
Message-ID: <20100225125746.D569B18582EA@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 08:02:06 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 08:02:06 -0500 (EST)
Subject: [BioCatalogue-developers] [1621] branches/integration-jan10: REST
 API work: more fixes from schema tests.
Message-ID: <20100225130206.930AF18582EA@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 08:49:37 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 08:49:37 -0500 (EST)
Subject: [BioCatalogue-developers] [1622]
 branches/integration-jan10/app/controllers/test_scripts_controller. rb:
 change permissions for who is allowed to create a test script
Message-ID: <20100225134937.3FA4F18582AC@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 09:26:37 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 09:26:37 -0500 (EST)
Subject: [BioCatalogue-developers] [1623]
 branches/integration-jan10/app/models/test_script.rb: Added some debugging
 logging.
Message-ID: <20100225142637.3FDC018582F4@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 09:27:43 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 09:27:43 -0500 (EST)
Subject: [BioCatalogue-developers] [1624]
 branches/integration-jan10/db/schema.rb: Updated db schema to latest .
Message-ID: <20100225142743.F057F18582DF@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 09:51:54 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 09:51:54 -0500 (EST)
Subject: [BioCatalogue-developers] [1625]
 branches/integration-jan10/app/views/api/filtering/_filters.xml. builder:
 REST API work: fixes.
Message-ID: <20100225145154.3630018582C2@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 10:13:54 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 10:13:54 -0500 (EST)
Subject: [BioCatalogue-developers] [1626] branches/integration-jan10: REST
 API work: implemented roots_only=( true|false) parameter for /categories.
Message-ID: <20100225151354.DCFF518582F4@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 10:19:12 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 10:19:12 -0500 (EST)
Subject: [BioCatalogue-developers] [Task #2926] external link open in a new
	tab or window
Message-ID: <20100225151912.3105918582DF@rubyforge.org>

Task #2926 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: external link open in a new tab or window
Complete: 0%
Status: Open

Description: Will be extremely useful if any external link e.g documentation URL could open in a new tab or window. otherwise navigation is sometimes  difficult (a lot of click on the 'go back' button on firefox) 

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

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2926&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Feb 25 10:55:20 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 10:55:20 -0500 (EST)
Subject: [BioCatalogue-developers] [1627] branches/integration-jan10/app:
 Fixes and consolidation for the ATOM feeds for services and announcements.
Message-ID: <20100225155520.B38D918582F3@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 11:17:16 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 11:17:16 -0500 (EST)
Subject: [BioCatalogue-developers] [1628] branches/integration-jan10/app:
 REST API work: change in the way redirects are handled for sub collections
 like / {resource_type}/{id}/services and /{resource_type}/{id}/annotations.
Message-ID: <20100225161716.2E52718582FA@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 11:19:11 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 11:19:11 -0500 (EST)
Subject: [BioCatalogue-developers] [1629]
 branches/integration-jan10/script/biocatalogue/api/tests/
 xml_schema_validations.rb: REST API work: removed some TODOs in the test.
Message-ID: <20100225161911.3C390185826F@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 11:31:25 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 11:31:25 -0500 (EST)
Subject: [BioCatalogue-developers] [1630]
 branches/integration-jan10/app/controllers/application_controller.rb :
 Updated the HTTP status codes that map to certain ActionController
 exceptions .
Message-ID: <20100225163125.5755418582F3@rubyforge.org>

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From jits at cs.man.ac.uk  Thu Feb 25 11:57:21 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Thu, 25 Feb 2010 16:57:21 +0000
Subject: [BioCatalogue-developers] Request
Message-ID: <4B86ABF1.2060207@cs.man.ac.uk>

Could I get this redirect put in place please...

http://apidocs.biocatalogue.org   ---->  
http://www.biocatalogue.org/wiki/doku.php?id=public:api

Jits

From noreply at rubyforge.org  Thu Feb 25 12:02:36 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 12:02:36 -0500 (EST)
Subject: [BioCatalogue-developers] [1631] branches/integration-jan10: REST
 API work: updated the root < biocatalogue> resource.
Message-ID: <20100225170236.91EF318582FA@rubyforge.org>

