From issues at mygrid.org.uk Wed Dec 1 10:47:52 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 1 Dec 2010 15:47:52 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-548) Investigate why there is a hughe number of search entries in the activity logs with empty search terms Message-ID: <9364871.312.1291218472813.JavaMail.jira@rosalind.cs.man.ac.uk> Investigate why there is a hughe number of search entries in the activity logs with empty search terms ------------------------------------------------------------------------------------------------------ Key: BIOCAT-548 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-548 Project: BioCatalogue Issue Type: Task Components: Data Reporter: Eric Nzuobontane Assignee: Jiten Bhagat It appears that the activity logs indicate a high number of searches. However, the majority of these search are not associated with any search term. This needs to be investigated. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Dec 1 10:49:52 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 1 Dec 2010 15:49:52 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-549) cleanup the application directory Message-ID: <11485269.313.1291218592822.JavaMail.jira@rosalind.cs.man.ac.uk> cleanup the application directory --------------------------------- Key: BIOCAT-549 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-549 Project: BioCatalogue Issue Type: Task Components: Misc Codebase Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane remove all redundant files and folders in the codebase -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Thu Dec 2 05:07:31 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 02 Dec 2010 10:07:31 +0000 Subject: [BioCatalogue-developers] BioCatalogue Live Update Message-ID: <4CF76FE3.7070002@ebi.ac.uk> Hi, The latest code base has been available on test site for a few days now. Live update which was planned for the 1st of December has now been postponed to the 7th of December. This will coincide with the planned maintenance of the systems. This update wil be the last update of the live site for this year except for any bug fixes. I may be away from mid December so we should either get this update in within the next week or may have to wait till the new year. I believe Franck has extensively tested the current codebase. However, further testing would probably not hurt. Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From utopia at cs.man.ac.uk Thu Dec 2 16:17:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 02 Dec 2010 21:17:33 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'BLASTatlas' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'BLASTatlas' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1690 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Dec 3 01:29:47 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 03 Dec 2010 06:29:47 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getPDBIdsFromLigandId' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getPDBIdsFromLigandId' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1107 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Mon Dec 6 12:44:20 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 06 Dec 2010 17:44:20 +0000 Subject: [BioCatalogue-developers] Fwd: [Production ERROR] annotations#create_inline (ActiveRecord::RecordNotSaved) "ActiveRecord::RecordNotSaved" Message-ID: <4CFD20F4.4030904@ebi.ac.uk> Hi Franck, Were you trying to test something? Documentation urls should now be validated for format, which was not happening before. Eric -------- Original Message -------- Subject: [Production ERROR] annotations#create_inline (ActiveRecord::RecordNotSaved) "ActiveRecord::RecordNotSaved" Date: Mon, 6 Dec 2010 16:50:06 +0000 From: BioCatalogue Errors To: ericnzuo at ebi.ac.uk, jits at cs.man.ac.uk, ytanoh at cs.man.ac.uk A ActiveRecord::RecordNotSaved occurred in annotations#create_inline: ActiveRecord::RecordNotSaved [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:2556:in `save_without_validation!' ------------------------------- Request: ------------------------------- * URL : http://test.biocatalogue.org/annotations/create_inline?partial=documentation_urls * Method : POST * IP address: 130.88.195.202 * Parameters: {"commit"=>"Add", "action"=>"create_inline", "authenticity_token"=>"Z0DNKIyz0dO6zFTP4YvQ33UXBZlmFsqIvyc8MHpwRKU=", "partial"=>"documentation_urls", "controller"=>"annotations", "annotation"=>{"value"=>"need to description here ", "annotatable_type"=>"SoapService", "attribute_name"=>"documentation_url", "annotatable_id"=>"2662", "source_type"=>"User", "source_id"=>27}} * Rails root: /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue ------------------------------- Session: ------------------------------- * session id: nil * data: nil ------------------------------- Environment: ------------------------------- * CONTENT_LENGTH : 262 * CONTENT_TYPE : application/x-www-form-urlencoded; charset=UTF-8 * DOCUMENT_ROOT : /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/public * HTTP_ACCEPT : text/javascript, text/html, application/xml, text/xml, */* * HTTP_ACCEPT_CHARSET : ISO-8859-1,utf-8;q=0.7,*;q=0.7 * HTTP_ACCEPT_ENCODING : gzip,deflate * HTTP_ACCEPT_LANGUAGE : en-us,en;q=0.5 * HTTP_CACHE_CONTROL : no-cache * HTTP_CONNECTION : keep-alive * HTTP_CONTENT_TYPE : application/x-www-form-urlencoded; charset=UTF-8 * HTTP_COOKIE : __utma=15951013.2016078177.1289908975.1291569467.1291653929.25; __utmz=15951013.1290603531.18.4.utmcsr=mygrid.org.uk|utmccn=(referral)|utmcmd=referral|utmcct=/; __utmc=15951013; __utmb=15951013.2.10.1291653929; _session_id=6739ca37013104c407ba35c9108a1f0e * HTTP_HOST : test.biocatalogue.org * HTTP_KEEP_ALIVE : 300 * HTTP_PRAGMA : no-cache * HTTP_REFERER : http://test.biocatalogue.org/services/2714 * HTTP_USER_AGENT : Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.15) Gecko/20101026 Firefox/3.5.15 * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 * HTTP_X_PROTOTYPE_VERSION : 1.6.0.3 * HTTP_X_REQUESTED_WITH : XMLHttpRequest * PATH_INFO : /annotations/create_inline * QUERY_STRING : partial=documentation_urls * REMOTE_ADDR : 130.88.195.202 * REMOTE_PORT : 57567 * REQUEST_METHOD : POST * REQUEST_URI : /annotations/create_inline?partial=documentation_urls * SCRIPT_NAME : * SERVER_ADDR : 172.18.1.107 * SERVER_ADMIN : root at localhost * SERVER_NAME : test.biocatalogue.org * SERVER_PORT : 80 * SERVER_PROTOCOL : HTTP/1.1 * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) * _ : _ * action_controller.request.query_parameters : partialdocumentation_urls * action_controller.request.request_parameters: commitAddauthenticity_tokenZ0DNKIyz0dO6zFTP4YvQ33UXBZlmFsqIvyc8MHpwRKU=annotationannotatable_typeSoapServicevalueneed to description here annotatable_id2662attribute_namedocumentation_url * action_controller.rescue.request : # * action_controller.rescue.response : # * rack.errors : # * rack.input : # * rack.multiprocess : true * rack.multithread : false * rack.request : # * rack.request.cookie_hash : __utma15951013.2016078177.1289908975.1291569467.1291653929.25__utmb15951013.2.10.1291653929__utmc15951013_session_id6739ca37013104c407ba35c9108a1f0e__utmz15951013.1290603531.18.4.utmcsr=mygrid.org.uk|utmccn=(referral)|utmcmd=referral|utmcct=/ * rack.request.cookie_string : __utma=15951013.2016078177.1289908975.1291569467.1291653929.25; __utmz=15951013.1290603531.18.4.utmcsr=mygrid.org.uk|utmccn=(referral)|utmcmd=referral|utmcct=/; __utmc=15951013; __utmb=15951013.2.10.1291653929; _session_id=6739ca37013104c407ba35c9108a1f0e * rack.request.form_hash : commitAddauthenticity_tokenZ0DNKIyz0dO6zFTP4YvQ33UXBZlmFsqIvyc8MHpwRKU=annotationvalueneed to description here annotatable_typeSoapServiceattribute_namedocumentation_urlannotatable_id2662 * rack.request.form_input : # * rack.request.form_vars : authenticity_token=Z0DNKIyz0dO6zFTP4YvQ33UXBZlmFsqIvyc8MHpwRKU%3D&annotation%5Bannotatable_type%5D=SoapService&annotation%5Bannotatable_id%5D=2662&annotation%5Battribute_name%5D=documentation_url&annotation%5Bvalue%5D=need%20to%20description%20here%20&commit=Add * rack.request.query_hash : partialdocumentation_urls * rack.request.query_string : partial=documentation_urls * rack.routing_args : actioncreate_inlinecontrollerannotations * rack.run_once : false * rack.session : user_id27previous_url/services/2714use_tab_cookiefalseservices_index_listing_typedetailed_csrf_tokenZ0DNKIyz0dO6zFTP4YvQ33UXBZlmFsqIvyc8MHpwRKU=flash * rack.session.options : securefalseexpire_afterkey_session_idid6739ca37013104c407ba35c9108a1f0ehttponlytruedomaincookie_onlytruepath/ * rack.session.record : # * rack.url_scheme : http * rack.version : 10 * Process: 30427 * Server : pweb-3a * request.format: text/javascript ------------------------------- Backtrace: ------------------------------- [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:2556:in `save_without_validation!' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/validations.rb:1019:in `save_without_dirty!' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/dirty.rb:87:in `save_without_transactions!' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:200:in `save!' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:200:in `save!' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:208:in `rollback_active_record_state!' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:200:in `save!' [RAILS_ROOT]/app/controllers/annotations_controller.rb:138:in `create_inline' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in `send' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in `perform_action_without_filters' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:617:in `call_filters' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:610:in `perform_action_without_benchmark' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in `ms' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:10:in `realtime' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in `ms' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rescue.rb:160:in `perform_action_without_flash' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb:141:in `perform_action' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in `send' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in `process_without_filters' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:606:in `process' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:391:in `process' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:386:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/route_set.rb:433:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:88:in `dispatch' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:111:in `_call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:82:in `initialize' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/methodoverride.rb:24:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/params_parser.rb:15:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rewindable_input.rb:25:in `call' [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in `call' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in `call' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in `cache' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in `cache' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in `call' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `synchronize' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in `call' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in `safe_fork' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in `start' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in `start' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 -------------- next part -------------- An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Dec 7 16:40:57 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 07 Dec 2010 21:40:57 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'NetOGlyc - Prediction of o-GalNAc (mucin type) glycosylation sites in mammalian proteins' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'NetOGlyc - Prediction of o-GalNAc (mucin type) glycosylation sites in mammalian proteins' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1628 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Wed Dec 8 00:51:12 2010 From: ericnzuo at ebi.ac.uk (ericnzuo at ebi.ac.uk) Date: Wed, 8 Dec 2010 05:51:12 -0000 (UTC) Subject: [BioCatalogue-developers] Problems with search Message-ID: <37811.213.106.89.217.1291787472.squirrel@webmail.ebi.ac.uk> Hi, There are problems with search at the moment which I am investigating. The search server is not accepting connections from the application all though it seems to be running. Eric From ericnzuo at ebi.ac.uk Wed Dec 8 01:04:16 2010 From: ericnzuo at ebi.ac.uk (ericnzuo at ebi.ac.uk) Date: Wed, 8 Dec 2010 06:04:16 -0000 (UTC) Subject: [BioCatalogue-developers] Problems with search Message-ID: <47293.213.106.89.217.1291788256.squirrel@webmail.ebi.ac.uk> Hi, There are problems with search at the moment which I am investigating. The search server is not accepting connections from the application all though it seems to be running. Eric From noreply at rubyforge.org Wed Dec 8 12:02:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 8 Dec 2010 12:02:42 -0500 (EST) Subject: [BioCatalogue-developers] [2324] branches/biocat-ree/: Running BioCatalogue under Enterprise Ruby Message-ID: <20101208170242.AB4BE1858357@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Dec 8 12:05:52 2010 From: issues at mygrid.org.uk (Alex Nenadic (JIRA)) Date: Wed, 8 Dec 2010 17:05:52 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-550) Add API BioCatalogue version number to the XML doc returned by GET on http://www.biocatalogue.org with Accept header "application/xml" Message-ID: <23132228.491.1291827952831.JavaMail.jira@rosalind.cs.man.ac.uk> Add API BioCatalogue version number to the XML doc returned by GET on http://www.biocatalogue.org with Accept header "application/xml" -------------------------------------------------------------------------------------------------------------------------------------- Key: BIOCAT-550 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-550 Project: BioCatalogue Issue Type: Bug Components: REST API Reporter: Alex Nenadic Assignee: Jiten Bhagat Fix For: 2010-12 Add API BioCatalogue version number to the XML doc returned by GET on http://www.biocatalogue.org with Accept header "application/xml" so that various plugins can check compliance with the current API. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Dec 9 06:03:18 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 9 Dec 2010 06:03:18 -0500 (EST) Subject: [BioCatalogue-developers] [2325] branches/biocat-ree/config: - added preinitializer config file Message-ID: <20101209110318.6C35A1858363@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Dec 9 06:04:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 9 Dec 2010 06:04:08 -0500 (EST) Subject: [BioCatalogue-developers] [2326] branches/biocat-ree/script/biocatalogue: move scripts from application base to scripts Message-ID: <20101209110408.24CBD185835A@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Dec 9 10:38:45 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 09 Dec 2010 15:38:45 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runNucleosomePotential' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runNucleosomePotential' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1112 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Thu Dec 9 11:30:46 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 9 Dec 2010 11:30:46 -0500 (EST) Subject: [BioCatalogue-developers] [2327] trunk/app/views/services/listing/_grid.html.erb: In the grid view, show "no description" for services without descriptions. Message-ID: <20101209163046.A565F185835E@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Dec 9 11:48:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 09 Dec 2010 16:48:28 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'pathfinding' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'pathfinding' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/2810 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Dec 9 12:10:48 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 09 Dec 2010 17:10:48 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getStructureFromPCZ' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getStructureFromPCZ' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1154 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Dec 9 17:30:15 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 09 Dec 2010 22:30:15 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getBFactorsFromPCZ_Report' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getBFactorsFromPCZ_Report' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1166 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Fri Dec 10 06:06:52 2010 From: issues at mygrid.org.uk (Alex Nenadic (JIRA)) Date: Fri, 10 Dec 2010 11:06:52 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-551) Add sorting by name for the parent Web services. Currenlty sorting only available by "newest" and "earliest". Message-ID: <12751319.530.1291979212833.JavaMail.jira@rosalind.cs.man.ac.uk> Add sorting by name for the parent Web services. Currenlty sorting only available by "newest" and "earliest". ------------------------------------------------------------------------------------------------------------- Key: BIOCAT-551 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-551 Project: BioCatalogue Issue Type: New Feature Components: REST API Reporter: Alex Nenadic Assignee: Jiten Bhagat This is needed for Taverna, see http://www.mygrid.org.uk/dev/issues/browse/T2-1556 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Dec 10 06:06:53 2010 From: issues at mygrid.org.uk (Alex Nenadic (JIRA)) Date: Fri, 10 Dec 2010 11:06:53 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-551) Add sorting by name for the parent Web services. Currenlty sorting only available by "newest" and "earliest". In-Reply-To: <12751319.530.1291979212833.