From ericnzuo at ebi.ac.uk Fri Mar 4 09:14:11 2011 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 04 Mar 2011 14:14:11 +0000 Subject: [BioCatalogue-developers] svn repository In-Reply-To: References: <4D70B303.1080903@ebi.ac.uk> Message-ID: <4D70F3B3.7030608@ebi.ac.uk> yes something has changed! Password authentication has been disabled. So now one has to setup ssh keys! http://www.eggheadcafe.com/software/aspnet/36326990/rubyforge-ssh-authentication-change.aspx On 04/03/2011 09:42, Jits at cs.man.ac.uk wrote: > Hi Eric, > > Nothing should have changed as far as I know. I'll investigate when I'm > back in the office on Tuesday. > > Jits > > >> Hi Jits, >> >> Has anything changed with the rubyforge repository? I just tried to >> update my code and hit permission issues. I thought maybe something to >> do with eclipse so I tried to checkout for a clean location and still >> hit the same permission issues. Just wondering if anything has changed. >> >> 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 >> ================================== >> >> -- 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 ericnzuo at ebi.ac.uk Fri Mar 4 11:48:59 2011 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 04 Mar 2011 16:48:59 +0000 Subject: [BioCatalogue-developers] test script server Message-ID: <4D7117FB.2050302@ebi.ac.uk> We need a way to submit the test scripts results without using my account. I am not sure how we go about that. Also, we need to decide which emails should receive the application error emails. Ideally this should not be personal emails as we will be in the same situation when other people leave 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 ericnzuo at ebi.ac.uk Mon Mar 7 05:36:31 2011 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 07 Mar 2011 10:36:31 +0000 Subject: [BioCatalogue-developers] rubyforge svn Message-ID: <4D74B52F.50506@ebi.ac.uk> http://rubyforge.org/tracker/index.php?func=detail&aid=29057&group_id=5&atid=102 -- 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 issues at mygrid.org.uk Mon Mar 7 08:18:28 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 7 Mar 2011 13:18:28 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-568) Double rendering problem when ssl is switched on! In-Reply-To: <27513129.446.1297168809437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3717172.87.1299503908003.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16546#comment-16546 ] Eric Nzuobontane commented on BIOCAT-568: ----------------------------------------- *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. ****** LinkedDataHandler metal app... Intial URL: /services Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000282) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true *** @current_filters = {} ****** LinkedDataHandler metal app... Intial URL: /services/2713 Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000328) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true ****** LinkedDataHandler metal app... Intial URL: /search/auto_complete 0.000000 0.000000 0.000000 ( 0.000016) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = Failed to get query suggestions. Error message: No such file or directory - / /data/search_query_suggestions.txt. ****** LinkedDataHandler metal app... Intial URL: /search?q=test&commit= Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.010000 0.010000 ( 0.002477) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true ****** LinkedDataHandler metal app... Intial URL: /search?page=2&q=test&scope=services Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000300) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true ****** LinkedDataHandler metal app... Intial URL: /search?page=3&q=test&scope=services Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000294) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true ****** LinkedDataHandler metal app... Intial URL: /services/2393 Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000290) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true [ pid=10365 file=ext/apache2/Hooks.cpp:676 time=2011-03-07 12:48:53.390 ]: Either the vistor clicked on the 'Stop' button in the web browser, or the visitor's connection has stalled and couldn't receive the data that Apache is sending to it. As a result, you will probably see a 'Broken Pipe' error in this log file. Please ignore it, this is normal. You might also want to increase Apache's TimeOut configuration option if you experience this problem often. *** Exception Errno::ECONNRESET in Passenger RequestHandler (Connection reset by peer) (process 10392): from ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:109:in `write' from ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:109:in `process_request' from trunk_2371/vendor/rails/actionpack/lib/action_controller/response.rb:155:in `each_line' from /trunk_2371/vendor/rails/actionpack/lib/action_controller/response.rb:155:in `each' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:108:in `process_request' from ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_request_handler.rb:207:in `main_loop' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:441:in `start_request_handler' from /build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:381:in `handle_spawn_application' from ruby/build/passenger-2.2.15/lib/phusion_passenger/utils.rb:252:in `safe_fork' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:377:in `handle_spawn_application' from ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:163:in `start' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:222:in `start' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:253:in `spawn_rails_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:247:in `spawn_rails_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:246:in `spawn_rails_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:145:in `spawn_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:278:in `handle_spawn_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' from /ruby/build/passenger-2.2.15/bin/passenger-spawn-server:61 ****** LinkedDataHandler metal app... Intial URL: /services Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000286) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true *** @current_filters = {} ****** LinkedDataHandler metal app... Intial URL: /services?su=%5B2%5D Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000300) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true *** @current_filters = {:su=>["2"]} ****** LinkedDataHandler metal app... Intial URL: /services/137 Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000332) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true ****** LinkedDataHandler metal app... Intial URL: /services/137 Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000357) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true ****** LinkedDataHandler metal app... Intial URL: /services/137 Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000295) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true ****** LinkedDataHandler metal app... Intial URL: /services/137 Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000285) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true > Double rendering problem when ssl is switched on! > ------------------------------------------------- > > Key: BIOCAT-568 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568 > Project: BioCatalogue > Issue Type: Bug > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > Application issues a double rendering error when ssl is switched on. This has a major impact on all secure pages like loggin -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Mar 7 08:20:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 7 Mar 2011 13:20:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-568) Double rendering problem when ssl is switched on! In-Reply-To: <27513129.446.1297168809437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5034671.88.1299504027775.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16547#comment-16547 ] Eric Nzuobontane commented on BIOCAT-568: ----------------------------------------- Error messages in the apache file above are not the most helpful. But that is all there is to this error. > Double rendering problem when ssl is switched on! > ------------------------------------------------- > > Key: BIOCAT-568 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568 > Project: BioCatalogue > Issue Type: Bug > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > Application issues a double rendering error when ssl is switched on. This has a major impact on all secure pages like loggin -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Tue Mar 8 05:27:19 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 08 Mar 2011 10:27:19 +0000 Subject: [BioCatalogue-developers] svn repository In-Reply-To: <4D70F3B3.7030608@ebi.ac.uk> References: <4D70B303.1080903@ebi.ac.uk> <4D70F3B3.7030608@ebi.ac.uk> Message-ID: <4D760487.7000707@cs.man.ac.uk> Ahhh! I have been using SSH keys all this time hence why I didn't notice this. Good to know! Thanks, Jits On 04/03/11 14:14, Eric Nzuobontane wrote: > yes something has changed! Password authentication has been disabled. > So now one has to setup ssh keys! > http://www.eggheadcafe.com/software/aspnet/36326990/rubyforge-ssh-authentication-change.aspx > > > > On 04/03/2011 09:42, Jits at cs.man.ac.uk wrote: >> Hi Eric, >> >> Nothing should have changed as far as I know. I'll investigate when I'm >> back in the office on Tuesday. >> >> Jits >> >> >>> Hi Jits, >>> >>> Has anything changed with the rubyforge repository? I just tried to >>> update my code and hit permission issues. I thought maybe something to >>> do with eclipse so I tried to checkout for a clean location and still >>> hit the same permission issues. Just wondering if anything has changed. >>> >>> 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 noreply at rubyforge.org Tue Mar 8 06:23:58 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 8 Mar 2011 06:23:58 -0500 (EST) Subject: [BioCatalogue-developers] [2372] trunk/app/views/services/show.html.erb: Potential fix for missing < script> begging tag not being rendered ( when running under REE in the new VM set up). Message-ID: <20110308112358.550F71858376@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 8 06:50:59 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 8 Mar 2011 06:50:59 -0500 (EST) Subject: [BioCatalogue-developers] [2373] trunk/app/views/services/show.html.erb: Edited the comments at the bottom of the file. Message-ID: <20110308115059.8AB871858376@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Mar 8 09:12:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 8 Mar 2011 14:12:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-568) Double rendering problem when ssl is switched on! In-Reply-To: <27513129.446.1297168809437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5048328.94.1299593547849.