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From noreply at rubyforge.org  Thu Feb 25 13:38:08 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 25 Feb 2010 13:38:08 -0500 (EST)
Subject: [BioCatalogue-developers] [1632]
 branches/integration-jan10/app/models/test_script.rb: allow other flavors
 of the zip content type
Message-ID: <20100225183808.7BFF118582C1@rubyforge.org>

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From ericnzuo at ebi.ac.uk  Thu Feb 25 14:06:25 2010
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 25 Feb 2010 19:06:25 +0000
Subject: [BioCatalogue-developers] Request
In-Reply-To: <4B86ABF1.2060207@cs.man.ac.uk>
References: <4B86ABF1.2060207@cs.man.ac.uk>
Message-ID: <4B86CA31.9020207@ebi.ac.uk>

Will follow this up..

Eric


Jiten Bhagat wrote:
> Could I get this redirect put in place please...
>
> http://apidocs.biocatalogue.org   ---->  
> http://www.biocatalogue.org/wiki/doku.php?id=public:api
>
> Jits
>   

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From ericnzuo at ebi.ac.uk  Thu Feb 25 14:16:46 2010
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 25 Feb 2010 19:16:46 +0000
Subject: [BioCatalogue-developers] content types on file upload
Message-ID: <4B86CC9E.5080708@ebi.ac.uk>

Hi Jits,

I have been reading around of what people do to determine the file type. 
The one that most people seem to use a system command 'file'. I am not 
keen on going down this route because the system dependencies. It turns 
out from my testing that adding a shebang line to the file make it to be 
interpreted properly. Also, i think it matters on whether the file has 
sufficient content. Could you try uploading a real ruby file like the 
one attached?

Eric

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From jits at cs.man.ac.uk  Fri Feb 26 09:45:45 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 26 Feb 2010 14:45:45 +0000
Subject: [BioCatalogue-developers] content types on file upload
In-Reply-To: <4B86CC9E.5080708@ebi.ac.uk>
References: <4B86CC9E.5080708@ebi.ac.uk>
Message-ID: <4B87DE99.8030602@cs.man.ac.uk>

> Also, i think it matters on whether the file has sufficient content.
> Could you try uploading a real ruby file like the one attached? 

I don't think this matters. I've tried with the file you mentioned and I
still get this...

"Content type is not allowed. Allowed file types are zip, xml, python,
perl, and ruby"

Jits


Eric Nzuobontane wrote:
> Hi Jits,
>
> I have been reading around of what people do to determine the file
> type. The one that most people seem to use a system command 'file'. I
> am not keen on going down this route because the system dependencies.
> It turns out from my testing that adding a shebang line to the file
> make it to be interpreted properly. Also, i think it matters on
> whether the file has sufficient content. Could you try uploading a
> real ruby file like the one attached?
>
> Eric
>


From noreply at rubyforge.org  Fri Feb 26 09:53:55 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 26 Feb 2010 09:53:55 -0500 (EST)
Subject: [BioCatalogue-developers] [1633]
 branches/integration-jan10/app/views/tags/api/_related_links.xml. builder:
 REST API work: bugfix for the /tags/{name} endpoint (XML).
Message-ID: <20100226145355.E729318582EE@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 26 11:09:21 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 26 Feb 2010 11:09:21 -0500 (EST)
Subject: [BioCatalogue-developers] [1634]
 branches/integration-jan10/app/controllers/application_controller.rb :
 Attempted fixes for IE8.
Message-ID: <20100226160922.0C92918582DD@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 26 13:00:04 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 26 Feb 2010 13:00:04 -0500 (EST)
Subject: [BioCatalogue-developers] [1635] trunk: Merged changesets 1391:1634
 from integration-jan10 into trunk .
Message-ID: <20100226180006.05C0318582F5@rubyforge.org>

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From jits at cs.man.ac.uk  Fri Feb 26 13:01:11 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 26 Feb 2010 18:01:11 +0000
Subject: [BioCatalogue-developers] IMPORTANT: merge for release
Message-ID: <4B880C67.5060508@cs.man.ac.uk>

Hi all,

I've just merged changesets 1391 to 1634 from the integration-jan10
branch into trunk, in prep for the release.

>From now...
- the integration-jan10 branch HAS BEEN DISCONTINUED. Please do not
commit any new code into this branch as it will never make it into
trunk. Best bet is to delete the local checkout from your dev environments.
- trunk needs to be stabilised for the release.