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24652457.531.1291979213791.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-551?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Alex Nenadic updated BIOCAT-551: -------------------------------- Description: Sorting of results needed for Taverna 2.30 release, see http://www.mygrid.org.uk/dev/issues/browse/T2-1556 (was: This is needed for Taverna, see http://www.mygrid.org.uk/dev/issues/browse/T2-1556) > Add sorting by name for the parent Web services. Currenlty sorting only available by "newest" and "earliest". > ------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-551 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-551 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Alex Nenadic > Assignee: Jiten Bhagat > > Sorting of results needed for Taverna 2.30 release, see http://www.mygrid.org.uk/dev/issues/browse/T2-1556 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Dec 10 06:08:52 2010 From: issues at mygrid.org.uk (Alex Nenadic (JIRA)) Date: Fri, 10 Dec 2010 11:08:52 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-551) Add sorting by name for the parent Web services. Currenlty sorting only available by "newest" and "earliest". In-Reply-To: <12751319.530.1291979212833.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7365204.532.1291979332815.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-551?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Alex Nenadic updated BIOCAT-551: -------------------------------- Fix Version/s: 2010-12 > Add sorting by name for the parent Web services. Currenlty sorting only available by "newest" and "earliest". > ------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-551 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-551 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Alex Nenadic > Assignee: Jiten Bhagat > Fix For: 2010-12 > > > Sorting of results needed for Taverna 2.30 release, see http://www.mygrid.org.uk/dev/issues/browse/T2-1556 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Dec 10 07:51:52 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 10 Dec 2010 12:51:52 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-552) Rebuild patched gems and push them to rubygems.org Message-ID: <13349919.538.1291985512811.JavaMail.jira@rosalind.cs.man.ac.uk> Rebuild patched gems and push them to rubygems.org -------------------------------------------------- Key: BIOCAT-552 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-552 Project: BioCatalogue Issue Type: Task Components: Misc Codebase Reporter: Eric Nzuobontane Assignee: Jiten Bhagat Patched: gem rubaidh-google_analytics (1.1.4) -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri Dec 10 09:56:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 10 Dec 2010 09:56:14 -0500 (EST) Subject: [BioCatalogue-developers] [2328] branches/biocat-ree: enable app to use bundler for gem management Message-ID: <20101210145614.C6683167831A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Dec 10 09:59:23 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 10 Dec 2010 09:59:23 -0500 (EST) Subject: [BioCatalogue-developers] [2329] branches/biocat-ree/config/preinitializer.rb.pre: complete commit for using bundler Message-ID: <20101210145923.52DDF185835A@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Dec 10 14:09:14 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 10 Dec 2010 19:09:14 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'ConsensusPathDB' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'ConsensusPathDB' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/188 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Dec 10 14:10:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 10 Dec 2010 19:10:10 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'ConsensusPathDB' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'ConsensusPathDB' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/188 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Dec 10 21:31:05 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 11 Dec 2010 02:31:05 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToMD_TrajectoryDCD' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToMD_TrajectoryDCD' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1125 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Dec 11 15:29:23 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 11 Dec 2010 20:29:23 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'GeneWiz' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'GeneWiz' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1840 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Dec 12 05:07:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 12 Dec 2010 10:07:10 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'BLASTatlas' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'BLASTatlas' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1690 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Dec 13 05:03:03 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 13 Dec 2010 10:03:03 