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16546#comment-16546 ] Eric Nzuobontane edited comment on BIOCAT-568 at 08/03/11 14:12: ----------------------------------------------------------------- *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true *** @current_filters = {} ****** [ pid=10365 file=ext/apache2/Hooks.cpp:676 time=2011-03-07 12:48:53.390 ]: Either the vistor clicked on the 'Stop' button in the web browser, or the visitor's connection has stalled and couldn't receive the data that Apache is sending to it. As a result, you will probably see a 'Broken Pipe' error in this log file. Please ignore it, this is normal. You might also want to increase Apache's TimeOut configuration option if you experience this problem often. *** Exception Errno::ECONNRESET in Passenger RequestHandler (Connection reset by peer) (process 10392): from ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:109:in `write' from ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:109:in `process_request' from trunk_2371/vendor/rails/actionpack/lib/action_controller/response.rb:155:in `each_line' from /trunk_2371/vendor/rails/actionpack/lib/action_controller/response.rb:155:in `each' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:108:in `process_request' from ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_request_handler.rb:207:in `main_loop' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:441:in `start_request_handler' from /build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:381:in `handle_spawn_application' from ruby/build/passenger-2.2.15/lib/phusion_passenger/utils.rb:252:in `safe_fork' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:377:in `handle_spawn_application' from ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:163:in `start' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:222:in `start' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:253:in `spawn_rails_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:247:in `spawn_rails_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:246:in `spawn_rails_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:145:in `spawn_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:278:in `handle_spawn_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' from /ruby/build/passenger-2.2.15/bin/passenger-spawn-server:61 was (Author: eric): *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. ****** LinkedDataHandler metal app... Intial URL: /services Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000282) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true *** @current_filters = {} ****** LinkedDataHandler metal app... Intial URL: /services/2713 Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000328) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true ****** LinkedDataHandler metal app... Intial URL: /search/auto_complete 0.000000 0.000000 0.000000 ( 0.000016) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = Failed to get query suggestions. Error message: No such file or directory - / /data/search_query_suggestions.txt. ****** LinkedDataHandler metal app... Intial URL: /search?q=test&commit= Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.010000 0.010000 ( 0.002477) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true ****** LinkedDataHandler metal app... Intial URL: /search?page=2&q=test&scope=services Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000300) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true ****** LinkedDataHandler metal app... Intial URL: /search?page=3&q=test&scope=services Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000294) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true ****** LinkedDataHandler metal app... Intial URL: /services/2393 Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000290) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true [ pid=10365 file=ext/apache2/Hooks.cpp:676 time=2011-03-07 12:48:53.390 ]: Either the vistor clicked on the 'Stop' button in the web browser, or the visitor's connection has stalled and couldn't receive the data that Apache is sending to it. As a result, you will probably see a 'Broken Pipe' error in this log file. Please ignore it, this is normal. You might also want to increase Apache's TimeOut configuration option if you experience this problem often. *** Exception Errno::ECONNRESET in Passenger RequestHandler (Connection reset by peer) (process 10392): from ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:109:in `write' from ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:109:in `process_request' from trunk_2371/vendor/rails/actionpack/lib/action_controller/response.rb:155:in `each_line' from /trunk_2371/vendor/rails/actionpack/lib/action_controller/response.rb:155:in `each' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:108:in `process_request' from ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_request_handler.rb:207:in `main_loop' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:441:in `start_request_handler' from /build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:381:in `handle_spawn_application' from ruby/build/passenger-2.2.15/lib/phusion_passenger/utils.rb:252:in `safe_fork' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:377:in `handle_spawn_application' from ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:163:in `start' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:222:in `start' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:253:in `spawn_rails_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:247:in `spawn_rails_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:246:in `spawn_rails_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:145:in `spawn_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:278:in `handle_spawn_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' from /ruby/build/passenger-2.2.15/bin/passenger-spawn-server:61 ****** LinkedDataHandler metal app... Intial URL: /services Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000286) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true *** @current_filters = {} ****** LinkedDataHandler metal app... Intial URL: /services?su=%5B2%5D Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000300) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true *** @current_filters = {:su=>["2"]} ****** LinkedDataHandler metal app... Intial URL: /services/137 Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000332) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true ****** LinkedDataHandler metal app... Intial URL: /services/137 Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000357) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true ****** LinkedDataHandler metal app... Intial URL: /services/137 Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000295) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true ****** LinkedDataHandler metal app... Intial URL: /services/137 Linked Data compliance: non XML, ATOM, JSON or BLJSON request, so not 303'ing for now... 0.000000 0.000000 0.000000 ( 0.000285) ****** *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true > Double rendering problem when ssl is switched on! > ------------------------------------------------- > > Key: BIOCAT-568 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568 > Project: BioCatalogue > Issue Type: Bug > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > Application issues a double rendering error when ssl is switched on. This has a major impact on all secure pages like loggin -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Mar 8 09:18:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 8 Mar 2011 14:18:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-568) Double rendering problem when ssl is switched on! In-Reply-To: <27513129.446.1297168809437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <368068.95.1299593907823.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16548#comment-16548 ] Eric Nzuobontane commented on BIOCAT-568: ----------------------------------------- Can't log out from browser session iff ssl is switched on for on an active connection(session) Processing SessionsController#destroy (for 172.22.68.234 at 2011-03-08 14:04:22) [DELETE] Parameters: {"action"=>"destroy", "_method"=>"delete", "authenticity_token"=>"7smX/EMgXgP32826ocPFj0+/pMmzWKxmSKIE/p4/1mw=", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/logout Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 7ms (DB: 4) | 302 Found [http://test.biocatalogue.org/logout] Processing ApplicationController#index (for 172.22.68.234 at 2011-03-08 14:04:44) [GET] ActionController::MethodNotAllowed (Only delete requests are allowed.): /passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:92:in `process_request' /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_request_handler.rb:207:in `main_loop' /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:441:in `start_request_handler' /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:381:in `handle_spawn_application' /ruby/build/passenger-2.2.15/lib/phusion_passenger/utils.rb:252:in `safe_fork' /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:377:in `handle_spawn_application' /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:163:in `start' /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:222:in `start' /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:253:in `spawn_rails_application' /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:247:in `spawn_rails_application' /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:246:in `spawn_rails_application' /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:145:in `spawn_application' /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:278:in `handle_spawn_application' /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' Rendering template within layouts/application_error Rendering /biocatalogue/test/trunk_2371/app/views/error/500.html.erb (500 Internal Server Error) Rendered layouts/_head_tabber_pre (6.7ms) Rendered layouts/_feed_link_tags (6.2ms) Rendered layouts/_head_browser_overrides (2.5ms) Rendered layouts/_head (50.0ms) > Double rendering problem when ssl is switched on! > ------------------------------------------------- > > Key: BIOCAT-568 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568 > Project: BioCatalogue > Issue Type: Bug > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > Application issues a double rendering error when ssl is switched on. This has a major impact on all secure pages like loggin -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Mar 8 09:22:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 8 Mar 2011 14:22:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-568) Double rendering problem when ssl is switched on! In-Reply-To: <27513129.446.1297168809437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9706828.96.1299594147815.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16549#comment-16549 ] Eric Nzuobontane commented on BIOCAT-568: ----------------------------------------- Processing SessionsController#create (for 172.22.68.234 at 2011-03-08 14:18:27) [POST] Parameters: {"commit"=>"Sign in", "action"=>"create", "authenticity_token"=>"MyPVloZv4E1ZGNeztzhatASkY6v1OgL1RIyKLpDGWAM=", "controller"=>"sessions", "login"=>"ericnzuo at ebi.ac.uk", "password"=>"[FILTERED]"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 4) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 11) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 13) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 14) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 20) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] > Double rendering problem when ssl is switched on! > ------------------------------------------------- > > Key: BIOCAT-568 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568 > Project: BioCatalogue > Issue Type: Bug > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > Application issues a double rendering error when ssl is switched on. This has a major impact on all secure pages like loggin -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Mar 8 09:24:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 8 Mar 2011 14:24:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-568) Double rendering problem when ssl is switched on! In-Reply-To: <27513129.446.1297168809437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11450632.97.1299594267797.