Mannie: I understand that you have some outstanding work left for the
REST services support which is for the next release after this one.
Please carry on working on this locally. Then hopefully some time next
week we'll start a new branch in which we can do all this new work.
Please could you also check one more time in trunk that the new REST
services support work is temporarily disabled and hasn't forgotten anything.

Cheers,
Jits

From noreply at rubyforge.org  Fri Feb 26 13:31:58 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 26 Feb 2010 13:31:58 -0500 (EST)
Subject: [BioCatalogue-developers] [1636]
 trunk/app/helpers/activity_feeds_helper.rb: Reduced size of activity logs
 initial queries.
Message-ID: <20100226183159.0DC3218582AC@rubyforge.org>

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From noreply at rubyforge.org  Fri Feb 26 14:06:30 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 26 Feb 2010 14:06:30 -0500 (EST)
Subject: [BioCatalogue-developers] [1637] trunk: REST API work: various
	fixes for schema.
Message-ID: <20100226190630.819FA18582D5@rubyforge.org>

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From mannie.tags at googlemail.com  Sun Feb 28 09:13:24 2010
From: mannie.tags at googlemail.com (Mannie Tagarira)
Date: Sun, 28 Feb 2010 14:13:24 +0000
Subject: [BioCatalogue-developers] IMPORTANT: merge for release
In-Reply-To: <4B880C67.5060508@cs.man.ac.uk>
References: <4B880C67.5060508@cs.man.ac.uk>
Message-ID: <E8C3077B-AF7D-40D1-B776-2AE899EE9C2A@gmail.com>

Hi Jits,

I have had a quick look at instance on the sandbox.  The REST support stuff has been disabled.  The activity feed still shows traces of some support, but that should not be an issue on the main site since there are ActivityLog objects that are REST support related.  The endpoint tab is disabled, and the edit, base endpoint SHOULD be as well for everyone.

Regards,
Mannie



On 26 Feb 2010, at 18:01, Jiten Bhagat wrote:

> Hi all,
> 
> I've just merged changesets 1391 to 1634 from the integration-jan10
> branch into trunk, in prep for the release.
> 
>> From now...
> - the integration-jan10 branch HAS BEEN DISCONTINUED. Please do not
> commit any new code into this branch as it will never make it into
> trunk. Best bet is to delete the local checkout from your dev environments.
> - trunk needs to be stabilised for the release.
> 
> Mannie: I understand that you have some outstanding work left for the
> REST services support which is for the next release after this one.
> Please carry on working on this locally. Then hopefully some time next
> week we'll start a new branch in which we can do all this new work.
> Please could you also check one more time in trunk that the new REST
> services support work is temporarily disabled and hasn't forgotten anything.
> 
> Cheers,
> Jits
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From noreply at rubyforge.org  Sun Feb 28 13:35:50 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 28 Feb 2010 13:35:50 -0500 (EST)
Subject: [BioCatalogue-developers] [1638] trunk: Work on event logging and
	error handling:
Message-ID: <20100228183550.573BB18582C7@rubyforge.org>

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From jits at cs.man.ac.uk  Sun Feb 28 13:36:42 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Sun, 28 Feb 2010 18:36:42 +0000
Subject: [BioCatalogue-developers] IMPORTANT: merge for release
In-Reply-To: <E8C3077B-AF7D-40D1-B776-2AE899EE9C2A@gmail.com>
References: <4B880C67.5060508@cs.man.ac.uk>
	<E8C3077B-AF7D-40D1-B776-2AE899EE9C2A@gmail.com>
Message-ID: <4B8AB7BA.4080204@cs.man.ac.uk>

Great, cheers Mannie.