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'pathfinding' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'pathfinding' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/2810 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Tue Dec 14 04:15:55 2010 From: ericnzuo at ebi.ac.uk (ericnzuo at ebi.ac.uk) Date: Tue, 14 Dec 2010 09:15:55 -0000 (UTC) Subject: [BioCatalogue-developers] @home sick Message-ID: <51160.213.106.89.217.1292318155.squirrel@webmail.ebi.ac.uk> I am not well so will be at home today. Will not be working as I have a bad headache. Eric From jits at cs.man.ac.uk Tue Dec 14 08:17:11 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 14 Dec 2010 13:17:11 +0000 Subject: [BioCatalogue-developers] @home sick In-Reply-To: <51160.213.106.89.217.1292318155.squirrel@webmail.ebi.ac.uk> References: <51160.213.106.89.217.1292318155.squirrel@webmail.ebi.ac.uk> Message-ID: <4D076E57.6030003@cs.man.ac.uk> Hi Eric, Hope you're feeling better! When you get a chance, could you put the latest database dump into the dropbox folder please? Thanks, Jits On 14/12/10 09:15, ericnzuo at ebi.ac.uk wrote: > I am not well so will be at home today. Will not be working as I have a > bad headache. > > Eric > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From issues at mygrid.org.uk Wed Dec 15 06:31:52 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 15 Dec 2010 11:31:52 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-553) Fix incorrect parsing of activity logs in similar_searches_report script Message-ID: <3977271.561.1292412712876.JavaMail.jira@rosalind.cs.man.ac.uk> Fix incorrect parsing of activity logs in similar_searches_report script ------------------------------------------------------------------------ Key: BIOCAT-553 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-553 Project: BioCatalogue Issue Type: Bug Components: Misc Codebase Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Minor There is a bug in the similar_searches_report script whereby the query term for search queries made on services index are not correctly taken parsed out. The code uses the 'query' key in the activity log data hash instead of 'q' for the services index activity logs. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Wed Dec 15 07:43:16 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 15 Dec 2010 07:43:16 -0500 (EST) Subject: [BioCatalogue-developers] [2330] trunk/script/biocatalogue/archived_services_report.rb: Initial implementation of a report generation script for archived services . Message-ID: <20101215124316.384AF1858379@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 15 11:50:10 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 15 Dec 2010 11:50:10 -0500 (EST) Subject: [BioCatalogue-developers] [2331] trunk/script/biocatalogue/archived_services_report.rb: Minor tweak to output. Message-ID: <20101215165010.27FFB185838D@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu Dec 16 05:34:11 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 16 Dec 2010 10:34:11 +0000 Subject: [BioCatalogue-developers] @home sick In-Reply-To: <4D076E57.6030003@cs.man.ac.uk> References: <51160.213.106.89.217.1292318155.squirrel@webmail.ebi.ac.uk> <4D076E57.6030003@cs.man.ac.uk> Message-ID: <4D09EB23.4020408@ebi.ac.uk> Done. On 14/12/2010 13:17, Jiten Bhagat wrote: > Hi Eric, > > Hope you're feeling better! > > When you get a chance, could you put the latest database dump into the > dropbox folder please? > > Thanks, > Jits > > > On 14/12/10 09:15, ericnzuo at ebi.ac.uk wrote: >> I am not well so will be at home today. Will not be working as I have a >> bad headache. >> >> Eric >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Thu Dec 16 08:32:18 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 16 Dec 2010 08:32:18 -0500 (EST) Subject: [BioCatalogue-developers] [2332] trunk/script/biocatalogue/api_usage_report.rb: Initial implementation of a report generation script for generating an API usage report . Message-ID: <20101216133218.B62D51858346@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Thu Dec 16 10:07:25 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 16 Dec 2010 15:07:25 +0000 Subject: [BioCatalogue-developers] new 2010 roadmap Message-ID: Hi guys, Take a look before it goes live: http://www.biocatalogue.org/wiki/doku.php?id=public_staging:roadmap Cheers, Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu Dec 16 10:55:56 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 16 Dec 2010 15:55:56 +0000 Subject: [BioCatalogue-developers] new 2010 roadmap In-Reply-To: References: Message-ID: <4D0A368C.4040904@cs.man.ac.uk> Hi, Pretty much all of Q4 belongs in 2011 because they haven't been released yet :( We need to think of other things to add for Q4. Eric, anything? For 2011 roadmap, please can you add the bits from my slides attached. Add these to the very top of the list. Jits On 16/12/10 15:07, Franck Tanoh wrote: > Hi guys, > > Take a look before it goes live: > http://www.biocatalogue.org/wiki/doku.php?id=public_staging:roadmap > > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ProposedTechRoadmap.ppt Type: application/vnd.ms-powerpoint Size: 104960 bytes Desc: not available URL: From ericnzuo at ebi.ac.uk Thu Dec 16 11:44:14 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 16 Dec 2010 16:44:14 +0000 Subject: [BioCatalogue-developers] new 2010 roadmap In-Reply-To: <4D0A368C.4040904@cs.man.ac.uk> References: <4D0A368C.4040904@cs.man.ac.uk> Message-ID: <4D0A41DE.1080608@ebi.ac.uk> I agree with Jits and nothing to add from here. I am going home now. Hopefully I will be well enough to be back tomorrow! Eric On 16/12/2010 15:55, Jiten Bhagat wrote: > Hi, > > Pretty much all of Q4 belongs in 2011 because they haven't been > released yet :( > > We need to think of other things to add for Q4. Eric, anything? > > For 2011 roadmap, please