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16549#comment-16549 ] Eric Nzuobontane edited comment on BIOCAT-568 at 08/03/11 14:22: ----------------------------------------------------------------- Processing SessionsController#create (for 172.22.68.234 at 2011-03-08 14:18:27) [POST] Parameters: {"commit"=>"Sign in", "action"=>"create", "authenticity_token"=>"MyPVloZv4E1ZGNeztzhatASkY6v1OgL1RIyKLpDGWAM=", "controller"=>"sessions", "login"=>"somebody at example.com", "password"=>"[FILTERED]"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 4) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 11) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 13) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 14) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 20) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] was (Author: eric): Processing SessionsController#create (for 172.22.68.234 at 2011-03-08 14:18:27) [POST] Parameters: {"commit"=>"Sign in", "action"=>"create", "authenticity_token"=>"MyPVloZv4E1ZGNeztzhatASkY6v1OgL1RIyKLpDGWAM=", "controller"=>"sessions", "login"=>"ericnzuo at ebi.ac.uk", "password"=>"[FILTERED]"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 4) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 11) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 13) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:27) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 14) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 20) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] Processing SessionsController#show (for 172.22.68.234 at 2011-03-08 14:18:28) [GET] Parameters: {"action"=>"show", "controller"=>"sessions"} Redirected to https://test.biocatalogue.org/session Filter chain halted as [:ensure_proper_protocol] rendered_or_redirected. Completed in 2ms (DB: 3) | 302 Found [http://test.biocatalogue.org/session] > Double rendering problem when ssl is switched on! > ------------------------------------------------- > > Key: BIOCAT-568 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568 > Project: BioCatalogue > Issue Type: Bug > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > Application issues a double rendering error when ssl is switched on. This has a major impact on all secure pages like loggin -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Mar 8 09:26:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 8 Mar 2011 14:26:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-568) Double rendering problem when ssl is switched on! In-Reply-To: <27513129.446.1297168809437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31435156.98.1299594387783.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane updated BIOCAT-568: ------------------------------------ Comment: was deleted (was: *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. Activity feed entry was blank for ActivityLog record: #. It could be that the activity_loggable, culprit or referenced has been deleted. *** DEBUG MESSAGES *** ActionController#request.format = # ActionController#request.format.html? = true *** @current_filters = {} ****** [ pid=10365 file=ext/apache2/Hooks.cpp:676 time=2011-03-07 12:48:53.390 ]: Either the vistor clicked on the 'Stop' button in the web browser, or the visitor's connection has stalled and couldn't receive the data that Apache is sending to it. As a result, you will probably see a 'Broken Pipe' error in this log file. Please ignore it, this is normal. You might also want to increase Apache's TimeOut configuration option if you experience this problem often. *** Exception Errno::ECONNRESET in Passenger RequestHandler (Connection reset by peer) (process 10392): from ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:109:in `write' from ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:109:in `process_request' from trunk_2371/vendor/rails/actionpack/lib/action_controller/response.rb:155:in `each_line' from /trunk_2371/vendor/rails/actionpack/lib/action_controller/response.rb:155:in `each' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:108:in `process_request' from ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_request_handler.rb:207:in `main_loop' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:441:in `start_request_handler' from /build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:381:in `handle_spawn_application' from ruby/build/passenger-2.2.15/lib/phusion_passenger/utils.rb:252:in `safe_fork' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:377:in `handle_spawn_application' from ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:163:in `start' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:222:in `start' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:253:in `spawn_rails_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:247:in `spawn_rails_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:246:in `spawn_rails_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:145:in `spawn_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:278:in `handle_spawn_application' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' from /ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' from /ruby/build/passenger-2.2.15/bin/passenger-spawn-server:61 ) > Double rendering problem when ssl is switched on! > ------------------------------------------------- > > Key: BIOCAT-568 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568 > Project: BioCatalogue > Issue Type: Bug > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > Application issues a double rendering error when ssl is switched on. This has a major impact on all secure pages like loggin -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Mar 9 05:43:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 9 Mar 2011 10:43:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-581) Service to look at as an example of a rest service with a wadl Message-ID: <10076359.100.1299667407766.JavaMail.jira@rosalind.cs.man.ac.uk> Service to look at as an example of a rest service with a wadl -------------------------------------------------------------- Key: BIOCAT-581 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-581 Project: BioCatalogue Issue Type: Task Reporter: Eric Nzuobontane Assignee: Jiten Bhagat Priority: Minor For a service with wadl to look at http://www.ebi.ac.uk/QuickGO/WebServices.html http://www.ebi.ac.uk/QuickGO/clients/QuickGO.wadl -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Mar 9 06:17:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 9 Mar 2011 11:17:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-582) Send a reminders to maintainers of services with tests that have been failing for a while to update their services/tests Message-ID: <27093980.101.1299669447777.JavaMail.jira@rosalind.cs.man.ac.uk> Send a reminders to maintainers of services with tests that have been failing for a while to update their services/tests ------------------------------------------------------------------------------------------------------------------------ Key: BIOCAT-582 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-582 Project: BioCatalogue Issue Type: Task Reporter: Eric Nzuobontane Assignee: Jiten Bhagat As the monitoring only sends out mail when there is a status change, some tests might fail for a while without the service owner noticing. A manual prompt could/should be made once in a while to remind service owners of services that need attention. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Mar 9 07:08:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 9 Mar 2011 12:08:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-583) Possible resource of interest! Message-ID: <13325920.102.1299672507778.JavaMail.jira@rosalind.cs.man.ac.uk> Possible resource of interest! ------------------------------ Key: BIOCAT-583 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-583 Project: BioCatalogue Issue Type: Task Reporter: Eric Nzuobontane Assignee: Jiten Bhagat EMAIL: maya.kennard at yahoo.com QUERY TYPE: EBI HELP: BioCatalogue Support DATE: Wednesday 11 February 2009, 17:24 Hello, I wanted to bring to your attention a web-resource for your resources list. VADLO - Biomedical & Life Sciences Search Engine Vadlo is an academic, open-access, life sciences search engine created by two biology scientists. In addition to other biology research related categories, it is also a good resource for academic lectures/powerpoints. References: vadlo.com/VADLO_References.html Daily Research Cartoons: vadlo.com/Daily_Research_Cartoon.html Website: vadlo.com Thanks. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Wed Mar 9 09:31:40 2011 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 09 Mar 2011 14:31:40 +0000 Subject: [BioCatalogue-developers] http://loadimpact.com/ Message-ID: <4D778F4C.70101@ebi.ac.uk> Might be of interest for quick free load test http://loadimpact.com/ -- 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 jits at cs.man.ac.uk Wed Mar 9 09:38:03 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 09 Mar 2011 14:38:03 +0000 Subject: [BioCatalogue-developers] http://loadimpact.com/ In-Reply-To: <4D778F4C.70101@ebi.ac.uk> References: <4D778F4C.70101@ebi.ac.uk> Message-ID: <4D7790CB.2040000@cs.man.ac.uk> LOL... sounds like an easy way for someone to carry out some denial of service attacks! Jits On 09/03/11 14:31, Eric Nzuobontane wrote: > Might be of interest for quick free load test http://loadimpact.com/ > From ericnzuo at ebi.ac.uk Wed Mar 9 10:29:57 2011 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 09 Mar 2011 15:29:57 +0000 Subject: [BioCatalogue-developers] http://loadimpact.com/ In-Reply-To: <4D7790CB.2040000@cs.man.ac.uk> References: <4D778F4C.70101@ebi.ac.uk> <4D7790CB.2040000@cs.man.ac.uk> Message-ID: <4D779CF5.5090203@ebi.ac.uk> Are we all that vulnerable? Maybe we should remove 'ab' from unix/linux systems as u can achieve the same with it... Eric On 09/03/2011 14:38, Jiten Bhagat wrote: > LOL... sounds like an easy way for someone to carry out some denial of > service attacks! > > Jits > > > On 09/03/11 14:31, Eric Nzuobontane wrote: >> Might be of interest for quick free load test http://loadimpact.com/ >> > > _______________________________________________ > 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 jits at cs.man.ac.uk Wed Mar 9 10:33:16 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 09 Mar 2011 15:33:16 +0000 Subject: [BioCatalogue-developers] http://loadimpact.com/ In-Reply-To: <4D779CF5.5090203@ebi.ac.uk> References: <4D778F4C.70101@ebi.ac.uk> <4D7790CB.2040000@cs.man.ac.uk> <4D779CF5.5090203@ebi.ac.uk> Message-ID: <4D779DBC.2010001@cs.man.ac.uk> Oh yeah; my comment was mostly tongue-in-cheek :) The first thought that came to me was "outsourcing DOS attacks" (which is essentially what DDOS is!) It does look like a very useful tool. Thanks. Jits On 09/03/11 15:29, Eric Nzuobontane wrote: > Are we all that vulnerable? Maybe we should remove 'ab' from > unix/linux systems as u can achieve the same with it... > > Eric > > > On 09/03/2011 14:38, Jiten Bhagat wrote: >> LOL... sounds like an easy way for someone to carry out some denial >> of service attacks! >> >> Jits >> >> >> On 09/03/11 14:31, Eric Nzuobontane wrote: >>> Might be of interest for quick free load test http://loadimpact.com/ >>> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > From noreply at rubyforge.org Mon Mar 14 08:33:27 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 14 Mar 2011 08:33:27 -0400 (EDT) Subject: [BioCatalogue-developers] [2374] trunk/app/controllers/users_controller.rb: fix ordering of status notification listing in user profile Message-ID: <20110314123330.6A30C185836C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 14 09:04:56 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 14 Mar 2011 09:04:56 -0400 (EDT) Subject: [BioCatalogue-developers] [2375] trunk/app/controllers/users_controller.rb: Message-ID: <20110314130456.E64B018581F3@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue Mar 15 05:28:29 2011 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 15 Mar 2011 09:28:29 +0000 Subject: [BioCatalogue-developers] Moving to REE and VM Message-ID: <4D7F313D.3000502@ebi.ac.uk> Hi Jits, Like I mentioned yesterday, we intend to switch the application environment to REE and VM this afternoon. I will let you know when that has happened. 