Jits


Mannie Tagarira wrote:
> Hi Jits,
>
> I have had a quick look at instance on the sandbox.  The REST support stuff has been disabled.  The activity feed still shows traces of some support, but that should not be an issue on the main site since there are ActivityLog objects that are REST support related.  The endpoint tab is disabled, and the edit, base endpoint SHOULD be as well for everyone.
>
> Regards,
> Mannie
>
>
>
> On 26 Feb 2010, at 18:01, Jiten Bhagat wrote:
>
>   
>> Hi all,
>>
>> I've just merged changesets 1391 to 1634 from the integration-jan10
>> branch into trunk, in prep for the release.
>>
>>     
>>> From now...
>>>       
>> - the integration-jan10 branch HAS BEEN DISCONTINUED. Please do not
>> commit any new code into this branch as it will never make it into
>> trunk. Best bet is to delete the local checkout from your dev environments.
>> - trunk needs to be stabilised for the release.
>>
>> Mannie: I understand that you have some outstanding work left for the
>> REST services support which is for the next release after this one.
>> Please carry on working on this locally. Then hopefully some time next
>> week we'll start a new branch in which we can do all this new work.
>> Please could you also check one more time in trunk that the new REST
>> services support work is temporarily disabled and hasn't forgotten anything.
>>
>> 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  Sun Feb 28 13:54:50 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Sun, 28 Feb 2010 18:54:50 +0000
Subject: [BioCatalogue-developers] Important Rails vulnerability - we need
	to fix for this release
Message-ID: <4B8ABBFA.3070900@cs.man.ac.uk>

Hi Eric,

I brought this up a while back; there's been a severe vulnerability in
Rails 2.x for a while now to do with Unicode characters and XSS injection.

See:
http://weblog.rubyonrails.org/2009/9/4/xss-vulnerability-in-ruby-on-rails
http://tomcopeland.blogs.com/juniordeveloper/2009/09/applying-the-rails-xss-vulnerability-patch.html

We need to urgently patch the live and test systems to fix this. *

I have a hunch that the recent error emails we have been getting is to
do with this. So we should fix this asap.

* Note: I have tried to upgrade our codebase to Rails 2.3.4+, which has
fixed this vulnerability, but was unsuccessful. More time would be
required to upgrade. In the meantime we should at least apply the patches.

Jits

From jits at cs.man.ac.uk  Sun Feb 28 13:57:48 2010
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Sun, 28 Feb 2010 18:57:48 +0000
Subject: [BioCatalogue-developers] Important Rails vulnerability - we
 need	to fix for this release
In-Reply-To: <4B8ABBFA.3070900@cs.man.ac.uk>
References: <4B8ABBFA.3070900@cs.man.ac.uk>
Message-ID: <4B8ABCAC.1050408@cs.man.ac.uk>

Btw, maybe we should freeze Rails into vendor and then apply the patch
to the local frozen version? What do you think?

Jits


Jiten Bhagat wrote:
> Hi Eric,
>
> I brought this up a while back; there's been a severe vulnerability in
> Rails 2.x for a while now to do with Unicode characters and XSS injection.
>
> See:
> http://weblog.rubyonrails.org/2009/9/4/xss-vulnerability-in-ruby-on-rails
> http://tomcopeland.blogs.com/juniordeveloper/2009/09/applying-the-rails-xss-vulnerability-patch.html
>
> We need to urgently patch the live and test systems to fix this. *
>
> I have a hunch that the recent error emails we have been getting is to
> do with this. So we should fix this asap.
>
> * Note: I have tried to upgrade our codebase to Rails 2.3.4+, which has
> fixed this vulnerability, but was unsuccessful. More time would be
> required to upgrade. In the meantime we should at least apply the patches.
>
> Jits
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From noreply at rubyforge.org  Sun Feb 28 16:41:07 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 28 Feb 2010 16:41:07 -0500 (EST)
Subject: [BioCatalogue-developers] [1639] trunk: Performance and style
	improvements for the activity feeds.
Message-ID: <20100228214107.77FDC18582CA@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 28 19:08:08 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 28 Feb 2010 19:08:08 -0500 (EST)
Subject: [BioCatalogue-developers] [1640] trunk: REST API work:
Message-ID: <20100301000808.58C10185828E@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 28 19:17:37 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 28 Feb 2010 19:17:37 -0500 (EST)
Subject: [BioCatalogue-developers] [1641]
	trunk/app/helpers/activity_feeds_helper.rb: Bugfix for some logging
Message-ID: <20100301001737.E2406185828E@rubyforge.org>

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From noreply at rubyforge.org  Sun Feb 28 19:38:14 2010
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 28 Feb 2010 19:38:14 -0500 (EST)
Subject: [BioCatalogue-developers] [1642]
	trunk/app/views/search/show.xml.builder: Some extra debugging code
Message-ID: <20100301003814.57C8018582D5@rubyforge.org>

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