can you add the bits from my slides attached. > Add these to the very top of the list. > > Jits > > > On 16/12/10 15:07, Franck Tanoh wrote: >> Hi guys, >> >> Take a look before it goes live: >> http://www.biocatalogue.org/wiki/doku.php?id=public_staging:roadmap >> >> 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 > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Thu Dec 16 11:57:57 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 16 Dec 2010 16:57:57 +0000 Subject: [BioCatalogue-developers] new 2010 roadmap In-Reply-To: <4D0A368C.4040904@cs.man.ac.uk> References: <4D0A368C.4040904@cs.man.ac.uk> Message-ID: >We need to think of other things to add for Q4. Eric, anything? If there's nothing I'll just leave it the way it is now. After all they are on the test site. >For 2011 roadmap, please can you add the bits from my slides attached. >Add these to the very top of the list. done Franck On 16 December 2010 15:55, Jiten Bhagat wrote: > Hi, > > Pretty much all of Q4 belongs in 2011 because they haven't been released > yet :( > > We need to think of other things to add for Q4. Eric, anything? > > For 2011 roadmap, please can you add the bits from my slides attached. Add > these to the very top of the list. > > Jits > > > > On 16/12/10 15:07, Franck Tanoh wrote: > > Hi guys, > > Take a look before it goes live: > http://www.biocatalogue.org/wiki/doku.php?id=public_staging:roadmap > > Cheers, > Franck > > -- > "Science knows no country, because knowledge belongs to humanity, and is > the torch which illuminates the world." - Louis Pasteur > > > _______________________________________________ > BioCatalogue-developers mailing listBioCatalogue-developers at rubyforge.orghttp://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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Sun Dec 19 02:10:27 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 19 Dec 2010 07:10:27 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runSLR' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runSLR' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1096 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Dec 19 02:12:42 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 19 Dec 2010 07:12:42 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getStatisticalLog' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getStatisticalLog' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1073 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Dec 19 02:31:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 19 Dec 2010 07:31:33 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'SIMPA protein secondary structure prediction (CNRS IBCP)' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'SIMPA protein secondary structure prediction (CNRS IBCP)' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/272 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Dec 20 02:40:01 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 20 Dec 2010 07:40:01 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'MkDom2' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'MkDom2' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1899 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Dec 20 07:01:50 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 20 Dec 2010 12:01:50 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'MkDom2' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'MkDom2' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1899 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Dec 20 07:02:07 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 20 Dec 2010 12:02:07 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'MkDom2' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'MkDom2' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1899 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue Dec 21 08:43:11 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 21 Dec 2010 08:43:11 -0500 (EST) Subject: [BioCatalogue-developers] [2333] trunk/lib/bio_catalogue/jobs/solr_delete.rb: background task to perform solr deletes Message-ID: <20101221134311.68797185837B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 21 08:45:50 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 21 Dec 2010 08:45:50 -0500 (EST) Subject: [BioCatalogue-developers] [2334] trunk/vendor/plugins/acts_as_solr/lib/common_methods.rb: perform solr delete in background process Message-ID: <20101221134551.7D88D185837F@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Dec 24 15:57:32 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 24 Dec 2010 20:57:32 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'phosphoELMdb' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'phosphoELMdb' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/115 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Dec 24 15:59:45 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 24 Dec 2010 20:59:45 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'phosphoELMdb' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'phosphoELMdb' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/115 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Dec 24 16:06:20 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 24 Dec 2010 21:06:20 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'phosphoELMdb' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'phosphoELMdb' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/115 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Dec 24 16:08:34 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 24 Dec 2010 21:08:34 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'phosphoELMdb' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'phosphoELMdb' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/115 