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 noreply at rubyforge.org Tue Mar 15 08:40:39 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 15 Mar 2011 08:40:39 -0400 (EDT) Subject: [BioCatalogue-developers] [2376] trunk/lib/tasks/eb-eye_dump.rake: fixed bug that was crashing eb-eye dump generation Message-ID: <20110315124040.369271678162@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue Mar 15 10:59:08 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 15 Mar 2011 14:59:08 +0000 Subject: [BioCatalogue-developers] Moving to REE and VM In-Reply-To: <4D7F313D.3000502@ebi.ac.uk> References: <4D7F313D.3000502@ebi.ac.uk> Message-ID: <4D7F7EBC.3000903@cs.man.ac.uk> Excellent! Thanks for letting me know, Eric. Best of luck... Jits On 15/03/11 09:28, Eric Nzuobontane wrote: > Hi Jits, > > Like I mentioned yesterday, we intend to switch the application > environment to REE and VM this afternoon. I will let you know when > that has happened. > > Eric > From ericnzuo at ebi.ac.uk Tue Mar 15 11:25:26 2011 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 15 Mar 2011 15:25:26 +0000 Subject: [BioCatalogue-developers] Moving to REE and VM In-Reply-To: <4D7F7EBC.3000903@cs.man.ac.uk> References: <4D7F313D.3000502@ebi.ac.uk> <4D7F7EBC.3000903@cs.man.ac.uk> Message-ID: <4D7F84E6.7000006@ebi.ac.uk> That is actually done now. So the live site is now also running on VMs. Eric On 15/03/2011 14:59, Jiten Bhagat wrote: > Excellent! Thanks for letting me know, Eric. > > Best of luck... > > Jits > > > On 15/03/11 09:28, Eric Nzuobontane wrote: >> Hi Jits, >> >> Like I mentioned yesterday, we intend to switch the application >> environment to REE and VM this afternoon. I will let you know when >> that has happened. >> >> 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 jits at cs.man.ac.uk Tue Mar 15 10:44:15 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 15 Mar 2011 14:44:15 +0000 Subject: [BioCatalogue-developers] Moving to REE and VM In-Reply-To: <4D7F313D.3000502@ebi.ac.uk> References: <4D7F313D.3000502@ebi.ac.uk> Message-ID: <4D7F7B3F.1060807@cs.man.ac.uk> Excellent! Thanks for letting me know, Eric. Best of luck... Jits On 15/03/11 09:28, Eric Nzuobontane wrote: > Hi Jits, > > Like I mentioned yesterday, we intend to switch the application > environment to REE and VM this afternoon. I will let you know when > that has happened. > > Eric > From noreply at rubyforge.org Tue Mar 15 13:11:13 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 15 Mar 2011 13:11:13 -0400 (EDT) Subject: [BioCatalogue-developers] [2377] trunk/lib/tasks/eb-eye_dump.rake: minor bugfix in eb-eye dump task Message-ID: <20110315171113.70F371858377@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Mar 17 06:18:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 17 Mar 2011 10:18:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-584) Stop monitoring of the test site Message-ID: <18223488.107.1300357107911.JavaMail.jira@rosalind.cs.man.ac.uk> Stop monitoring of the test site -------------------------------- Key: BIOCAT-584 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-584 Project: BioCatalogue Issue Type: Task Components: Service Monitoring Affects Versions: 1.0.0 Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Priority: Minor Fix For: 1.0.0 Stop monitoring of the test site as no one is really checking these and they are redundant given the live site monitoring -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Mar 17 07:02:38 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 17 Mar 2011 11:02:38 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-584) Stop monitoring of the test site In-Reply-To: <18223488.107.1300357107911.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14171968.108.1300359758999.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-584?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16566#comment-16566 ] Jiten Bhagat commented on BIOCAT-584: ------------------------------------- Isn't the point of this to check that the monitoring sub-system is working as expected? Maybe it's worth limiting the monitoring on the test site to a handful of services only? > Stop monitoring of the test site > -------------------------------- > > Key: BIOCAT-584 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-584 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Priority: Minor > Fix For: 1.0.0 > > Original Estimate: 1 hour > Remaining Estimate: 1 hour > > Stop monitoring of the test site as no one is really checking these and they are redundant given the live site monitoring -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Thu Mar 17 08:55:57 2011 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 17 Mar 2011 12:55:57 +0000 Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-584) Stop monitoring of the test site In-Reply-To: <14171968.108.1300359758999.JavaMail.jira@rosalind.cs.man.ac.uk> References: <14171968.108.1300359758999.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4D8204DD.7080104@ebi.ac.uk> I do not know what the best solution is. The test script monitoring can easily be limited. The availability would certainly need some work to restrict it. Eric On 17/03/2011 11:02, Jiten Bhagat (JIRA) wrote: > [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-584?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16566#comment-16566 ] > > Jiten Bhagat commented on BIOCAT-584: > ------------------------------------- > > Isn't the point of this to check that the monitoring sub-system is working as expected? > > Maybe it's worth limiting the monitoring on the test site to a handful of services only? > >> Stop monitoring of the test site >> -------------------------------- >> >> Key: BIOCAT-584 >> URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-584 >> Project: BioCatalogue >> Issue Type: Task >> Components: Service Monitoring >> Affects Versions: 1.0.0 >> Reporter: Eric Nzuobontane >> Assignee: Eric Nzuobontane >> Priority: Minor >> Fix For: 1.0.0 >> >> Original Estimate: 1 hour >> Remaining Estimate: 1 hour >> >> Stop monitoring of the test site as no one is really checking these and they are redundant given the live site monitoring -- 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 issues at mygrid.org.uk Thu Mar 17 12:29:37 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 17 Mar 2011 16:29:37 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-123) Get the reliability profile of a service Message-ID: <31683165.110.1300379377824.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-123?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-123. ------------------------------------- Resolution: No longer relevant > Get the reliability profile of a service > ---------------------------------------- > > Key: BIOCAT-123 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-123 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard, Service Monitoring, Web Interface > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > > From the 20Q's, Q3 - > "What is the reliability profile of service X?", "Can I see the usage history of service X?", "who is the provider?", "is it free?" > - Each service should have a profile (reliability, history of use, free, licenses etc) -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Mar 17 12:29:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 17 Mar 2011 16:29:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-123) Get the reliability profile of a service Message-ID: <9159516.109.1300379367943.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-123?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-123. ------------------------------------- Resolution: Incomplete > Get the reliability profile of a service > ---------------------------------------- > > Key: BIOCAT-123 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-123 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard, Service Monitoring, Web Interface > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > > From the 20Q's, Q3 - > "What is the reliability profile of service X?", "Can I see the usage history of service X?", "who is the provider?", "is it free?" > - Each service should have a profile (reliability, history of use, free, licenses etc) -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Mar 17 12:29:42 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 17 Mar 2011 16:29:42 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Reopened: (BIOCAT-123) Get the reliability profile of a service Message-ID: <17870749.111.1300379382415.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-123?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reopened BIOCAT-123: ------------------------------------- > Get the reliability profile of a service > ---------------------------------------- > > Key: BIOCAT-123 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-123 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard, Service Monitoring, Web Interface > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > > From the 20Q's, Q3 - > "What is the reliability profile of service X?", "Can I see the usage history of service X?", "who is the provider?", "is it free?" > - Each service should have a profile (reliability, history of use, free, licenses etc) -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Mar 17 12:32:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 17 Mar 2011 16:32:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-304) Investigate twittering failure on live site Message-ID: <6616078.112.1300379547817.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-304?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-304. ------------------------------------- Resolution: Duplicate > Investigate twittering failure on live site > ------------------------------------------- > > Key: BIOCAT-304 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-304 > Project: BioCatalogue > Issue Type: Bug > Components: Server Management > Environment: RoR > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Priority: Minor > > Tweets fail to be created/sent from the live site to the biocatalogue twitter account. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Mar 17 12:34:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 17 Mar 2011 16:34:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-571) Fix the eb-eye indexing of the biocatalogue database In-Reply-To: <4302731.599.1297418109380.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3045875.113.1300379667797.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-571?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-571. ------------------------------------- Resolution: Fixed eb-eye reads the dumps from data/eb-eye/ > Fix the eb-eye indexing of the biocatalogue database > ---------------------------------------------------- > > Key: BIOCAT-571 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-571 > Project: BioCatalogue > Issue Type: Task > Components: Data > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Labels: indexing > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > BioCatalogue indexing by eb-eye failed when the new codebase was checked out. Investigate!! -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Mar 17 12:34:30 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 17 Mar 2011 16:34:30 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-524) Remove Disqus In-Reply-To: <21784102.541.1289909489152.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3122362.114.1300379670457.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-524?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-524. ------------------------------------- Resolution: Fixed > Remove Disqus > ------------- > > Key: BIOCAT-524 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-524 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > Fix For: 1.0.1 > > > Remove Disqus integration from the site as it has not proven to be effective enough. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Mar 17 12:36:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 17 Mar 2011 16:36:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-52) Write server update script Message-ID: <130988.115.1300379787802.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-52?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-52. ------------------------------------ Resolution: Fixed now available in the local repository > Write server update script > -------------------------- > > Key: BIOCAT-52 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-52 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Write a script for the server update process. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Mar 17 12:38:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 17 Mar 2011 16:38:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-506) Add documentation on how to setup the monitoring on the wiki (BioCatalogue installation) In-Reply-To: <12444050.10333.1288256115454.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6604720.116.1300379907817.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-506?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-506. ------------------------------------- Resolution: Fixed > Add documentation on how to setup the monitoring on the wiki (BioCatalogue installation) > ---------------------------------------------------------------------------------------- > > Key: BIOCAT-506 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-506 > Project: BioCatalogue > Issue Type: Task > Components: Wiki > Environment: wiki > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > Complete the BioCatalogue installation process by adding the monitoring setup instructions. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Mar 17 12:38:30 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 17 Mar 2011 16:38:30 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-76) Add progress bar to soaplab services upload Message-ID: <5912959.117.1300379910250.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-76?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-76. ------------------------------------ Resolution: No longer relevant > Add progress bar to soaplab services upload > ------------------------------------------- > > Key: BIOCAT-76 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-76 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Submission > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > > Uploading hundreds of services from soaplab server can take a while. It will be useful to feedback to the user through a progress bar or some other mechanism -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Mar 17 12:38:32 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 17 Mar 2011 16:38:32 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-477) Parse the biocatalogue content to flag any dead links In-Reply-To: <16018195.9859.1285599555309.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3033998.118.1300379912562.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-477?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-477. ------------------------------------- Resolution: Fixed > Parse the biocatalogue content to flag any dead links > ----------------------------------------------------- > > Key: BIOCAT-477 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-477 > Project: BioCatalogue > Issue Type: Task > Components: Data > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Links within the biocatalogue will become inaccessible from time to time. The object of this task is to flag such links thereby generating a curation event which should be followed up by a human curator. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Mar 17 12:40:27 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 17 Mar 2011 16:40:27 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-210) Setup cron job to reindex on a regular basis Message-ID: <28578770.119.1300380027788.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-210?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-210. ------------------------------------- Resolution: Won't Fix > Setup cron job to reindex on a regular basis > -------------------------------------------- > > Key: BIOCAT-210 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-210 > Project: BioCatalogue > Issue Type: Task > Components: Search / Filtering / Browsing, Server Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > the cron job would make the sure the index is fairly up to date -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon Mar 21 10:19:34 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 21 Mar 2011 10:19:34 -0400 (EDT) Subject: [BioCatalogue-developers] [2378] trunk/app: allow user to be assigned curator privileges from UI by admins Message-ID: <20110321141934.DDA5E185836B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 21 10:25:36 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 21 Mar 2011 10:25:36 -0400 (EDT) Subject: [BioCatalogue-developers] [2379] trunk/config/routes.rb: routes for assigning user curation privileges Message-ID: <20110321142536.599E3185836C@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Mon Mar 21 11:19:24 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 21 Mar 2011 15:19:24 +0000 Subject: [BioCatalogue-developers] Server VM specs etc Message-ID: <4D876C7C.3090506@cs.man.ac.uk> Hi Eric, I've had a look at the info on the new Drupal based docs site, which is very useful. Could you also add info on the exact specs of the VMs? I.e.: how much RAM, what CPU, what OS, what versions of libraries (MySQL, etc). Thanks, Jits From jits at cs.man.ac.uk Mon Mar 21 11:21:50 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 21 Mar 2011 15:21:50 +0000 Subject: [BioCatalogue-developers] Server VM specs etc In-Reply-To: <4D876C7C.3090506@cs.man.ac.uk> References: <4D876C7C.3090506@cs.man.ac.uk> Message-ID: <4D876D0E.4070503@cs.man.ac.uk> Also, info on the Solr and memcache set ups. Thanks, Jits On 21/03/11 15:19, Jiten Bhagat wrote: > Hi Eric, > > I've had a look at the info on the new Drupal based docs site, which > is very useful. Could you also add info on the exact specs of the VMs? > I.e.: how much RAM, what CPU, what OS, what versions of libraries > (MySQL, etc). > > Thanks, > Jits From noreply at rubyforge.org Tue Mar 22 07:08:34 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 22 Mar 2011 07:08:34 -0400 (EDT) Subject: [BioCatalogue-developers] [2380] trunk/config/routes.rb: Minor cleanup Message-ID: <20110322110834.C78CF18583B0@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue Mar 22 07:11:31 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 22 Mar 2011 11:11:31 +0000 Subject: [BioCatalogue-developers] Fwd: [2378] trunk/app: allow user to be assigned curator privileges from UI by admins Message-ID: <4D8883E3.8020707@cs.man.ac.uk> Eric, You introduced the 'new' and 'create' actions to service_responsibles_controller, but looks to me like they are left open for anyone to create ServiceResponsible objects. I.e.: no login or authorisation is currently required. Is this the expected behaviour? Jits -------- Original Message -------- Subject: [BioCatalogue-developers] [2378] trunk/app: allow user to be assigned curator privileges from UI by admins Date: Mon, 21 Mar 2011 10:19:34 -0400 (EDT) From: noreply at rubyforge.org To: biocatalogue-developers at rubyforge.org Revision 2378 Author ebontane Date 2011-03-21 10:19:34 -0400 (Mon, 21 Mar 2011) Log Message allow user to be assigned curator privileges from UI by admins Modified Paths * trunk/app/controllers/service_responsibles_controller.rb <#trunkappcontrollersservice_responsibles_controllerrb> * trunk/app/controllers/users_controller.rb <#trunkappcontrollersusers_controllerrb> * trunk/app/models/user.rb <#trunkappmodelsuserrb> * trunk/app/views/users/show.html.erb <#trunkappviewsusersshowhtmlerb> Diff Modified: trunk/app/controllers/service_responsibles_controller.rb (2377 => 2378) --- trunk/app/controllers/service_responsibles_controller.rb 2011-03-15 17:11:13 UTC (rev 2377) +++ trunk/app/controllers/service_responsibles_controller.rb 2011-03-21 14:19:34 UTC (rev 2378) @@ -13,12 +13,38 @@ before_filter :authorise, :only => [:activate, :deactivate] + def new + @service_responsible = ServiceResponsible.new + + respond_to do |format| + format.html {redirect_to @service_responsible.service} + end + + end + + def create + @service_responsible = ServiceResponsible.new(params[:service_responsible]) + + respond_to do |format| + if @service_responsible.save + flash[:notice] = "New Responsible has been assigned" + format.html{ redirect_to @service_responsible.service} + format.xml {disable_action} + else + flash[:error] = "Could not assign new responsible" + format.html { redirect_to(@service) } + format.xml {disable_action} + end + end + end + + def deactivate respond_to do |format| if @service_responsible.deactivate! flash[:notice] = "
You have been removed from the status notification list for #{@service_responsible.service.display_name}
.
" - format.html{redirect_to(user_url(@service_responsible.user, :id => @service_responsible.user.id, :anchor =>'status-notifications')) } + format.html{redirect_to(user_url(@service_responsible.user, :id => @service_responsible.user.id, :page => @page, :anchor =>'status-notifications')) } format.xml { disable_action } else flash[:notice] = "
Could not remove you from status notification list for #{@service_responsible.service.display_name}
.
" @@ -34,7 +60,7 @@ if @service_responsible if @service_responsible.activate! flash[:notice] = "
You have been added to status notification list for #{@service_responsible.service.display_name}
.
" - format.html{ redirect_to(user_url(@service_responsible.user, :id => @service_responsible.user.id, :anchor =>'status-notifications')) } + format.html{ redirect_to(user_url(@service_responsible.user, :id => @service_responsible.user.id, :page => @page, :anchor =>'status-notifications')) } format.xml { disable_action } else flash[:error] = "
Could not add you to the status notification list for #{@service_responsible.service.display_name}
.
" Modified: trunk/app/controllers/users_controller.rb (2377 => 2378) --- trunk/app/controllers/users_controller.rb 2011-03-15 17:11:13 UTC (rev 2377) +++ trunk/app/controllers/users_controller.rb 2011-03-21 14:19:34 UTC (rev 2378) @@ -30,10 +30,14 @@ before_filter :find_users, :only => [ :index, :filtered_index ] - before_filter :find_user, :only => [ :show, :edit, :update, :change_password, :rpx_update, :annotations_by, :favourites, :services_responsible ] + before_filter :find_user, :only => [ :show, :edit, :update, :change_password, + :rpx_update, :annotations_by, :favourites, + :services_responsible, :make_curator, :remove_curator ] before_filter :add_use_tab_cookie_to_session, :only => [ :show ] + before_filter :authorise, :only => [:make_curator, :remove_curator] + oauth_authorize :saved_searches if ENABLE_SSL&& Rails.env.production? @@ -354,6 +358,38 @@ format.json { render :json => BioCatalogue::Api::Json.collection(@user.active_services_responsible_for) } end end + + def make_curator + respond_to do |format| + if @user + if @user.make_curator! + flash[:notice] = "
#{@user.display_name} is now a curator
.