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Dec 24 16:15:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 24 Dec 2010 21:15:10 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'phosphoELMdb' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'phosphoELMdb' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/115 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Dec 24 16:17:25 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 24 Dec 2010 21:17:25 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'phosphoELMdb' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'phosphoELMdb' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/115 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Dec 26 14:02:46 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 26 Dec 2010 19:02:46 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:zipTrajectory' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:zipTrajectory' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1168 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Dec 28 10:27:59 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 28 Dec 2010 15:27:59 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'The ELM Resource Structure Filter' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'The ELM Resource Structure Filter' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1620 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Dec 29 22:04:03 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 30 Dec 2010 03:04:03 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getPropertySequenceFromFeatureAASequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getPropertySequenceFromFeatureAASequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1167 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Dec 30 18:14:47 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 30 Dec 2010 23:14:47 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getHingePointsWithFCMethodFromPCZ_Report' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getHingePointsWithFCMethodFromPCZ_Report' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1159 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Dec 30 18:26:23 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 30 Dec 2010 23:26:23 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getStiffnessFromPCZ_Report' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getStiffnessFromPCZ_Report' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1162 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Dec 30 21:02:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 31 Dec 2010 02:02:33 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getAverageStructure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getAverageStructure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1150 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Dec 30 21:08:19 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 31 Dec 2010 02:08:19 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToMD_TrajectoryCRD' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToMD_TrajectoryCRD' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1120 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Dec 30 21:19:54 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 31 Dec 2010 02:19:54 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:cleanStructureFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:cleanStructureFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1142 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Fri Dec 31 10:02:52 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 31 Dec 2010 15:02:52 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-554) Tab not remembered on Service Provider page Message-ID: <5817156.591.1293807772914.JavaMail.jira@rosalind.cs.man.ac.uk> Tab not remembered on Service Provider page ------------------------------------------- Key: BIOCAT-554 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-554 Project: BioCatalogue Issue Type: Bug Components: Web Interface Reporter: Carole Goble Assignee: Jiten Bhagat Priority: Critical Fix For: 2010-12 When browsing on a Service Provider's page in the catalogue the last selected tab is not remembered when paging through the services. Use the same cookie mechanism used on other tabbed pages (eg: service profile page) to ensure the right tab is selected on page loads. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Dec 31 10:06:52 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 31 Dec 2010 15:06:52 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-555) Ability to search within collections of Services Message-ID: <27592347.592.1293808012808.JavaMail.jira@rosalind.cs.man.ac.uk> Ability to search within collections of Services ------------------------------------------------ Key: BIOCAT-555 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-555 Project: BioCatalogue Issue Type: New Feature Components: Search / Filtering / Browsing, Web Interface Reporter: Carole Goble Assignee: Jiten Bhagat When browsing collections of services, for example the 'Services' tab on the Service Provider or User pages, it is currently not possible to *search within* just that collection. Have the ability to browse within that set of services only. This is an alternative way of browsing for services, similar to filtering. It may be possible to reuse the filtering mechanism here. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Fri Dec 31 13:52:08 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 31 Dec 2010 18:52:08 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'UniProt' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'UniProt' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/162 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team