" + format.html{ redirect_to(user_url(@user)) } + format.xml { disable_action } + else + flash[:error] = "
Could not make user a curator
.
" + format.html{ redirect_to(user_url(@user)) } + format.xml { disable_action } + end + end + end + end + + def remove_curator + respond_to do |format| + if @user + if @user.remove_curator! + flash[:notice] = "
#{@user.display_name} is no longer a curator
.
" + format.html{ redirect_to(user_url(@user)) } + format.xml { disable_action } + else + flash[:error] = "
Could not remove user as a curator
.
" + format.html{ redirect_to(user_url(@user)) } + format.xml { disable_action } + end + end + end + end private @@ -444,5 +480,12 @@ @updated_user.password = nil @updated_user.password_confirmation = nil end + + def authorise + unless logged_in?&& current_user.is_admin? + flash[:error] =" You are not authorised to perform this action" + redirect to @user + end + end end Modified: trunk/app/models/user.rb (2377 => 2378) --- trunk/app/models/user.rb 2011-03-15 17:11:13 UTC (rev 2377) +++ trunk/app/models/user.rb 2011-03-21 14:19:34 UTC (rev 2378) @@ -239,6 +239,33 @@ User.find_all_by_role_id(2) end + # make user an admin + def make_curator! + unless self.is_curator? + begin + self.role_id = 2 + self.save! + return true + rescue Exception => ex + logger.error("There was a problem making user a curator"); + logger.error(ex) + end + end + end + # remove admin privileges + def remove_curator! + unless !self.is_curator? + begin + self.role_id = nil + self.save! + return true + rescue Exception => ex + logger.error("There was a problem removing user as a curator"); + logger.error(ex) + end + end + end + private # Encrypts password with the salt. Modified: trunk/app/views/users/show.html.erb (2377 => 2378) --- trunk/app/views/users/show.html.erb 2011-03-15 17:11:13 UTC (rev 2377) +++ trunk/app/views/users/show.html.erb 2011-03-21 14:19:34 UTC (rev 2378) @@ -9,6 +9,29 @@ %> <% t "#{display_name(@user)}" -%> +<%if logged_in?&& current_user.is_admin? %> + + + + + +<%end%>

<% if mine? @user %> @@ -99,7 +122,6 @@
- <% if mine? @user %>
-------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Attached Message Part URL: From jits at cs.man.ac.uk Tue Mar 22 07:26:53 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 22 Mar 2011 11:26:53 +0000 Subject: [BioCatalogue-developers] test script server In-Reply-To: <4D7117FB.2050302@ebi.ac.uk> References: <4D7117FB.2050302@ebi.ac.uk> Message-ID: <4D88877D.9010209@cs.man.ac.uk> Hi Eric, Did you come up with a solution to this (even if temporary)? Jits On 04/03/11 16:48, Eric Nzuobontane wrote: > We need a way to submit the test scripts results without using my > account. I am not sure how we go about that. Also, we need to decide > which emails should receive the application error emails. Ideally this > should not be personal emails as we will be in the same situation when > other people leave > > Eric > From ericnzuo at ebi.ac.uk Tue Mar 22 08:28:36 2011 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 22 Mar 2011 12:28:36 +0000 Subject: [BioCatalogue-developers] Fwd: [2378] trunk/app: allow user to be assigned curator privileges from UI by admins In-Reply-To: <4D8883E3.8020707@cs.man.ac.uk> References: <4D8883E3.8020707@cs.man.ac.uk> Message-ID: <4D8895F4.3070705@ebi.ac.uk> Sorry, that is a mistake. That was not meant to be committed as it has nothing to do with the commit message. It is part of some uncompleted work which was meant to allow people to assign responsibility. At the moment, it is one way only, from the request side. Please revert that change. Eric On 22/03/2011 11:11, Jiten Bhagat wrote: > Eric, > > You introduced the 'new' and 'create' actions to > service_responsibles_controller, but looks to me like they are left > open for anyone to create ServiceResponsible objects. I.e.: no login > or authorisation is currently required. > > Is this the expected behaviour? > > Jits > > > -------- Original Message -------- > Subject: [BioCatalogue-developers] [2378] trunk/app: allow user to be > assigned curator privileges from UI by admins > Date: Mon, 21 Mar 2011 10:19:34 -0400 (EDT) > From: noreply at rubyforge.org > To: biocatalogue-developers at rubyforge.org > > > > Revision > 2378 > Author > ebontane > Date > 2011-03-21 10:19:34 -0400 (Mon, 21 Mar 2011) > > > Log Message > > allow user to be assigned curator privileges from UI by admins > > > Modified Paths > > * trunk/app/controllers/service_responsibles_controller.rb > <#trunkappcontrollersservice_responsibles_controllerrb> > * trunk/app/controllers/users_controller.rb > <#trunkappcontrollersusers_controllerrb> > * trunk/app/models/user.rb <#trunkappmodelsuserrb> > * trunk/app/views/users/show.html.erb <#trunkappviewsusersshowhtmlerb> > > > Diff > > > Modified: > trunk/app/controllers/service_responsibles_controller.rb (2377 > => 2378) > > > --- trunk/app/controllers/service_responsibles_controller.rb 2011-03-15 17:11:13 UTC (rev 2377) > +++ trunk/app/controllers/service_responsibles_controller.rb 2011-03-21 14:19:34 UTC (rev 2378) > @@ -13,12 +13,38 @@ > before_filter :authorise, :only => [:activate, :deactivate] > > > + def new > + @service_responsible = ServiceResponsible.new > + > + respond_to do |format| > + format.html {redirect_to @service_responsible.service} > + end > + > + end > + > + def create > + @service_responsible = ServiceResponsible.new(params[:service_responsible]) > + > + respond_to do |format| > + if @service_responsible.save > + flash[:notice] = "New Responsible has been assigned" > + format.html{ redirect_to @service_responsible.service} > + format.xml {disable_action} > + else > + flash[:error] = "Could not assign new responsible" > + format.html { redirect_to(@service) } > + format.xml {disable_action} > + end > + end > + end > + > + > def deactivate > > respond_to do |format| > if @service_responsible.deactivate! > flash[:notice] = "
You have been removed from the status notification list for #{@service_responsible.service.display_name}
.
" > - format.html{redirect_to(user_url(@service_responsible.user, :id => @service_responsible.user.id, :anchor =>'status-notifications')) } > + format.html{redirect_to(user_url(@service_responsible.user, :id => @service_responsible.user.id, :page => @page, :anchor =>'status-notifications')) } > format.xml { disable_action } > else > flash[:notice] = "
Could not remove you from status notification list for #{@service_responsible.service.display_name}
.
" > @@ -34,7 +60,7 @@ > if @service_responsible > if @service_responsible.activate! > flash[:notice] = "
You have been added to status notification list for #{@service_responsible.service.display_name}
.
" > - format.html{ redirect_to(user_url(@service_responsible.user, :id => @service_responsible.user.id, :anchor =>'status-notifications')) } > + format.html{ redirect_to(user_url(@service_responsible.user, :id => @service_responsible.user.id, :page => @page, :anchor =>'status-notifications')) } > format.xml { disable_action } > else > flash[:error] = "
Could not add you to the status notification list for #{@service_responsible.service.display_name}
.
" > > > Modified: trunk/app/controllers/users_controller.rb (2377 => 2378) > > > --- trunk/app/controllers/users_controller.rb 2011-03-15 17:11:13 UTC (rev 2377) > +++ trunk/app/controllers/users_controller.rb 2011-03-21 14:19:34 UTC (rev 2378) > @@ -30,10 +30,14 @@ > > before_filter :find_users, :only => [ :index, :filtered_index ] > > - before_filter :find_user, :only => [ :show, :edit, :update, :change_password, :rpx_update, :annotations_by, :favourites, :services_responsible ] > + before_filter :find_user, :only => [ :show, :edit, :update, :change_password, > + :rpx_update, :annotations_by, :favourites, > + :services_responsible, :make_curator, :remove_curator ] > > before_filter :add_use_tab_cookie_to_session, :only => [ :show ] > > + before_filter :authorise, :only => [:make_curator, :remove_curator] > + > oauth_authorize :saved_searches > > if ENABLE_SSL&& Rails.env.production? > @@ -354,6 +358,38 @@ > format.json { render :json => BioCatalogue::Api::Json.collection(@user.active_services_responsible_for) } > end > end > + > + def make_curator > + respond_to do |format| > + if @user > + if @user.make_curator! > + flash[:notice] = "
#{@user.display_name} is now a curator
.
" > + format.html{ redirect_to(user_url(@user)) } > + format.xml { disable_action } > + else > + flash[:error] = "
Could not make user a curator
.
" > + format.html{ redirect_to(user_url(@user)) } > + format.xml { disable_action } > + end > + end > + end > + end > + > + def remove_curator > + respond_to do |format| > + if @user > + if @user.remove_curator! > + flash[:notice] = "
#{@user.display_name} is no longer a curator
.
" > + format.html{ redirect_to(user_url(@user)) } > + format.xml { disable_action } > + else > + flash[:error] = "
Could not remove user as a curator
.
" > + format.html{ redirect_to(user_url(@user)) } > + format.xml { disable_action } > + end > + end > + end > + end > > private > > @@ -444,5 +480,12 @@ > @updated_user.password = nil > @updated_user.password_confirmation = nil > end > + > + def authorise > + unless logged_in?&& current_user.is_admin? > + flash[:error] =" You are not authorised to perform this action" > + redirect to @user > + end > + end > > end > > > Modified: trunk/app/models/user.rb (2377 => 2378) > > > --- trunk/app/models/user.rb 2011-03-15 17:11:13 UTC (rev 2377) > +++ trunk/app/models/user.rb 2011-03-21 14:19:34 UTC (rev 2378) > @@ -239,6 +239,33 @@ > User.find_all_by_role_id(2) > end > > + # make user an admin > + def make_curator! > + unless self.is_curator? > + begin > + self.role_id = 2 > + self.save! > + return true > + rescue Exception => ex > + logger.error("There was a problem making user a curator"); > + logger.error(ex) > + end > + end > + end > + # remove admin privileges > + def remove_curator! > + unless !self.is_curator? > + begin > + self.role_id = nil > + self.save! > + return true > + rescue Exception => ex > + logger.error("There was a problem removing user as a curator"); > + logger.error(ex) > + end > + end > + end > + > private > > # Encrypts password with the salt. > > > Modified: trunk/app/views/users/show.html.erb (2377 => 2378) > > > --- trunk/app/views/users/show.html.erb 2011-03-15 17:11:13 UTC (rev 2377) > +++ trunk/app/views/users/show.html.erb 2011-03-21 14:19:34 UTC (rev 2378) > @@ -9,6 +9,29 @@ > %> > > <% t "#{display_name(@user)}" -%> > +<%if logged_in?&& current_user.is_admin? %> > + > + > + > + > + > +<%end%> > >

> <% if mine? @user %> > @@ -99,7 +122,6 @@ >

> >
> - > <% if mine? @user %> > >
-- 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 noreply at rubyforge.org Tue Mar 22 08:46:54 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 22 Mar 2011 08:46:54 -0400 (EDT) Subject: [BioCatalogue-developers] [2381] trunk/app/controllers/service_responsibles_controller.rb: reverting a commit made in error Message-ID: <20110322124654.45AF01858375@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue Mar 22 09:18:25 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 22 Mar 2011 13:18:25 +0000 Subject: [BioCatalogue-developers] Fwd: [2378] trunk/app: allow user to be assigned curator privileges from UI by admins In-Reply-To: <4D8895F4.3070705@ebi.ac.uk> References: <4D8883E3.8020707@cs.man.ac.uk> <4D8895F4.3070705@ebi.ac.uk> Message-ID: <4D88A1A1.9000807@cs.man.ac.uk> Ahh, okay. Thanks for the explanation! Jits On 22/03/11 12:28, Eric Nzuobontane wrote: > Sorry, that is a mistake. That was not meant to be committed as it has > nothing to do with the commit message. It is part of some uncompleted > work which was meant to allow people to assign responsibility. At the > moment, it is one way only, from the request side. > > Please revert that change. > > Eric > > > On 22/03/2011 11:11, Jiten Bhagat wrote: >> Eric, >> >> You introduced the 'new' and 'create' actions to >> service_responsibles_controller, but looks to me like they are left >> open for anyone to create ServiceResponsible objects. I.e.: no login >> or authorisation is currently required. >> >> Is this the expected behaviour? >> >> Jits >> >> >> -------- Original Message -------- >> Subject: [BioCatalogue-developers] [2378] trunk/app: allow user to >> be assigned curator privileges from UI by admins >> Date: Mon, 21 Mar 2011 10:19:34 -0400 (EDT) >> From: noreply at rubyforge.org >> To: biocatalogue-developers at rubyforge.org >> >> >> >> Revision >> 2378 >> Author >> ebontane >> Date >> 2011-03-21 10:19:34 -0400 (Mon, 21 Mar 2011) >> >> >> Log Message >> >> allow user to be assigned curator privileges from UI by admins >> >> >> Modified Paths >> >> * trunk/app/controllers/service_responsibles_controller.rb >> <#trunkappcontrollersservice_responsibles_controllerrb> >> * trunk/app/controllers/users_controller.rb >> <#trunkappcontrollersusers_controllerrb> >> * trunk/app/models/user.rb <#trunkappmodelsuserrb> >> * trunk/app/views/users/show.html.erb >> <#trunkappviewsusersshowhtmlerb> >> >> >> Diff >> >> >> Modified: >> trunk/app/controllers/service_responsibles_controller.rb >> (2377 => 2378) >> >> >> --- trunk/app/controllers/service_responsibles_controller.rb 2011-03-15 17:11:13 UTC (rev 2377) >> +++ trunk/app/controllers/service_responsibles_controller.rb 2011-03-21 14:19:34 UTC (rev 2378) >> @@ -13,12 +13,38 @@ >> before_filter :authorise, :only => [:activate, :deactivate] >> >> >> + def new >> + @service_responsible = ServiceResponsible.new >> + >> + respond_to do |format| >> + format.html {redirect_to @service_responsible.service} >> + end >> + >> + end >> + >> + def create >> + @service_responsible = ServiceResponsible.new(params[:service_responsible]) >> + >> + respond_to do |format| >> + if @service_responsible.save >> + flash[:notice] = "New Responsible has been assigned" >> + format.html{ redirect_to @service_responsible.service} >> + format.xml {disable_action} >> + else >> + flash[:error] = "Could not assign new responsible" >> + format.html { redirect_to(@service) } >> + format.xml {disable_action} >> + end >> + end >> + end >> + >> + >> def deactivate >> >> respond_to do |format| >> if @service_responsible.deactivate! >> flash[:notice] = "
You have been removed from the status notification list for #{@service_responsible.service.display_name}
.
" >> - format.html{redirect_to(user_url(@service_responsible.user, :id => @service_responsible.user.id, :anchor =>'status-notifications')) } >> + format.html{redirect_to(user_url(@service_responsible.user, :id => @service_responsible.user.id, :page => @page, :anchor =>'status-notifications')) } >> format.xml { disable_action } >> else >> flash[:notice] = "
Could not remove you from status notification list for #{@service_responsible.service.display_name}
.
" >> @@ -34,7 +60,7 @@ >> if @service_responsible >> if @service_responsible.activate! >> flash[:notice] = "
You have been added to status notification list for #{@service_responsible.service.display_name}
.
" >> - format.html{ redirect_to(user_url(@service_responsible.user, :id => @service_responsible.user.id, :anchor =>'status-notifications')) } >> + format.html{ redirect_to(user_url(@service_responsible.user, :id => @service_responsible.user.id, :page => @page, :anchor =>'status-notifications')) } >> format.xml { disable_action } >> else >> flash[:error] = "
Could not add you to the status notification list for #{@service_responsible.service.display_name}
.
" >> >> >> Modified: trunk/app/controllers/users_controller.rb (2377 => >> 2378) >> >> >> --- trunk/app/controllers/users_controller.rb 2011-03-15 17:11:13 UTC (rev 2377) >> +++ trunk/app/controllers/users_controller.rb 2011-03-21 14:19:34 UTC (rev 2378) >> @@ -30,10 +30,14 @@ >> >> before_filter :find_users, :only => [ :index, :filtered_index ] >> >> - before_filter :find_user, :only => [ :show, :edit, :update, :change_password, :rpx_update, :annotations_by, :favourites, :services_responsible ] >> + before_filter :find_user, :only => [ :show, :edit, :update, :change_password, >> + :rpx_update, :annotations_by, :favourites, >> + :services_responsible, :make_curator, :remove_curator ] >> >> before_filter :add_use_tab_cookie_to_session, :only => [ :show ] >> >> + before_filter :authorise, :only => [:make_curator, :remove_curator] >> + >> oauth_authorize :saved_searches >> >> if ENABLE_SSL&& Rails.env.production? >> @@ -354,6 +358,38 @@ >> format.json { render :json => BioCatalogue::Api::Json.collection(@user.active_services_responsible_for) } >> end >> end >> + >> + def make_curator >> + respond_to do |format| >> + if @user >> + if @user.make_curator! >> + flash[:notice] = "
#{@user.display_name} is now a curator
.
" >> + format.html{ redirect_to(user_url(@user)) } >> + format.xml { disable_action } >> + else >> + flash[:error] = "
Could not make user a curator
.
" >> + format.html{ redirect_to(user_url(@user)) } >> + format.xml { disable_action } >> + end >> + end >> + end >> + end >> + >> + def remove_curator >> + respond_to do |format| >> + if @user >> + if @user.remove_curator! >> + flash[:notice] = "
#{@user.display_name} is no longer a curator
.
" >> + format.html{ redirect_to(user_url(@user)) } >> + format.xml { disable_action } >> + else >> + flash[:error] = "
Could not remove user as a curator
.
" >> + format.html{ redirect_to(user_url(@user)) } >> + format.xml { disable_action } >> + end >> + end >> + end >> + end >> >> private >> >> @@ -444,5 +480,12 @@ >> @updated_user.password = nil >> @updated_user.password_confirmation = nil >> end >> + >> + def authorise >> + unless logged_in?&& current_user.is_admin? >> + flash[:error] =" You are not authorised to perform this action" >> + redirect to @user >> + end >> + end >> >> end >> >> >> Modified: trunk/app/models/user.rb (2377 => 2378) >> >> >> --- trunk/app/models/user.rb 2011-03-15 17:11:13 UTC (rev 2377) >> +++ trunk/app/models/user.rb 2011-03-21 14:19:34 UTC (rev 2378) >> @@ -239,6 +239,33 @@ >> User.find_all_by_role_id(2) >> end >> >> + # make user an admin >> + def make_curator! >> + unless self.is_curator? >> + begin >> + self.role_id = 2 >> + self.save! >> + return true >> + rescue Exception => ex >> + logger.error("There was a problem making user a curator"); >> + logger.error(ex) >> + end >> + end >> + end >> + # remove admin privileges >> + def remove_curator! >> + unless !self.is_curator? >> + begin >> + self.role_id = nil >> + self.save! >> + return true >> + rescue Exception => ex >> + logger.error("There was a problem removing user as a curator"); >> + logger.error(ex) >> + end >> + end >> + end >> + >> private >> >> # Encrypts password with the salt. >> >> >> Modified: trunk/app/views/users/show.html.erb (2377 => 2378) >> >> >> --- trunk/app/views/users/show.html.erb 2011-03-15 17:11:13 UTC (rev 2377) >> +++ trunk/app/views/users/show.html.erb 2011-03-21 14:19:34 UTC (rev 2378) >> @@ -9,6 +9,29 @@ >> %> >> >> <% t "#{display_name(@user)}" -%> >> +<%if logged_in?&& current_user.is_admin? %> >> + >> + >> +
    >> +
  • >> + >> + Actions >> + <%= image_tag icon_filename_for(:dropdown), :alt=> "dropdown menu" -%> >> + >> +
      >> +
    • >> + <% if @user.is_curator? -%> >> + <%= link_to("Remove Curator", remove_curator_user_url(@user), :method => :put, :confirm => "Are you sure?", :class => "button_slim") -%> >> + <%else%> >> + <%= link_to("Make Curator", make_curator_user_url(@user), :method => :put, :confirm => "Are you sure?", :class => "button_slim") -%> >> + <%end%> >> +
      • >> +
    >> +
    • >> +
>> + >> + >> +<%end%> >> >>

>> <% if mine? @user %> >> @@ -99,7 +122,6 @@ >>

>> >>
>> - >> <% if mine? @user %> >> >>
> > > -- > 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 MAILER-DAEMON at nicmail3.iomart.com Thu Mar 24 16:32:39 2011 From: MAILER-DAEMON at nicmail3.iomart.com (Mail Delivery Subsystem) Date: Thu, 24 Mar 2011 20:32:39 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201103242032.p2OKWdBA028375@nicmail3.iomart.com> The original message was received at Thu, 24 Mar 2011 20:31:34 GMT from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/rfc822-headers Size: 1001 bytes Desc: not available URL: From noreply at rubyforge.org Fri Mar 25 11:59:58 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 25 Mar 2011 11:59:58 -0400 (EDT) Subject: [BioCatalogue-developers] [2382] trunk/vendor/wsdl-parsing-service/README.txt: Added PHP dependencies info for WSDLUtils service Message-ID: <20110325155958.F2BE018583B2@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 25 12:47:42 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 25 Mar 2011 12:47:42 -0400 (EDT) Subject: [BioCatalogue-developers] [2383] trunk/vendor/wsdl-parsing-service/README.txt: Added another PHP dependency for WSDLUtils service Message-ID: <20110325164742.89E5118583B2@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Mar 25 13:03:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 25 Mar 2011 17:03:55 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-585) WSDLUtils service not working in Debian 5 Message-ID: <23216200.9.1301072635381.JavaMail.jira@rosalind.cs.man.ac.uk> WSDLUtils service not working in Debian 5 ----------------------------------------- Key: BIOCAT-585 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-585 Project: BioCatalogue Issue Type: Bug Components: SOAP Services Support Environment: Debian 5, PHP 5.2.6 Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical WSDL files are failing to parse when using a WSDLUtils service running on Debian 5. More investigation is required into this. Example URL: {code} http://localhost/WSDLUtils/WSDLUtils.php?method=parse&wsdl_uri=http://www.biocatalogue.org/soap_services/2709/latest_wsdl {code} Error report: {code} Warning: DOMDocument::load(): supplied argument is not a valid Stream-Context resource in /var/www/WSDLUtils/WSDLParser/WSDLXmlSchemaParser.php on line 24 Warning: Cannot modify header information - headers already sent by (output started at /var/www/WSDLUtils/WSDLParser/WSDLXmlSchemaParser.php:24) in /var/www/WSDLUtils/WSDLUtils.php on line 247 2Retrieving document at 'http://www.biocatalogue.org/soap_services/2709/latest_wsdl'. Retrieving document at 'http://www.biocatalogue.org/soap_services/2709/latest_wsdl'. Analyzer Stopped By Exception: Version null of the "null" document is not compatible with this version of the test tools. 1http://www.bioinf.manchester.ac.uk/http://schemas.xmlsoap.org/soap/httphttp://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/minotaur/services/minotaurPrecis.cgiTakes a UniProt ID list as input; returns the associated PRECIS report. {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From MAILER-DAEMON at nicmail3.iomart.com Sun Mar 27 23:28:48 2011 From: MAILER-DAEMON at nicmail3.iomart.com (Mail Delivery Subsystem) Date: Mon, 28 Mar 2011 04:28:48 +0100 Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201103280328.p2S3SmVB029638@nicmail3.iomart.com> The original message was received at Mon, 28 Mar 2011 04:27:47 +0100 from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/rfc822-headers Size: 1005 bytes Desc: not available URL: From MAILER-DAEMON at nicmail3.iomart.com Sun Mar 27 23:29:49 2011 From: MAILER-DAEMON at nicmail3.iomart.com (Mail Delivery Subsystem) Date: Mon, 28 Mar 2011 04:29:49 +0100 Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201103280329.p2S3Tngs029932@nicmail3.iomart.com> The original message was received at Mon, 28 Mar 2011 04:28:48 +0100 from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/rfc822-headers Size: 1005 bytes Desc: not available URL: From MAILER-DAEMON at nicmail3.iomart.com Mon Mar 28 00:15:56 2011 From: MAILER-DAEMON at nicmail3.iomart.com (Mail Delivery Subsystem) Date: Mon, 28 Mar 2011 05:15:56 +0100 Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201103280415.p2S447QC013063@nicmail3.iomart.com> The original message was received at Mon, 28 Mar 2011 04:29:48 +0100 from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/rfc822-headers Size: 1005 bytes Desc: not available URL: From MAILER-DAEMON at nicmail3.iomart.com Tue Mar 29 07:29:05 2011 From: MAILER-DAEMON at nicmail3.iomart.com (Mail Delivery Subsystem) Date: Tue, 29 Mar 2011 12:29:05 +0100 Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201103291129.p2TBT5iv001227@nicmail3.iomart.com> The original message was received at Tue, 29 Mar 2011 12:28:04 +0100 from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/rfc822-headers Size: 1004 bytes Desc: not available URL: From MAILER-DAEMON at nicmail3.iomart.com Tue Mar 29 17:48:06 2011 From: MAILER-DAEMON at nicmail3.iomart.com (Mail Delivery Subsystem) Date: Tue, 29 Mar 2011 22:48:06 +0100 Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201103292148.p2TLm6wA030341@nicmail3.iomart.com> The original message was received at Tue, 29 Mar 2011 22:47:05 +0100 from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/rfc822-headers Size: 1002 bytes Desc: not available URL: From MAILER-DAEMON at nicmail3.iomart.com Thu Mar 31 21:08:36 2011 From: MAILER-DAEMON at nicmail3.iomart.com (Mail Delivery Subsystem) Date: Fri, 1 Apr 2011 02:08:36 +0100 Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201104010108.p3118a8q013658@nicmail3.iomart.com> The original message was received at Fri, 1 Apr 2011 02:07:34 +0100 from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/rfc822-headers Size: 1001 bytes Desc: not available URL: