From noreply at rubyforge.org Wed Sep 1 05:24:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 1 Sep 2010 05:24:47 -0400 (EDT) Subject: [BioCatalogue-developers] [2225] trunk: - bug fixes for the ssl_requirement Message-ID: <20100901092448.0B2BF1858361@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Sep 1 05:35:12 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 1 Sep 2010 05:35:12 -0400 (EDT) Subject: [BioCatalogue-developers] [2226] trunk/app/controllers/users_controller.rb: - updated ssl_required for users_controller Message-ID: <20100901093512.6F1731858346@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Sep 1 05:46:41 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 1 Sep 2010 05:46:41 -0400 (EDT) Subject: [BioCatalogue-developers] [2227] trunk/app/views: - updated the protocol in the forms in the views - resource_url(: protocol => default_protocol ) Message-ID: <20100901094642.3F06E1858317@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Sep 1 11:27:41 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 1 Sep 2010 11:27:41 -0400 (EDT) Subject: [BioCatalogue-developers] [2228] trunk: - implemented the functionality to POST filters ( as a work around for the 256 uri length limit). Message-ID: <20100901152741.B67FE177993F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Sep 2 06:39:46 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 2 Sep 2010 06:39:46 -0400 (EDT) Subject: [BioCatalogue-developers] [2229] trunk: - updated /annotations/bulk_create to use the collection form Message-ID: <20100902103946.88AFF1858373@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Sep 2 07:53:35 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 2 Sep 2010 07:53:35 -0400 (EDT) Subject: [BioCatalogue-developers] [2230] trunk: - bug fixes Message-ID: <20100902115335.1DCA51858370@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Sep 2 10:44:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 2 Sep 2010 15:44:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-461) Fix inconsistencies with the "counts" of results between /soap_operations/filters and /soap_operations Message-ID: <22675401.8171.1283438655431.JavaMail.jira@rosalind.cs.man.ac.uk> Fix inconsistencies with the "counts" of results between /soap_operations/filters and /soap_operations ------------------------------------------------------------------------------------------------------ Key: BIOCAT-461 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-461 Project: BioCatalogue Issue Type: Bug Reporter: Mannie Tagarira Assignee: Jiten Bhagat Using the tag "blast" as an example: Under "Tags" in "/soap_operations/filters.format", the count for "blast" if 4 (for example) The same tag used as a filter ("/soap_operations.format?tag=[blast]") returns 3 more results. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Sep 2 11:03:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 2 Sep 2010 16:03:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-451) Update the models to include #associated_service as well as other methods to improve performance In-Reply-To: <25831151.8036.1281523995361.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10019416.8172.1283439795326.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-451?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-451 started by Mannie Tagarira. > Update the models to include #associated_service as well as other methods to improve performance > ------------------------------------------------------------------------------------------------ > > Key: BIOCAT-451 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-451 > Project: BioCatalogue > Issue Type: Task > Components: Performance / Optimisations > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Sep 2 12:09:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 2 Sep 2010 17:09:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-451) Update the models to include #associated_service as well as other methods to improve performance In-Reply-To: <25831151.8036.1281523995361.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1323980.8184.1283443755324.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-451?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-451 stopped by Mannie Tagarira. > Update the models to include #associated_service as well as other methods to improve performance > ------------------------------------------------------------------------------------------------ > > Key: BIOCAT-451 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-451 > Project: BioCatalogue > Issue Type: Task > Components: Performance / Optimisations > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Sep 2 12:12:31 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 2 Sep 2010 12:12:31 -0400 (EDT) Subject: [BioCatalogue-developers] [2231] trunk/app/models: - added the method "associated_service" amongst others to the models Message-ID: <20100902161231.9F14E1678316@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Sep 3 05:06:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 3 Sep 2010 10:06:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-451) Update the models to include #associated_service as well as other methods to improve performance In-Reply-To: <25831151.8036.1281523995361.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1300756.8185.1283504775437.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-451?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-451. ------------------------------------ Resolution: Fixed > Update the models to include #associated_service as well as other methods to improve performance > ------------------------------------------------------------------------------------------------ > > Key: BIOCAT-451 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-451 > Project: BioCatalogue > Issue Type: Task > Components: Performance / Optimisations > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri Sep 3 06:30:20 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 3 Sep 2010 06:30:20 -0400 (EDT) Subject: [BioCatalogue-developers] [2232] trunk: - added endpoint /rest_services/{id}/methods Message-ID: <20100903103020.A59AC185836F@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Sep 3 07:47:50 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 03 Sep 2010 12:47:50 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:genome.imim.es:runRepeatMaskerCollection' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:genome.imim.es:runRepeatMaskerCollection' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1034 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Sep 3 10:43:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 3 Sep 2010 10:43:22 -0400 (EDT) Subject: [BioCatalogue-developers] [2233] trunk/app: - implemented XML for POST /{resource}/filtered_index Message-ID: <20100903144323.0E9E819782F8@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Sep 3 16:49:30 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 03 Sep 2010 21:49:30 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getTrajectoryBfactorPerResidueFromMD_Trajectory' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getTrajectoryBfactorPerResidueFromMD_Trajectory' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1123 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue Sep 7 07:44:13 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 7 Sep 2010 07:44:13 -0400 (EDT) Subject: [BioCatalogue-developers] [2234] trunk: - added the field "archived_at" for REST services and all the REST components, and SoapService Message-ID: <20100907114413.AA75D1678318@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Sep 7 11:49:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 7 Sep 2010 16:49:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-462) Expose archived services and service components in the API Message-ID: <9943135.8517.1283874555417.JavaMail.jira@rosalind.cs.man.ac.uk> Expose archived services and service components in the API ---------------------------------------------------------- Key: BIOCAT-462 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-462 Project: BioCatalogue Issue Type: Task Components: REST API Reporter: Mannie Tagarira Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Sep 8 05:13:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 8 Sep 2010 10:13:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-463) Allow test scripts to be run on demand Message-ID: <16413607.8521.1283937195300.JavaMail.jira@rosalind.cs.man.ac.uk> Allow test scripts to be run on demand -------------------------------------- Key: BIOCAT-463 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-463 Project: BioCatalogue Issue Type: Improvement Components: Misc Codebase Reporter: Mannie Tagarira Assignee: Jiten Bhagat At the moment, tests are run as background processes after a given time interval. It would be nice for users (via external tools such as Taverna) to check the monitoring status of a service on demand... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Sep 9 09:27:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 9 Sep 2010 14:27:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-464) Exclude archived items from the API index RestMethods if sorted by name Message-ID: <29023845.8998.1284038835382.JavaMail.jira@rosalind.cs.man.ac.uk> Exclude archived items from the API index RestMethods if sorted by name ----------------------------------------------------------------------- Key: BIOCAT-464 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-464 Project: BioCatalogue Issue Type: Bug Components: REST API, REST Services Support Reporter: Mannie Tagarira Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Sep 9 09:33:24 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 9 Sep 2010 09:33:24 -0400 (EDT) Subject: [BioCatalogue-developers] [2235] trunk: - updated the filters in the API to show the display name for tags as opposed to the unique identifier Message-ID: <20100909133324.954C2177993F@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Sep 9 10:31:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 9 Sep 2010 15:31:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-460) Document updates to the API In-Reply-To: <6899755.8166.1282752315321.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23461108.8999.1284042675391.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-460?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira reassigned BIOCAT-460: -------------------------------------- Assignee: Jiten Bhagat (was: Mannie Tagarira) > Document updates to the API > --------------------------- > > Key: BIOCAT-460 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-460 > Project: BioCatalogue > Issue Type: Task > Components: REST API, Wiki > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Sep 9 10:33:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 9 Sep 2010 15:33:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-465) Test OAuth on the live site Message-ID: <10881481.9000.1284042795322.JavaMail.jira@rosalind.cs.man.ac.uk> Test OAuth on the live site --------------------------- Key: BIOCAT-465 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-465 Project: BioCatalogue Issue Type: Task Components: REST API Reporter: Mannie Tagarira Assignee: Jiten Bhagat Priority: Critical -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Sep 9 10:35:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 9 Sep 2010 15:35:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-440) Implement activity limits for REST API calls In-Reply-To: <483658.7233.1278603854488.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18717216.9002.1284042916259.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-440?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira reassigned BIOCAT-440: -------------------------------------- Assignee: Jiten Bhagat (was: Mannie Tagarira) > Implement activity limits for REST API calls > -------------------------------------------- > > Key: BIOCAT-440 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-440 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Sep 9 10:37:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 9 Sep 2010 15:37:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-466) Expose other BioCatalogue functionality via the API Message-ID: <13403444.9003.1284043035308.JavaMail.jira@rosalind.cs.man.ac.uk> Expose other BioCatalogue functionality via the API --------------------------------------------------- Key: BIOCAT-466 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-466 Project: BioCatalogue Issue Type: Task Components: REST API Reporter: Mannie Tagarira Assignee: Jiten Bhagat - saved searches - favourites - other -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Sep 9 10:35:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 9 Sep 2010 15:35:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-317) Allow for filtering of services using hostname Message-ID: <13532440.9001.1284042915339.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-317?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira reassigned BIOCAT-317: -------------------------------------- Assignee: Jiten Bhagat (was: Mannie Tagarira) > Allow for filtering of services using hostname > ---------------------------------------------- > > Key: BIOCAT-317 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-317 > Project: BioCatalogue > Issue Type: New Feature > Components: Search / Filtering / Browsing > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Priority: Minor > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Sep 9 10:42:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 9 Sep 2010 15:42:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-467) Enhanced write support for the REST API Message-ID: <28646784.9004.1284043335312.JavaMail.jira@rosalind.cs.man.ac.uk> Enhanced write support for the REST API --------------------------------------- Key: BIOCAT-467 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-467 Project: BioCatalogue Issue Type: Improvement Components: REST API Reporter: Mannie Tagarira Assignee: Jiten Bhagat - user registration and update - extended rest support (submission and update of rest methods, rest parameters, and rest representations) - service update and deletion - annotation update and deletion - other -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Sep 10 06:12:19 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Sep 2010 11:12:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-468) Do not show archived items in BLJSON Message-ID: <24041041.9044.1284113539275.JavaMail.jira@rosalind.cs.man.ac.uk> Do not show archived items in BLJSON ------------------------------------ Key: BIOCAT-468 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-468 Project: BioCatalogue Issue Type: Bug Components: REST API Reporter: Mannie Tagarira Assignee: Jiten Bhagat Priority: Blocker -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Sep 10 06:48:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Sep 2010 11:48:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-469) Update the app to use OAuth as opposed to basic auth Message-ID: <11927937.9091.1284115695344.JavaMail.jira@rosalind.cs.man.ac.uk> Update the app to use OAuth as opposed to basic auth ---------------------------------------------------- Key: BIOCAT-469 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-469 Project: BioCatalogue Issue Type: Sub-task Reporter: Mannie Tagarira Assignee: Mannie Tagarira -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Sep 13 08:51:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 13 Sep 2010 13:51:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-470) Reindex the live data and restart the tomcat server Message-ID: <26696124.9321.1284382275368.JavaMail.jira@rosalind.cs.man.ac.uk> Reindex the live data and restart the tomcat server --------------------------------------------------- Key: BIOCAT-470 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-470 Project: BioCatalogue Issue Type: Task Components: Server Management Environment: Solr & tomcat Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Tue Sep 14 06:51:30 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 14 Sep 2010 11:51:30 +0100 Subject: [BioCatalogue-developers] Mail for the friend's list Message-ID: <4C8F53B2.5070302@ebi.ac.uk> Dear all, As you are probably aware already, BioCatalogue monitors services submitted to the registry. In order to help improve the quality of the services in the registry, we intend to enable the feature to notify providers( or anyone responsible for the service) about service status changes we detect. It will be very helpful if you would follow up on these notifications, so that together we can make the BioCatalogue a better registry. Kind regards, The BioCatalogue Team -- 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 Tue Sep 14 07:25:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 14 Sep 2010 12:25:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-471) Test and then switch service test status change notifications in production( for providers) Message-ID: <8770585.9354.1284463515313.JavaMail.jira@rosalind.cs.man.ac.uk> Test and then switch service test status change notifications in production( for providers) ------------------------------------------------------------------------------------------- Key: BIOCAT-471 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-471 Project: BioCatalogue Issue Type: Task Components: Service Monitoring Reporter: Eric Nzuobontane Assignee: Jiten Bhagat BioCatalogue monitors services and detects status changes for service tests. Notifications should be sent to providers and administrators of the services when changes are detected. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 14 07:27:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 14 Sep 2010 12:27:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-471) Test and then switch service test status change notifications in production( for providers) In-Reply-To: <8770585.9354.1284463515313.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14139429.9355.1284463635333.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-471?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-471: --------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > Test and then switch service test status change notifications in production( for providers) > ------------------------------------------------------------------------------------------- > > Key: BIOCAT-471 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-471 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 hour > Remaining Estimate: 1 hour > > BioCatalogue monitors services and detects status changes for service tests. Notifications should be sent to providers and administrators of the services when changes are detected. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From alekses6 at cs.man.ac.uk Tue Sep 14 12:12:26 2010 From: alekses6 at cs.man.ac.uk (Sergejs Aleksejevs) Date: Tue, 14 Sep 2010 17:12:26 +0100 Subject: [BioCatalogue-developers] API does not return any descriptions for REST methods even though there are descriptions on the website In-Reply-To: <4C8F68E6.9070002@cs.man.ac.uk> References: <4C8F68E6.9070002@cs.man.ac.uk> Message-ID: <4C8F9EEA.1070106@cs.man.ac.uk> Hi Jits, Just to check -- Mannie was trying to explain me that descriptions returned in the API are the ones added by the submitter of the service. Those that are added later are not visible through the API (as they are annotations?). Mannie said he has changed it the way that the "preferred" description is returned via the API, but I'm not sure whether he's made it live on sandbox (I think he did). I cannot confirm that this works - e.g. for http://sandbox.biocatalogue.org/rest_methods/79.xml there is no description in the XML, even though there is one on Sandbox. It would be great to have this fixed at some point, so that the BioCatalogue plugin can pick this data up. Thank you, Sergey From alekses6 at cs.man.ac.uk Tue Sep 14 08:21:58 2010 From: alekses6 at cs.man.ac.uk (Sergejs Aleksejevs) Date: Tue, 14 Sep 2010 13:21:58 +0100 Subject: [BioCatalogue-developers] Search returns error 500 if query contains semicolon Message-ID: <4C8F68E6.9070002@cs.man.ac.uk> Hi Jits, This is for when you get back to work. I have noticed that with this search query (http://sandbox.biocatalogue.org/soap_operations.bljson?per_page=20&q=%3Bldsajjfdsaljfsakjsa%3Bld%3Blsdfasdf&include=ancestors) I do get an error 500 back. This is somehow to do with ";" symbols ("%3B" in the URL-encoded form) in the search query. The same happens on the website, too -- it shows an error message saying "Sorry, search didn't work this time. Try with different keyword(s). Please report this if it fails for other searches too". (And the same happens for /search.xml in the API). It's not a high priority or anything - just looks like a minor bug! Thank you, Sergey -------------- next part -------------- An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Sep 14 21:59:37 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 15 Sep 2010 02:59:37 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'COILS predict protein coiled-coil regions (CNRS IBCP)' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'COILS predict protein coiled-coil regions (CNRS IBCP)' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/274 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Wed Sep 15 06:39:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 15 Sep 2010 11:39:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-230) Allow users to register themselves as "contacts" for a service Message-ID: <27412051.9361.1284547155392.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-230?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-230: --------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > Allow users to register themselves as "contacts" for a service > -------------------------------------------------------------- > > Key: BIOCAT-230 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-230 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > > These can then be shown in the "Contacts" annotations section above all free text annotations. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From alekses6 at cs.man.ac.uk Wed Sep 15 12:09:48 2010 From: alekses6 at cs.man.ac.uk (Sergejs Aleksejevs) Date: Wed, 15 Sep 2010 17:09:48 +0100 Subject: [BioCatalogue-developers] Formatting in the API output Message-ID: <4C90EFCC.10004@cs.man.ac.uk> Hi Jits, Could I ask you to fix the formatting in the API output a little bit? If I access this endpoint -- http://www.biocatalogue.org/services/2712/monitoring.xml, I get ... The last check failed

Note : Test is failing since Tuesday September 14 , 2010

2010-09-14T19:13:04Z ... ( can also look like this: The last check for this test was successful) ----------------------- In , could you please put a dot at the end of the message in both cases. Also, there's an extra space after "Note" and before the colon. The reason for these changes is that I'm stripping out HTML and using these as a plain text in Taverna, in which case it's not understandable without the ".". Thank you, Sergey From issues at mygrid.org.uk Thu Sep 16 06:03:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 16 Sep 2010 11:03:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-301) Clean up script for the test execution directories Message-ID: <8126720.9371.1284631395357.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-301?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-301 started by Eric Nzuobontane. > Clean up script for the test execution directories > -------------------------------------------------- > > Key: BIOCAT-301 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-301 > Project: BioCatalogue > Issue Type: Task > Components: Server Management, Service Monitoring > Environment: Linux, python > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Write a script that will clean up the log directories where the test scripts are executed. Logs are kept for a month then scheduled for delete. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Sep 16 06:05:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 16 Sep 2010 11:05:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-301) Clean up script for the test execution directories Message-ID: <19592645.9372.1284631515317.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-301?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15900#action_15900 ] Eric Nzuobontane commented on BIOCAT-301: ----------------------------------------- The harness logs will be kept for a week. The individual job logs(i.e the test script logs) will be kept for a least two months. A cron job will regular archive these logs and clean of the logs directories > Clean up script for the test execution directories > -------------------------------------------------- > > Key: BIOCAT-301 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-301 > Project: BioCatalogue > Issue Type: Task > Components: Server Management, Service Monitoring > Environment: Linux, python > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Write a script that will clean up the log directories where the test scripts are executed. Logs are kept for a month then scheduled for delete. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Thu Sep 16 10:23:01 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 16 Sep 2010 15:23:01 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'engineDB_06_08' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'engineDB_06_08' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/214 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Sep 16 10:23:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 16 Sep 2010 15:23:10 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'engineDB_06_08' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'engineDB_06_08' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/214 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From MAILER-DAEMON at ebi.ac.uk Thu Sep 16 11:06:16 2010 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 16 Sep 2010 16:06:16 +0100 Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201009161506.o8GF6Gvq003385@spike.ebi.ac.uk> The original message was received at Thu, 16 Sep 2010 16:06:07 +0100 from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 This message contains a virus (Exploit.E107).) ----- Transcript of session follows ----- ... while talking to mx1.cs.man.ac.uk.: >>> DATA <<< 550 This message contains a virus (Exploit.E107). 554 5.0.0 Service unavailable -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] search#show (ActionController::InvalidAuthenticityToken) "ActionController::InvalidAuthenticityToken" Date: Thu, 16 Sep 2010 16:06:07 +0100 Size: 11852 URL: From issues at mygrid.org.uk Fri Sep 17 05:57:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 17 Sep 2010 10:57:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-472) Submitters(responsibles) should be able to remove their uploaded tests Message-ID: <9613162.9376.1284717435488.JavaMail.jira@rosalind.cs.man.ac.uk> Submitters(responsibles) should be able to remove their uploaded tests ---------------------------------------------------------------------- Key: BIOCAT-472 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-472 Project: BioCatalogue Issue Type: Improvement Components: Service Monitoring Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Users should be given the possibility to remove their own tests. Removing test however would mean that all the monitoring data associated with that test would be lost as well. At the moment, the policy has been to disable tests rather than to remove them. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri Sep 17 06:15:29 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 17 Sep 2010 06:15:29 -0400 (EDT) Subject: [BioCatalogue-developers] [2236] trunk: -added indicator for description annotation coverage. Message-ID: <20100917101529.4868219782D4@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Fri Sep 17 06:29:24 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 17 Sep 2010 11:29:24 +0100 Subject: [BioCatalogue-developers] Status of Rest Service & API work Message-ID: <4C934304.9070808@ebi.ac.uk> Hi Mannie, I understand that you are back to Uni. Thanks for all the help with BioCatalogue. I just wanted to know what the final state of thing is with respect to the rest service and api work. If you have a pointer to documentation/notes anywhere, then please let me know. I am planning for a release soon and therefore would like to clearly understand what will be available for the release or not. -- 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 Sep 17 09:49:01 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 17 Sep 2010 14:49:01 +0100 Subject: [BioCatalogue-developers] hmmmmmm Message-ID: <4C9371CD.9090202@ebi.ac.uk> I just tried to update the test site and hit this problem! http://groups.google.com/group/ruby-twitter-gem/browse_thread/thread/262ef086bc00be9a/7824331203144950#7824331203144950 I am not not sure I can upgrade to ruby I.8.6 or higher. Hmmmm!!! -- 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 Fri Sep 17 11:44:53 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 17 Sep 2010 11:44:53 -0400 (EDT) Subject: [BioCatalogue-developers] [2237] trunk: downgrading oauth gem version to 0.3.6 from 0.4. 1 bec of incompatibility with ruby 1.8.5 Message-ID: <20100917154453.85D8F1678310@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Sep 17 13:39:51 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 17 Sep 2010 18:39:51 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runLeapWithLigandsFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runLeapWithLigandsFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1174 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Mon Sep 20 04:46:29 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 20 Sep 2010 09:46:29 +0100 Subject: [BioCatalogue-developers] test site down Message-ID: <4C971F65.40106@ebi.ac.uk> Hi, The test site, test.biocatalogue.org is currently down because of connection issues with the database. I have informed systems about the situation and I hoping this will get fixed urgently. cheers, 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 Mon Sep 20 09:43:39 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 20 Sep 2010 09:43:39 -0400 (EDT) Subject: [BioCatalogue-developers] [2238] trunk: - Allow users to delete their uploaded test scripts Message-ID: <20100920134339.30C071678316@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Sep 20 11:45:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 20 Sep 2010 16:45:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-473) Missing method in module : undefined method `get_filters_for_soap_input_tags' for BioCatalogue::Filtering::Services:Module Message-ID: <28153708.9565.1284997515321.JavaMail.jira@rosalind.cs.man.ac.uk> Missing method in module : undefined method `get_filters_for_soap_input_tags' for BioCatalogue::Filtering::Services:Module --------------------------------------------------------------------------------------------------------------------------- Key: BIOCAT-473 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-473 Project: BioCatalogue Issue Type: Bug Components: Search / Filtering / Browsing Reporter: Eric Nzuobontane Assignee: Jiten Bhagat There is a bug in the service filtering module. The error message generated is attached below: undefined method `get_filters_for_soap_input_tags' for BioCatalogue::Filtering::Services:Module On line #64 of app/views/services/_index_filters.html.erb 61: :filter_type => :tag_ops } -%> 62: 63: 64: <% inputs_tags_filters = BioCatalogue::Filtering::Services.get_filters_for_soap_input_tags %> 65: <%= render :partial => "filtering/filter_options_generic", 66: :locals => { :filters => inputs_tags_filters, 67: :filter_type => :tag_ins } -%> app/views/services/_index_filters.html.erb:64 app/views/services/_index_filters.html.erb:11 app/views/services/index.html.erb:29 app/controllers/services_controller.rb:40:in `index' -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Tue Sep 21 05:22:18 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 21 Sep 2010 10:22:18 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'WHAT IF Web Services' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'WHAT IF Web Services' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/2777 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Sep 21 05:42:45 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 21 Sep 2010 10:42:45 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'WHAT IF Web Services' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'WHAT IF Web Services' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/2777 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Tue Sep 21 07:05:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 21 Sep 2010 12:05:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-458) Investigate biocatalogue db encoding problems and fix any inconsistencies with the rails application In-Reply-To: <27122381.8114.1282212375444.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11962437.9660.1285067115330.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-458?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-458 started by Eric Nzuobontane. > Investigate biocatalogue db encoding problems and fix any inconsistencies with the rails application > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-458 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-458 > Project: BioCatalogue > Issue Type: Task > Components: Data > Environment: MySQL, Rails > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > From Mannie: > There is a concerning issue regarding database encodings in which some characters are stored in the database in an inconsistent way; most European character sets are not being handled properly. Accented characters, for example, will appear as symbols, which is clearly not the desired effect. Take for example, the user with ID 234 (not yet activated), whose name is "Jos? Mar?a Fern?ndez"; this may appear in the BioCatalogue as "Jos?? Mar? a Fern??ndez" or something similar depending on the database encoding used. > So far, this has been the case on my machine, Jits's machine, as well as the sandbox. Could you please look into this just to make sure this issue does not affect the test and live sites as well... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 21 07:09:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 21 Sep 2010 12:09:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-458) Investigate biocatalogue db encoding problems and fix any inconsistencies with the rails application In-Reply-To: <27122381.8114.1282212375444.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9991656.9661.1285067355305.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-458?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15959#action_15959 ] Eric Nzuobontane commented on BIOCAT-458: ----------------------------------------- As far as I can see, rails actually decodes this properly. However, there is an issue with a mix of encodings in the database. There is one table, activity_logs, which uses 'utf8' while the rest are latine1. > Investigate biocatalogue db encoding problems and fix any inconsistencies with the rails application > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-458 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-458 > Project: BioCatalogue > Issue Type: Task > Components: Data > Environment: MySQL, Rails > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > From Mannie: > There is a concerning issue regarding database encodings in which some characters are stored in the database in an inconsistent way; most European character sets are not being handled properly. Accented characters, for example, will appear as symbols, which is clearly not the desired effect. Take for example, the user with ID 234 (not yet activated), whose name is "Jos? Mar?a Fern?ndez"; this may appear in the BioCatalogue as "Jos?? Mar? a Fern??ndez" or something similar depending on the database encoding used. > So far, this has been the case on my machine, Jits's machine, as well as the sandbox. Could you please look into this just to make sure this issue does not affect the test and live sites as well... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue Sep 21 08:44:44 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 21 Sep 2010 08:44:44 -0400 (EDT) Subject: [BioCatalogue-developers] [2239] trunk/app/models/service_test.rb: delete redundant function Message-ID: <20100921124444.46BE118582E2@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Sep 21 08:47:48 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 21 Sep 2010 08:47:48 -0400 (EDT) Subject: [BioCatalogue-developers] [2240] branches/service-states/: creating branch for service life cycle states Message-ID: <20100921124748.6529919782F8@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Sep 21 10:19:05 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 21 Sep 2010 10:19:05 -0400 (EDT) Subject: [BioCatalogue-developers] [2241] branches/test-scripts/: delete redundant branch Message-ID: <20100921141905.64C171678317@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Sep 21 10:21:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 21 Sep 2010 10:21:07 -0400 (EDT) Subject: [BioCatalogue-developers] [2242] branches/web-service-ownership/: delete web service ownership branch Message-ID: <20100921142107.86F1C1678317@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue Sep 21 10:57:33 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 21 Sep 2010 15:57:33 +0100 Subject: [BioCatalogue-developers] Agenda for Next Week in Manchester Message-ID: <4C98C7DD.6000404@ebi.ac.uk> Hi Rodrigo, During my time in Manchester next week, we intend to discuss and work on the following amongst other things: 1) Review the roadmap - Determine which requirements have been met, wholly or partially and evaluate what is needed to complete the partially complete ones - Come up with a proposal of the way forward in terms of what outstanding requirements should be prioritized. This would cover discussions on semantic annotations(using EDAM) & BioXSD 2) Test and document the current codebase in preparation for a release the following week. Note that this includes testing for the write API 3) Review the architecture with an aim to reducing the maintenance overhead( especially as project will move to OAM phase next year) 4) Discuss the final EMBRACE import and how to handle future access to the embrace registry url 5) Come up with a plan on how to manage content like flagging & cleaning up dead links 6) Some design work on any quick wins that come out of our discussions If you have anything in mind that you think will be good to discuss/work on during my time in Manchester, then please let me know. cheers, 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 Sep 21 10:59:58 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 21 Sep 2010 10:59:58 -0400 (EDT) Subject: [BioCatalogue-developers] [2243] branches/soaplab-and-monitoring/: delete soaplab and monitoring branch Message-ID: <20100921145958.143031858367@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue Sep 21 11:14:09 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 21 Sep 2010 16:14:09 +0100 Subject: [BioCatalogue-developers] Agenda for Next Week in Manchester In-Reply-To: <4C98C7DD.6000404@ebi.ac.uk> References: <4C98C7DD.6000404@ebi.ac.uk> Message-ID: <4C98CBC1.9080400@ebi.ac.uk> I think one other thing that would be good to discuss is a plan to clean up and structure the documentation for easier reference. Eric On 21/09/2010 15:57, Eric Nzuobontane wrote: > Hi Rodrigo, > > During my time in Manchester next week, we intend to discuss and work > on the following amongst other things: > > 1) Review the roadmap > - Determine which requirements have been met, wholly or partially > and evaluate what is needed to complete the partially complete ones > - Come up with a proposal of the way forward in terms of what > outstanding requirements should be prioritized. This would cover > discussions on semantic annotations(using EDAM) & BioXSD > > 2) Test and document the current codebase in preparation for a release > the following week. Note that this includes testing for the write API > > 3) Review the architecture with an aim to reducing the maintenance > overhead( especially as project will move to OAM phase next year) > > 4) Discuss the final EMBRACE import and how to handle future access to > the embrace registry url > > 5) Come up with a plan on how to manage content like flagging & > cleaning up dead links > > 6) Some design work on any quick wins that come out of our discussions > > If you have anything in mind that you think will be good to > discuss/work on during my time in Manchester, then please let me know. > > cheers, > > 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 ytanoh at cs.man.ac.uk Tue Sep 21 11:39:08 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 21 Sep 2010 16:39:08 +0100 Subject: [BioCatalogue-developers] [Production ERROR] services#index (ActionView::TemplateError) "undefined method `get_filters_for_soap_input_tags' for BioCatalogue::Filtering::Services:Module" In-Reply-To: <4c975c96204fe_762d1590512a7fc81bd@pweb-3a.ebi.ac.uk.tmail> References: <4c975c96204fe_762d1590512a7fc81bd@pweb-3a.ebi.ac.uk.tmail> Message-ID: Hi guys, We are receiving a lot of message from the test site, is everything OK? Franck On 20 September 2010 14:07, BioCatalogue Errors < biocatalogue-developers at rubyforge.org> wrote: > A ActionView::TemplateError occurred in services#index: > > undefined method `get_filters_for_soap_input_tags' for > BioCatalogue::Filtering::Services:Module > On line #64 of app/views/services/_index_filters.html.erb > > 61: > :filter_type => :tag_ops > } -%> > 62: > 63: > 64: <% inputs_tags_filters = > BioCatalogue::Filtering::Services.get_filters_for_soap_input_tags %> > 65: <%= render :partial => > "filtering/filter_options_generic", > 66: > :locals => { :filters => inputs_tags_filters, > 67: > :filter_type => :tag_ins > } -%> > > app/views/services/_index_filters.html.erb:64 > app/views/services/_index_filters.html.erb:11 > app/views/services/index.html.erb:29 > app/controllers/services_controller.rb:40:in `index' > passenger (2.2.4) lib/phusion_passenger/rack/request_handler.rb:91:in > `process_request' > passenger (2.2.4) > lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:376:in > `start_request_handler' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:334:in > `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in `safe_fork' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:332:in > `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in > `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in > `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in > `start_synchronously' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in > `start' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in > `spawn_rails_application' > passenger (2.2.4) > lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in > `spawn_rails_application' > passenger (2.2.4) > lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > passenger (2.2.4) > lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in > `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in > `spawn_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in > `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in > `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in > `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in > `start_synchronously' > > ------------------------------- > Request: > ------------------------------- > > * URL : > http://test.biocatalogue.org/services?cat=%5B15%5D&tag_filters=on > * Method : GET > * IP address: 66.249.66.116 > * Parameters: {"cat"=>"[15]", "tag_filters"=>"on", "action"=>"index", > "controller"=>"services"} > * Rails root: > /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue > > ------------------------------- > Session: > ------------------------------- > > * session id: nil > * data: nil > > ------------------------------- > Environment: > ------------------------------- > > * DOCUMENT_ROOT : > /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/public > * HTTP_ACCEPT : */* > * HTTP_ACCEPT_ENCODING : gzip,deflate > * HTTP_CONNECTION : Keep-alive > * HTTP_FROM : googlebot(at) > googlebot.com > * HTTP_HOST : test.biocatalogue.org > * HTTP_USER_AGENT : Mozilla/5.0 (compatible; > Googlebot/2.1; +http://www.google.com/bot.html) > * HTTP_X_CLUSTER_CLIENT_IP : 66.249.66.116 > * PATH_INFO : /services > * QUERY_STRING : > cat=%5B15%5D&tag_filters=on > * REMOTE_ADDR : 66.249.66.116 > * REMOTE_PORT : 39607 > * REQUEST_METHOD : GET > * REQUEST_URI : > /services?cat=%5B15%5D&tag_filters=on > * SCRIPT_NAME : > * SERVER_ADDR : 172.18.1.107 > * SERVER_ADMIN : root at localhost > * SERVER_NAME : test.biocatalogue.org > * SERVER_PORT : 80 > * SERVER_PROTOCOL : HTTP/1.1 > * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) > * _ : _ > * action_controller.request.query_parameters : tag_filtersoncat[15] > * action_controller.request.request_parameters: > * action_controller.rescue.request : > # > * action_controller.rescue.response : > # > * rack.errors : # > * rack.input : # > * rack.multiprocess : true > * rack.multithread : false > * rack.request : > # > * rack.request.query_hash : tag_filtersoncat[15] > * rack.request.query_string : > cat=%5B15%5D&tag_filters=on > * rack.routing_args : > actionindexcontrollerservices > * rack.run_once : false > * rack.session : > use_tab_cookiefalseservices_index_listing_typedetailedprevious_url/services?cat=%5B15%5D&tag_filters=on > * rack.session.options : > expire_afterhttponlytruesecurefalsecookie_onlytruekey_session_ididd46113119cf90644452b7f6760677628domainpath/ > * rack.session.record : > # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 30253 > * Server : pweb-3a > > * request.format: */* > > ------------------------------- > Backtrace: > ------------------------------- > > On line #64 of app/views/services/_index_filters.html.erb > > 61: > :filter_type => :tag_ops > } -%> > 62: > 63: > 64: <% inputs_tags_filters = > BioCatalogue::Filtering::Services.get_filters_for_soap_input_tags %> > 65: <%= render :partial => > "filtering/filter_options_generic", > 66: > :locals => { :filters => inputs_tags_filters, > 67: > :filter_type => :tag_ins > } -%> > > app/views/services/_index_filters.html.erb:64 > app/views/services/_index_filters.html.erb:11 > app/views/services/index.html.erb:29 > app/controllers/services_controller.rb:40:in `index' > passenger (2.2.4) lib/phusion_passenger/rack/request_handler.rb:91:in > `process_request' > passenger (2.2.4) > lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:376:in > `start_request_handler' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:334:in > `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in `safe_fork' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:332:in > `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in > `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in > `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in > `start_synchronously' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in > `start' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in > `spawn_rails_application' > passenger (2.2.4) > lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in > `spawn_rails_application' > passenger (2.2.4) > lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > passenger (2.2.4) > lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in > `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in > `spawn_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in > `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in > `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in > `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in > `start_synchronously' > > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue Sep 21 12:03:26 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 21 Sep 2010 17:03:26 +0100 Subject: [BioCatalogue-developers] [Production ERROR] services#index (ActionView::TemplateError) "undefined method `get_filters_for_soap_input_tags' for BioCatalogue::Filtering::Services:Module" In-Reply-To: References: <4c975c96204fe_762d1590512a7fc81bd@pweb-3a.ebi.ac.uk.tmail> Message-ID: <4C98D74E.4040707@ebi.ac.uk> Hi Franck, This is a bug. I am not exactly sure about what to do to do in order to fix it. It not clear to me if the intention was to define this method which is used or it is a typo. So I created a jira task for this while waiting for Jits to come back. I also do not want to mask the problem by putting in a fix which may not be appropriate. Eric On 21/09/2010 16:39, Franck Tanoh wrote: > Hi guys, > > We are receiving a lot of message from the test site, is everything OK? > > Franck > > > > > On 20 September 2010 14:07, BioCatalogue Errors > > wrote: > > A ActionView::TemplateError occurred in services#index: > > undefined method `get_filters_for_soap_input_tags' for > BioCatalogue::Filtering::Services:Module > On line #64 of app/views/services/_index_filters.html.erb > > 61: > > :filter_type => :tag_ops } -%> > 62: > 63: > 64: <% inputs_tags_filters = > BioCatalogue::Filtering::Services.get_filters_for_soap_input_tags %> > 65: <%= render :partial => "filtering/filter_options_generic", > 66: > :locals => { :filters => inputs_tags_filters, > 67: > > :filter_type => :tag_ins } -%> > > app/views/services/_index_filters.html.erb:64 > app/views/services/_index_filters.html.erb:11 > app/views/services/index.html.erb:29 > app/controllers/services_controller.rb:40:in `index' > passenger (2.2.4) > lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' > passenger (2.2.4) > lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:376:in > `start_request_handler' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:334:in > `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in `safe_fork' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:332:in > `handle_spawn_application' > passenger (2.2.4) > lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) > lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) > lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > passenger (2.2.4) > lib/phusion_passenger/abstract_server.rb:162:in `start' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in > `spawn_rails_application' > passenger (2.2.4) > lib/phusion_passenger/abstract_server_collection.rb:126:in > `lookup_or_add' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in > `spawn_rails_application' > passenger (2.2.4) > lib/phusion_passenger/abstract_server_collection.rb:80:in > `synchronize' > passenger (2.2.4) > lib/phusion_passenger/abstract_server_collection.rb:79:in > `synchronize' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in > `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in > `spawn_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in > `handle_spawn_application' > passenger (2.2.4) > lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) > lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) > lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > > ------------------------------- > Request: > ------------------------------- > > * URL : > http://test.biocatalogue.org/services?cat=%5B15%5D&tag_filters=on > > * Method : GET > * IP address: 66.249.66.116 > * Parameters: {"cat"=>"[15]", "tag_filters"=>"on", > "action"=>"index", "controller"=>"services"} > * Rails root: > /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue > > ------------------------------- > Session: > ------------------------------- > > * session id: nil > * data: nil > > ------------------------------- > Environment: > ------------------------------- > > * DOCUMENT_ROOT : > /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/public > * HTTP_ACCEPT : */* > * HTTP_ACCEPT_ENCODING : gzip,deflate > * HTTP_CONNECTION : Keep-alive > * HTTP_FROM : > googlebot(at)googlebot.com > * HTTP_HOST : > test.biocatalogue.org > * HTTP_USER_AGENT : Mozilla/5.0 > (compatible; Googlebot/2.1; +http://www.google.com/bot.html) > * HTTP_X_CLUSTER_CLIENT_IP : 66.249.66.116 > * PATH_INFO : /services > * QUERY_STRING : > cat=%5B15%5D&tag_filters=on > * REMOTE_ADDR : 66.249.66.116 > * REMOTE_PORT : 39607 > * REQUEST_METHOD : GET > * REQUEST_URI : > /services?cat=%5B15%5D&tag_filters=on > * SCRIPT_NAME : > * SERVER_ADDR : 172.18.1.107 > * SERVER_ADMIN : root at localhost > * SERVER_NAME : > test.biocatalogue.org > * SERVER_PORT : 80 > * SERVER_PROTOCOL : HTTP/1.1 > * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) > * _ : _ > * action_controller.request.query_parameters : tag_filtersoncat[15] > * action_controller.request.request_parameters: > * action_controller.rescue.request : > # > * action_controller.rescue.response : > # > * rack.errors : # > * rack.input : > # > * rack.multiprocess : true > * rack.multithread : false > * rack.request : > # > * rack.request.query_hash : tag_filtersoncat[15] > * rack.request.query_string : > cat=%5B15%5D&tag_filters=on > * rack.routing_args : > actionindexcontrollerservices > * rack.run_once : false > * rack.session : > use_tab_cookiefalseservices_index_listing_typedetailedprevious_url/services?cat=%5B15%5D&tag_filters=on > * rack.session.options : > expire_afterhttponlytruesecurefalsecookie_onlytruekey_session_ididd46113119cf90644452b7f6760677628domainpath/ > * rack.session.record : > # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 30253 > * Server : pweb-3a > > * request.format: */* > > ------------------------------- > Backtrace: > ------------------------------- > > On line #64 of app/views/services/_index_filters.html.erb > > 61: > > :filter_type => :tag_ops } -%> > 62: > 63: > 64: <% inputs_tags_filters = > BioCatalogue::Filtering::Services.get_filters_for_soap_input_tags %> > 65: <%= render :partial => "filtering/filter_options_generic", > 66: > :locals => { :filters => inputs_tags_filters, > 67: > > :filter_type => :tag_ins } -%> > > app/views/services/_index_filters.html.erb:64 > app/views/services/_index_filters.html.erb:11 > app/views/services/index.html.erb:29 > app/controllers/services_controller.rb:40:in `index' > passenger (2.2.4) > lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' > passenger (2.2.4) > lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:376:in > `start_request_handler' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:334:in > `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in > `safe_fork' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:332:in > `handle_spawn_application' > passenger (2.2.4) > lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) > lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) > lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > passenger (2.2.4) > lib/phusion_passenger/abstract_server.rb:162:in `start' > passenger (2.2.4) > lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > passenger (2.2.4) > lib/phusion_passenger/spawn_manager.rb:261:in > `spawn_rails_application' > passenger (2.2.4) > lib/phusion_passenger/abstract_server_collection.rb:126:in > `lookup_or_add' > passenger (2.2.4) > lib/phusion_passenger/spawn_manager.rb:255:in > `spawn_rails_application' > passenger (2.2.4) > lib/phusion_passenger/abstract_server_collection.rb:80:in > `synchronize' > passenger (2.2.4) > lib/phusion_passenger/abstract_server_collection.rb:79:in > `synchronize' > passenger (2.2.4) > lib/phusion_passenger/spawn_manager.rb:254:in > `spawn_rails_application' > passenger (2.2.4) > lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' > passenger (2.2.4) > lib/phusion_passenger/spawn_manager.rb:286:in > `handle_spawn_application' > passenger (2.2.4) > lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) > lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) > lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > > > > > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers -- 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 rls at ebi.ac.uk Tue Sep 21 15:51:23 2010 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Tue, 21 Sep 2010 20:51:23 +0100 Subject: [BioCatalogue-developers] Agenda for Next Week in Manchester In-Reply-To: <4C98C7DD.6000404@ebi.ac.uk> References: <4C98C7DD.6000404@ebi.ac.uk> Message-ID: <4C990CBB.80707@ebi.ac.uk> One additional item would be to discuss an evaluation of all the features of the portal with the aim of identifying the non-to-useful ones (that is why I was asking earlier for some measures) and potentially remove these in order to simply and focus present and future work. Just my two cents. R:) On 21/09/2010 15:57, Eric Nzuobontane wrote: > Hi Rodrigo, > > During my time in Manchester next week, we intend to discuss and work on > the following amongst other things: > > 1) Review the roadmap > - Determine which requirements have been met, wholly or partially and > evaluate what is needed to complete the partially complete ones > - Come up with a proposal of the way forward in terms of what > outstanding requirements should be prioritized. This would cover > discussions on semantic annotations(using EDAM) & BioXSD > > 2) Test and document the current codebase in preparation for a release > the following week. Note that this includes testing for the write API > > 3) Review the architecture with an aim to reducing the maintenance > overhead( especially as project will move to OAM phase next year) > > 4) Discuss the final EMBRACE import and how to handle future access to > the embrace registry url > > 5) Come up with a plan on how to manage content like flagging & cleaning > up dead links > > 6) Some design work on any quick wins that come out of our discussions > > If you have anything in mind that you think will be good to discuss/work > on during my time in Manchester, then please let me know. > > cheers, > > Eric > From issues at mygrid.org.uk Wed Sep 22 07:04:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 22 Sep 2010 12:04:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-474) Error page return when attempting to submit a service before sign in. A redirect was expected Message-ID: <9915096.9712.1285153455393.JavaMail.jira@rosalind.cs.man.ac.uk> Error page return when attempting to submit a service before sign in. A redirect was expected --------------------------------------------------------------------------------------------- Key: BIOCAT-474 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-474 Project: BioCatalogue Issue Type: Bug Components: Service Submission Environment: UI Reporter: Eric Nzuobontane Assignee: Jiten Bhagat If one attempts to submit a service before sign in, the expectation is that the user will be redirected to the login page. However, an error page is returned instead. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Wed Sep 22 10:44:28 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 22 Sep 2010 10:44:28 -0400 (EDT) Subject: [BioCatalogue-developers] [2244] trunk: - allow users to delete(hide) their uploaded tests. Message-ID: <20100922144429.188AB1678316@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Sep 22 12:08:21 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 22 Sep 2010 12:08:21 -0400 (EDT) Subject: [BioCatalogue-developers] [2245] trunk/app/controllers/service_tests_controller.rb: bugfix - only admins should access hidden tests Message-ID: <20100922160821.63E831858321@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Sep 22 12:15:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 22 Sep 2010 17:15:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-472) Submitters(responsibles) should be able to remove their uploaded tests In-Reply-To: <9613162.9376.1284717435488.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2875324.9734.1285172115377.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-472?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-472 started by Eric Nzuobontane. > Submitters(responsibles) should be able to remove their uploaded tests > ---------------------------------------------------------------------- > > Key: BIOCAT-472 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-472 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Users should be given the possibility to remove their own tests. Removing test however would mean that all the monitoring data associated with that test would be lost as well. At the moment, the policy has been to disable tests rather than to remove them. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Sep 22 12:19:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 22 Sep 2010 17:19:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-472) Submitters(responsibles) should be able to remove their uploaded tests In-Reply-To: <9613162.9376.1284717435488.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16395217.9735.1285172355333.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-472?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15966#action_15966 ] Eric Nzuobontane commented on BIOCAT-472: ----------------------------------------- People responsible for a service will be given permission to delete tests. On delete, the test will be hidden from users and may only be accessible to admins though the UI. It will decided in the future if these tests should actually be deleted. As their status no longer affect the overall service status, they are kept for purely historical reasons. > Submitters(responsibles) should be able to remove their uploaded tests > ---------------------------------------------------------------------- > > Key: BIOCAT-472 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-472 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Users should be given the possibility to remove their own tests. Removing test however would mean that all the monitoring data associated with that test would be lost as well. At the moment, the policy has been to disable tests rather than to remove them. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Sep 22 16:45:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 22 Sep 2010 21:45:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-475) Rendering problem in safari when rendering search results Message-ID: <32851103.9736.1285188315321.JavaMail.jira@rosalind.cs.man.ac.uk> Rendering problem in safari when rendering search results --------------------------------------------------------- Key: BIOCAT-475 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-475 Project: BioCatalogue Issue Type: Bug Components: Web Interface Reporter: Eric Nzuobontane Assignee: Jiten Bhagat buttons and listing are misaligned in safari when search results are returned. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Sep 22 16:47:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 22 Sep 2010 21:47:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-475) Rendering problem in safari when rendering search results In-Reply-To: <32851103.9736.1285188315321.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15323836.9737.1285188435319.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-475?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane updated BIOCAT-475: ------------------------------------ Attachment: screenshot-1.jpg scroll to the right to see the misalignment > Rendering problem in safari when rendering search results > --------------------------------------------------------- > > Key: BIOCAT-475 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-475 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Attachments: screenshot-1.jpg > > > buttons and listing are misaligned in safari when search results are returned. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Thu Sep 23 06:41:42 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 23 Sep 2010 11:41:42 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'engineDB_06_08' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'engineDB_06_08' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/214 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Mon Sep 27 05:56:15 2010 From: issues at mygrid.org.uk (Alex Nenadic (JIRA)) Date: Mon, 27 Sep 2010 10:56:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-476) BioCat API needs a single cal to get operations (methods) of a REST service Message-ID: <20858522.9801.1285581375410.JavaMail.jira@rosalind.cs.man.ac.uk> BioCat API needs a single cal to get operations (methods) of a REST service --------------------------------------------------------------------------- Key: BIOCAT-476 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-476 Project: BioCatalogue Issue Type: Improvement Reporter: Alex Nenadic Assignee: Jiten Bhagat BioCat API needs a single cal to get operations (methods) of a REST service. At the moment - 2 REST calls are needed to get this info and Sergejs did not want to use this in the BioCat plugin for Taverna as it was to heavy. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Sep 27 10:59:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 27 Sep 2010 15:59:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-477) Parse the biocatalogue content to flag any dead links Message-ID: <16018195.9859.1285599555309.JavaMail.jira@rosalind.cs.man.ac.uk> 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: Jiten Bhagat Links with the biocatalogue will become inaccessible from time to time. The object of this task is to flag such likes thereby generating a curation event (for the curator). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Sep 27 11:01:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 27 Sep 2010 16:01:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (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: <14199849.9860.1285599675307.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 updated BIOCAT-477: ------------------------------------ Description: 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. was: Links with the biocatalogue will become inaccessible from time to time. The object of this task is to flag such likes thereby generating a curation event (for the curator). > 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: Jiten Bhagat > > 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. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Mon Sep 27 10:46:23 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 27 Sep 2010 15:46:23 +0100 Subject: [BioCatalogue-developers] Agenda for Next Week in Manchester In-Reply-To: <4C990CBB.80707@ebi.ac.uk> References: <4C98C7DD.6000404@ebi.ac.uk> <4C990CBB.80707@ebi.ac.uk> Message-ID: <4CA0AE3F.5010908@cs.man.ac.uk> Rodrigo, Did you have any particular features in mind (or have some feedback on from others)? We've already identified the Disqus commenting* and Ratings as candidates for removal. Cheers, Jits * We are aiming to replace the Disqus commenting with a new "Discussions" tab which will allow threaded discussions to take place (without external user accounts, ie: better integrated into the BioCatalogue). We will, of course, properly run this through users first before releasing such a thing, Rodrigo Lopez wrote: > One additional item would be to discuss an evaluation of all the > features of the portal with the aim of identifying the non-to-useful > ones (that is why I was asking earlier for some measures) and > potentially remove these in order to simply and focus present and > future work. > Just my two cents. > > R:) > > On 21/09/2010 15:57, Eric Nzuobontane wrote: >> Hi Rodrigo, >> >> During my time in Manchester next week, we intend to discuss and work on >> the following amongst other things: >> >> 1) Review the roadmap >> - Determine which requirements have been met, wholly or partially and >> evaluate what is needed to complete the partially complete ones >> - Come up with a proposal of the way forward in terms of what >> outstanding requirements should be prioritized. This would cover >> discussions on semantic annotations(using EDAM) & BioXSD >> >> 2) Test and document the current codebase in preparation for a release >> the following week. Note that this includes testing for the write API >> >> 3) Review the architecture with an aim to reducing the maintenance >> overhead( especially as project will move to OAM phase next year) >> >> 4) Discuss the final EMBRACE import and how to handle future access to >> the embrace registry url >> >> 5) Come up with a plan on how to manage content like flagging & cleaning >> up dead links >> >> 6) Some design work on any quick wins that come out of our discussions >> >> If you have anything in mind that you think will be good to discuss/work >> on during my time in Manchester, then please let me know. >> >> cheers, >> >> Eric >> > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From hpm at ebi.ac.uk Mon Sep 27 11:46:20 2010 From: hpm at ebi.ac.uk (Hamish McWilliam) Date: Mon, 27 Sep 2010 16:46:20 +0100 Subject: [BioCatalogue-developers] Agenda for Next Week in Manchester In-Reply-To: <4CA0AE3F.5010908@cs.man.ac.uk> References: <4C98C7DD.6000404@ebi.ac.uk> <4C990CBB.80707@ebi.ac.uk> <4CA0AE3F.5010908@cs.man.ac.uk> Message-ID: <4CA0BC4C.8040804@ebi.ac.uk> Hi Jits, > Did you have any particular features in mind (or have some feedback on > from others)? > > We've already identified the Disqus commenting* and Ratings as > candidates for removal. After a little discussion to draw the memories to the surface, the main things that were mentioned in the BioCatalogue feedback discussion during the EMBRACE meeting in June were: 1. Results page white space. For the workshop we were all using laptops, so needing to scroll a lot when searching the catalogue or browsing the services was something that was commented on quite a bit. While there was some discussion about which information could be removed from the service summaries, there was no consensus on which information could be removed, however it was felt that the information could be rearranged to reduce the amount of "whitespace", and the padding and pitch of the text tightened. 2. Services page tag cloud. Convention for tag coluds on web pages seems to be moving towards them being a feature for a sidebar, commonly the right sidebar. This would move the service information up, so less scrolling. 3. More services per-page. Having 10 services per page was seen as too limiting, and leading to more page navigation than they were happy with. While this will increase the amount of scrolling it was felt that this was better than paging. 4. Service page whitespace. Again too much scrolling, especially for fields which do not contain information. 5. Reduce the header size. Another scrolling suggestion was to reduce the height of the header. 6. Commenting Wasn't seen as useful. This may be just a case of being unable to show useful comments meaning that they didn't see it as being used/useful. It may also reflect the feeling that since we can annotate the service what would we be writing as a comment? 7. Ratings Again not seen as useful. Not much support for rankings, partly since this is a provider audience, also many of the rankings in the catalogue being self-rankings, and thus a bit suspect. An other thing that has cropped up in discussions is: 8. Three flavors of result page. The "Services" page, results page 1 and results page 2+ have different features and look-and-feel. Was felt that one form of results page, with the faceted features of the "Services" page would be better. This is ignoring the lists of services in things like a provider description. Given the remaining development time available, these issues are only really worth addressing if the effort required is minimal, and fits with the schedule for the other required features. > * We are aiming to replace the Disqus commenting with a new > "Discussions" tab which will allow threaded discussions to take place > (without external user accounts, ie: better integrated into the > BioCatalogue). We will, of course, properly run this through users first > before releasing such a thing, Nice idea, but I'm not sure it would be used much, for the same reasons commenting has not been used. For the moment this seems low priority, has anyone been requesting this functionality? Hamish > > > > Rodrigo Lopez wrote: >> One additional item would be to discuss an evaluation of all the >> features of the portal with the aim of identifying the non-to-useful >> ones (that is why I was asking earlier for some measures) and >> potentially remove these in order to simply and focus present and >> future work. >> Just my two cents. >> >> R:) >> >> On 21/09/2010 15:57, Eric Nzuobontane wrote: >>> Hi Rodrigo, >>> >>> During my time in Manchester next week, we intend to discuss and work on >>> the following amongst other things: >>> >>> 1) Review the roadmap >>> - Determine which requirements have been met, wholly or partially and >>> evaluate what is needed to complete the partially complete ones >>> - Come up with a proposal of the way forward in terms of what >>> outstanding requirements should be prioritized. This would cover >>> discussions on semantic annotations(using EDAM) & BioXSD >>> >>> 2) Test and document the current codebase in preparation for a release >>> the following week. Note that this includes testing for the write API >>> >>> 3) Review the architecture with an aim to reducing the maintenance >>> overhead( especially as project will move to OAM phase next year) >>> >>> 4) Discuss the final EMBRACE import and how to handle future access to >>> the embrace registry url >>> >>> 5) Come up with a plan on how to manage content like flagging & cleaning >>> up dead links >>> >>> 6) Some design work on any quick wins that come out of our discussions >>> >>> If you have anything in mind that you think will be good to discuss/work >>> on during my time in Manchester, then please let me know. >>> >>> cheers, >>> >>> Eric >>> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers -- ============================================================ Mr Hamish McWilliam European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD, UK URL: http://www.ebi.ac.uk/ ============================================================ From jits at cs.man.ac.uk Mon Sep 27 12:00:49 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 27 Sep 2010 17:00:49 +0100 Subject: [BioCatalogue-developers] Agenda for Next Week in Manchester In-Reply-To: <4CA0BC4C.8040804@ebi.ac.uk> References: <4C98C7DD.6000404@ebi.ac.uk> <4C990CBB.80707@ebi.ac.uk> <4CA0AE3F.5010908@cs.man.ac.uk> <4CA0BC4C.8040804@ebi.ac.uk> Message-ID: <4CA0BFB1.4060404@cs.man.ac.uk> Hi Hamish, Thanks for reminding us about these! Very useful feedback here. Regarding discussions - agreed that this is low priority compared to other things. In terms of requesting this feature, it's more of a "nice to have" and "build it and see if providers and consumers communicate using it". Communications between folks is something that was part of the original proposal but isn't something that has happened in the catalogue yet. The discussions thing is something that has been done in other systems here and would be "easy" to integrate, so I figured it *might* be a quick win. But we'll see about this later on. Cheers, Jits Hamish McWilliam wrote: > Hi Jits, > >> Did you have any particular features in mind (or have some feedback on >> from others)? >> >> We've already identified the Disqus commenting* and Ratings as >> candidates for removal. > > After a little discussion to draw the memories to the surface, the > main things that were mentioned in the BioCatalogue feedback > discussion during the EMBRACE meeting in June were: > > 1. Results page white space. > For the workshop we were all using laptops, so needing to scroll a lot > when searching the catalogue or browsing the services was something > that was commented on quite a bit. While there was some discussion > about which information could be removed from the service summaries, > there was no consensus on which information could be removed, however > it was felt that the information could be rearranged to reduce the > amount of "whitespace", and the padding and pitch of the text tightened. > > 2. Services page tag cloud. > Convention for tag coluds on web pages seems to be moving towards them > being a feature for a sidebar, commonly the right sidebar. This would > move the service information up, so less scrolling. > > 3. More services per-page. > Having 10 services per page was seen as too limiting, and leading to > more page navigation than they were happy with. While this will > increase the amount of scrolling it was felt that this was better than > paging. > > 4. Service page whitespace. > Again too much scrolling, especially for fields which do not contain > information. > > 5. Reduce the header size. > Another scrolling suggestion was to reduce the height of the header. > > 6. Commenting > Wasn't seen as useful. This may be just a case of being unable to show > useful comments meaning that they didn't see it as being used/useful. > It may also reflect the feeling that since we can annotate the service > what would we be writing as a comment? > > 7. Ratings > Again not seen as useful. Not much support for rankings, partly since > this is a provider audience, also many of the rankings in the > catalogue being self-rankings, and thus a bit suspect. > > An other thing that has cropped up in discussions is: > > 8. Three flavors of result page. > The "Services" page, results page 1 and results page 2+ have different > features and look-and-feel. Was felt that one form of results page, > with the faceted features of the "Services" page would be better. This > is ignoring the lists of services in things like a provider description. > > Given the remaining development time available, these issues are only > really worth addressing if the effort required is minimal, and fits > with the schedule for the other required features. > >> * We are aiming to replace the Disqus commenting with a new >> "Discussions" tab which will allow threaded discussions to take place >> (without external user accounts, ie: better integrated into the >> BioCatalogue). We will, of course, properly run this through users first >> before releasing such a thing, > > Nice idea, but I'm not sure it would be used much, for the same > reasons commenting has not been used. For the moment this seems low > priority, has anyone been requesting this functionality? > > > Hamish > >> >> >> >> Rodrigo Lopez wrote: >>> One additional item would be to discuss an evaluation of all the >>> features of the portal with the aim of identifying the non-to-useful >>> ones (that is why I was asking earlier for some measures) and >>> potentially remove these in order to simply and focus present and >>> future work. >>> Just my two cents. >>> >>> R:) >>> >>> On 21/09/2010 15:57, Eric Nzuobontane wrote: >>>> Hi Rodrigo, >>>> >>>> During my time in Manchester next week, we intend to discuss and >>>> work on >>>> the following amongst other things: >>>> >>>> 1) Review the roadmap >>>> - Determine which requirements have been met, wholly or partially and >>>> evaluate what is needed to complete the partially complete ones >>>> - Come up with a proposal of the way forward in terms of what >>>> outstanding requirements should be prioritized. This would cover >>>> discussions on semantic annotations(using EDAM) & BioXSD >>>> >>>> 2) Test and document the current codebase in preparation for a release >>>> the following week. Note that this includes testing for the write API >>>> >>>> 3) Review the architecture with an aim to reducing the maintenance >>>> overhead( especially as project will move to OAM phase next year) >>>> >>>> 4) Discuss the final EMBRACE import and how to handle future access to >>>> the embrace registry url >>>> >>>> 5) Come up with a plan on how to manage content like flagging & >>>> cleaning >>>> up dead links >>>> >>>> 6) Some design work on any quick wins that come out of our discussions >>>> >>>> If you have anything in mind that you think will be good to >>>> discuss/work >>>> on during my time in Manchester, then please let me know. >>>> >>>> cheers, >>>> >>>> Eric >>>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > From issues at mygrid.org.uk Tue Sep 28 06:52:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 28 Sep 2010 11:52:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-478) Disable the annotation level work Message-ID: <13556670.9867.1285671135330.JavaMail.jira@rosalind.cs.man.ac.uk> Disable the annotation level work --------------------------------- Key: BIOCAT-478 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-478 Project: BioCatalogue Issue Type: Task Components: Web Interface Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Disable the annotation level in the UI and revert the views to the previous state -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 06:55:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 28 Sep 2010 11:55:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-479) Change the queries that do count to use the ActiveRecord count method Message-ID: <33188271.9868.1285671315305.JavaMail.jira@rosalind.cs.man.ac.uk> Change the queries that do count to use the ActiveRecord count method --------------------------------------------------------------------- Key: BIOCAT-479 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-479 Project: BioCatalogue Issue Type: Task Components: Performance / Optimisations Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Use the ActiveRecord count method instead of loading records in memory to count. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 06:59:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 28 Sep 2010 11:59:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-480) Rename the update_success rate methods Message-ID: <28078060.9869.1285671555306.JavaMail.jira@rosalind.cs.man.ac.uk> Rename the update_success rate methods -------------------------------------- Key: BIOCAT-480 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-480 Project: BioCatalogue Issue Type: Task Components: Service Monitoring Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Consistently rename the update success rate method, use the submit_job and update notions -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 07:12:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 28 Sep 2010 12:12:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-481) Actually allow users to delete test scripts only, not URL monitors. Message-ID: <18563836.9870.1285672335308.JavaMail.jira@rosalind.cs.man.ac.uk> Actually allow users to delete test scripts only, not URL monitors. -------------------------------------------------------------------- Key: BIOCAT-481 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-481 Project: BioCatalogue Issue Type: Task Components: Service Monitoring Reporter: Eric Nzuobontane Assignee: Jiten Bhagat Deleting test scripts would completely remove their history from BioCatalogue as well. The history of the script is longer relevant to the service if the test itself is not longer relevant, so it is not necessary to keep it. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 07:14:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 28 Sep 2010 12:14:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-481) Actually allow users to delete test scripts only, not URL monitors. In-Reply-To: <18563836.9870.1285672335308.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22535116.9871.1285672455332.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-481?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-481: --------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > Actually allow users to delete test scripts only, not URL monitors. > -------------------------------------------------------------------- > > Key: BIOCAT-481 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-481 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Deleting test scripts would completely remove their history from BioCatalogue as well. The history of the script is longer relevant to the service if the test itself is not longer relevant, so it is not necessary to keep it. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 07:16:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 12:16:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-481) Actually allow users to delete test scripts only, not URL monitors. In-Reply-To: <18563836.9870.1285672335308.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31486843.9872.1285672575321.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-481?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15988#action_15988 ] Jiten Bhagat commented on BIOCAT-481: ------------------------------------- Remember that this is only for user submitted tests, eg: Test Scripts. The URL Monitors should not be able to be deleted by users (only admiins). > Actually allow users to delete test scripts only, not URL monitors. > -------------------------------------------------------------------- > > Key: BIOCAT-481 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-481 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Deleting test scripts would completely remove their history from BioCatalogue as well. The history of the script is longer relevant to the service if the test itself is not longer relevant, so it is not necessary to keep it. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue Sep 28 08:42:16 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 28 Sep 2010 08:42:16 -0400 (EDT) Subject: [BioCatalogue-developers] [2246] trunk/vendor/plugins/acts_as_solr/lib/tasks/solr.rake: Hack fix for the rake solr: start issue that occurs only with certain versions of Ruby 1.8.7 (see: http ://www.mygrid.org.uk/dev/issues/browse/SYSMO-348 and http://redmine. ruby-lang.org/issues/show/2708). Message-ID: <20100928124216.DD135177993F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Sep 28 08:42:24 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 28 Sep 2010 08:42:24 -0400 (EDT) Subject: [BioCatalogue-developers] [2247] trunk: - rename the methods to update_success rate of a test to make them more consistent Message-ID: <20100928124224.E98A819782CD@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Sep 28 08:47:12 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 28 Sep 2010 08:47:12 -0400 (EDT) Subject: [BioCatalogue-developers] [2248] trunk/vendor/plugins/acts_as_solr/lib/tasks/solr.rake: Oops typo! Message-ID: <20100928124713.05580177993F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Sep 28 09:02:48 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 28 Sep 2010 09:02:48 -0400 (EDT) Subject: [BioCatalogue-developers] [2249] trunk/app/views/services: - revert the changes to the _listings.html .erb & name_section.html.erb which included the annotation level stuff Message-ID: <20100928130248.AADB21858370@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Sep 28 09:11:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 28 Sep 2010 14:11:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-478) Disable the annotation level work In-Reply-To: <13556670.9867.1285671135330.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26702316.9873.1285679475330.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-478?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-478 started by Eric Nzuobontane. > Disable the annotation level work > --------------------------------- > > Key: BIOCAT-478 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-478 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Disable the annotation level in the UI and revert the views to the previous state -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 09:13:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 28 Sep 2010 14:13:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-478) Disable the annotation level work In-Reply-To: <13556670.9867.1285671135330.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10643565.9874.1285679595334.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-478?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15989#action_15989 ] Eric Nzuobontane commented on BIOCAT-478: ----------------------------------------- This has been disabled in trunk. This work can be continued in developer branch accompanied with the discussion that needs to had in parallel with the development. > Disable the annotation level work > --------------------------------- > > Key: BIOCAT-478 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-478 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Disable the annotation level in the UI and revert the views to the previous state -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 09:13:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 28 Sep 2010 14:13:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-482) Continue development in a branch Message-ID: <9174203.9875.1285679596210.JavaMail.jira@rosalind.cs.man.ac.uk> Continue development in a branch -------------------------------- Key: BIOCAT-482 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-482 Project: BioCatalogue Issue Type: Sub-task Components: Web Interface Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue Sep 28 10:13:03 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 28 Sep 2010 10:13:03 -0400 (EDT) Subject: [BioCatalogue-developers] [2250] trunk/app/helpers/activity_feeds_helper.rb: Minor bugfix to the generation of the status change icons in the monitoring status changes activity feed . Message-ID: <20100928141303.D72CF1858371@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Sep 28 10:13:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 28 Sep 2010 10:13:42 -0400 (EDT) Subject: [BioCatalogue-developers] [2251] trunk/app/views/shared/_login_form.html.erb: Fix to the login form due to bug introduced in a previous commit. Message-ID: <20100928141342.600FB19782DB@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Sep 28 10:18:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 28 Sep 2010 15:18:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-483) Monitoring should only send status updates to humans, not virtual submitters like registries. Message-ID: <17780554.9880.1285683495310.JavaMail.jira@rosalind.cs.man.ac.uk> Monitoring should only send status updates to humans, not virtual submitters like registries. --------------------------------------------------------------------------------------------- Key: BIOCAT-483 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-483 Project: BioCatalogue Issue Type: Bug Components: Service Monitoring Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane The monitoring piece should only send mail to humans and the sending of mail and the submission of test results should be decoupled. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 10:34:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 15:34:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-484) Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) In-Reply-To: <20152521.9882.1285684455326.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23139521.9883.1285684456550.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-484: -------------------------------- Summary: Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) (was: Improve the service_annotation_report script) Description: Need: # To take into account REST services # To take into account the Soaplab descriptions # To add percentages # To add more breakdowns was: Need: # To take into REST services # To take into account the Soaplab descriptions # To add percentages # To add more breakdowns > Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-484 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > Need: > # To take into account REST services > # To take into account the Soaplab descriptions > # To add percentages > # To add more breakdowns -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 10:34:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 15:34:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-484) Improve the service_annotation_report script Message-ID: <20152521.9882.1285684455326.JavaMail.jira@rosalind.cs.man.ac.uk> Improve the service_annotation_report script -------------------------------------------- Key: BIOCAT-484 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484 Project: BioCatalogue Issue Type: New Feature Reporter: Jiten Bhagat Assignee: Jiten Bhagat Need: # To take into REST services # To take into account the Soaplab descriptions # To add percentages # To add more breakdowns -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 10:30:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 15:30:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-343) Implement a "News" tab on a service's page In-Reply-To: <29654500.520.1274178676994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32594210.9881.1285684215361.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-343 stopped by Jiten Bhagat. > Implement a "News" tab on a service's page > ------------------------------------------ > > Key: BIOCAT-343 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 days > Time Spent: 1 day, 1 hour > Remaining Estimate: 7 hours > > This should show a full activity list/feed for the service, showing events that have happened, like new annotations, WSDL changes, etc. > Maybe have the WSDL changes in a separate column on the right hand side? -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue Sep 28 10:43:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 28 Sep 2010 10:43:47 -0400 (EDT) Subject: [BioCatalogue-developers] [2252] trunk/app/views/services/_index_filters.html.erb: [BIOCAT-473] Bugfix Message-ID: <20100928144347.5C248177993F@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Sep 28 10:47:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 15:47:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-473) Missing method in module : undefined method `get_filters_for_soap_input_tags' for BioCatalogue::Filtering::Services:Module In-Reply-To: <28153708.9565.1284997515321.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6958292.9884.1285685235358.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-473?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-473. --------------------------------- Resolution: Fixed Issue found and fixed > Missing method in module : undefined method `get_filters_for_soap_input_tags' for BioCatalogue::Filtering::Services:Module > --------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-473 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-473 > Project: BioCatalogue > Issue Type: Bug > Components: Search / Filtering / Browsing > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > There is a bug in the service filtering module. The error message generated is attached below: > undefined method `get_filters_for_soap_input_tags' for BioCatalogue::Filtering::Services:Module > On line #64 of app/views/services/_index_filters.html.erb > 61: :filter_type => :tag_ops } -%> > 62: > 63: > 64: <% inputs_tags_filters = BioCatalogue::Filtering::Services.get_filters_for_soap_input_tags %> > 65: <%= render :partial => "filtering/filter_options_generic", > 66: :locals => { :filters => inputs_tags_filters, > 67: :filter_type => :tag_ins } -%> > app/views/services/_index_filters.html.erb:64 > app/views/services/_index_filters.html.erb:11 > app/views/services/index.html.erb:29 > app/controllers/services_controller.rb:40:in `index' -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 10:47:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 15:47:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-473) Missing method in module : undefined method `get_filters_for_soap_input_tags' for BioCatalogue::Filtering::Services:Module In-Reply-To: <28153708.9565.1284997515321.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8415988.9885.1285685236635.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-473?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-473. ------------------------------- > Missing method in module : undefined method `get_filters_for_soap_input_tags' for BioCatalogue::Filtering::Services:Module > --------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-473 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-473 > Project: BioCatalogue > Issue Type: Bug > Components: Search / Filtering / Browsing > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > There is a bug in the service filtering module. The error message generated is attached below: > undefined method `get_filters_for_soap_input_tags' for BioCatalogue::Filtering::Services:Module > On line #64 of app/views/services/_index_filters.html.erb > 61: :filter_type => :tag_ops } -%> > 62: > 63: > 64: <% inputs_tags_filters = BioCatalogue::Filtering::Services.get_filters_for_soap_input_tags %> > 65: <%= render :partial => "filtering/filter_options_generic", > 66: :locals => { :filters => inputs_tags_filters, > 67: :filter_type => :tag_ins } -%> > app/views/services/_index_filters.html.erb:64 > app/views/services/_index_filters.html.erb:11 > app/views/services/index.html.erb:29 > app/controllers/services_controller.rb:40:in `index' -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 10:53:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 15:53:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-474) Error page return when attempting to submit a service before sign in. A redirect was expected In-Reply-To: <9915096.9712.1285153455393.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <218524.9886.1285685595352.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-474?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-474. --------------------------------- Resolution: Fixed This was caused due to an issue in the log in form which has since been fixed. > Error page return when attempting to submit a service before sign in. A redirect was expected > --------------------------------------------------------------------------------------------- > > Key: BIOCAT-474 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-474 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Environment: UI > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > If one attempts to submit a service before sign in, the expectation is that the user will be redirected to the login page. However, an error page is returned instead. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 10:53:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 15:53:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-474) Error page return when attempting to submit a service before sign in. A redirect was expected In-Reply-To: <9915096.9712.1285153455393.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21636485.9887.1285685596769.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-474?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-474. ------------------------------- > Error page return when attempting to submit a service before sign in. A redirect was expected > --------------------------------------------------------------------------------------------- > > Key: BIOCAT-474 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-474 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Environment: UI > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > If one attempts to submit a service before sign in, the expectation is that the user will be redirected to the login page. However, an error page is returned instead. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 10:30:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 15:30:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-343) Implement a "News" tab on a service's page In-Reply-To: <29654500.520.1274178676994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32594210.9881.1285684215361.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-343 stopped by Jiten Bhagat. > Implement a "News" tab on a service's page > ------------------------------------------ > > Key: BIOCAT-343 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 days > Time Spent: 1 day, 1 hour > Remaining Estimate: 7 hours > > This should show a full activity list/feed for the service, showing events that have happened, like new annotations, WSDL changes, etc. > Maybe have the WSDL changes in a separate column on the right hand side? -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 11:08:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 28 Sep 2010 16:08:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-472) Submitters(responsibles) should be able to remove their uploaded tests In-Reply-To: <9613162.9376.1284717435488.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30296739.9888.1285686495335.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-472?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15992#action_15992 ] Eric Nzuobontane commented on BIOCAT-472: ----------------------------------------- Having given some more thought to the issue, we have now decided to allow users to delete their own test scripts with all their associated meta data like test results. Users are also able to enable/disable their tests > Submitters(responsibles) should be able to remove their uploaded tests > ---------------------------------------------------------------------- > > Key: BIOCAT-472 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-472 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Users should be given the possibility to remove their own tests. Removing test however would mean that all the monitoring data associated with that test would be lost as well. At the moment, the policy has been to disable tests rather than to remove them. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 12:33:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 17:33:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-485) Stats generation is failing due to recent changes in the Tags module Message-ID: <8877172.9889.1285691595325.JavaMail.jira@rosalind.cs.man.ac.uk> Stats generation is failing due to recent changes in the Tags module -------------------------------------------------------------------- Key: BIOCAT-485 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-485 Project: BioCatalogue Issue Type: Bug Components: Stats Dashboard Environment: UI, Backend Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical This is important as we need to generate stats for Carole -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 12:33:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 17:33:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-485) Stats generation is failing due to recent changes in the Tags module Message-ID: <8877172.9889.1285691595325.JavaMail.jira@rosalind.cs.man.ac.uk> Stats generation is failing due to recent changes in the Tags module -------------------------------------------------------------------- Key: BIOCAT-485 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-485 Project: BioCatalogue Issue Type: Bug Components: Stats Dashboard Environment: UI, Backend Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical This is important as we need to generate stats for Carole -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 12:33:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 17:33:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-485) Stats generation is failing due to recent changes in the Tags module Message-ID: <8877172.9889.1285691595325.JavaMail.jira@rosalind.cs.man.ac.uk> Stats generation is failing due to recent changes in the Tags module -------------------------------------------------------------------- Key: BIOCAT-485 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-485 Project: BioCatalogue Issue Type: Bug Components: Stats Dashboard Environment: UI, Backend Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical This is important as we need to generate stats for Carole -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 12:33:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 17:33:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-485) Stats generation is failing due to recent changes in the Tags module Message-ID: <8877172.9889.1285691595325.JavaMail.jira@rosalind.cs.man.ac.uk> Stats generation is failing due to recent changes in the Tags module -------------------------------------------------------------------- Key: BIOCAT-485 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-485 Project: BioCatalogue Issue Type: Bug Components: Stats Dashboard Environment: UI, Backend Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical This is important as we need to generate stats for Carole -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue Sep 28 12:49:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 28 Sep 2010 12:49:02 -0400 (EDT) Subject: [BioCatalogue-developers] [2253] trunk: [BIOCAT-485] Fixed: stats generation is failing due to recent changes in the Tags module. Message-ID: <20100928164902.DD7FC1858361@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Sep 28 12:51:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 17:51:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-485) Stats generation is failing due to recent changes in the Tags module In-Reply-To: <8877172.9889.1285691595325.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3135970.9890.1285692675361.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-485?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10438 ] Jiten Bhagat logged work on BIOCAT-485: --------------------------------------- Author: Jiten Bhagat Created on: 2010-09-28 17:49 Start Date: 2010-09-28 15:49 Worklog Time Spent: 2 hours Issue Time Tracking ------------------- Remaining Estimate: 1 hour (was: 3 hours) Time Spent: 2 hours > Stats generation is failing due to recent changes in the Tags module > -------------------------------------------------------------------- > > Key: BIOCAT-485 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-485 > Project: BioCatalogue > Issue Type: Bug > Components: Stats Dashboard > Environment: UI, Backend > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Original Estimate: 3 hours > Time Spent: 2 hours > Remaining Estimate: 1 hour > > This is important as we need to generate stats for Carole -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 12:51:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 17:51:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-485) Stats generation is failing due to recent changes in the Tags module In-Reply-To: <8877172.9889.1285691595325.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14687713.9891.1285692676597.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-485?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-485. --------------------------------- Remaining Estimate: 0 minutes (was: 1 hour) Resolution: Fixed Fixed > Stats generation is failing due to recent changes in the Tags module > -------------------------------------------------------------------- > > Key: BIOCAT-485 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-485 > Project: BioCatalogue > Issue Type: Bug > Components: Stats Dashboard > Environment: UI, Backend > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Original Estimate: 3 hours > Time Spent: 2 hours > Remaining Estimate: 0 minutes > > This is important as we need to generate stats for Carole -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Sep 28 12:51:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Sep 2010 17:51:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-485) Stats generation is failing due to recent changes in the Tags module In-Reply-To: <8877172.9889.1285691595325.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29016707.9892.1285692677550.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-485?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-485. ------------------------------- > Stats generation is failing due to recent changes in the Tags module > -------------------------------------------------------------------- > > Key: BIOCAT-485 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-485 > Project: BioCatalogue > Issue Type: Bug > Components: Stats Dashboard > Environment: UI, Backend > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Original Estimate: 3 hours > Time Spent: 2 hours > Remaining Estimate: 0 minutes > > This is important as we need to generate stats for Carole -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Wed Sep 29 05:50:20 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 29 Sep 2010 10:50:20 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getMaskTrajectoryFromMD_Trajectory' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getMaskTrajectoryFromMD_Trajectory' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1148 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Sep 29 06:14:26 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Sep 2010 06:14:26 -0400 (EDT) Subject: [BioCatalogue-developers] [2254] trunk: - allow users to delete their test scripts Message-ID: <20100929101427.0D0081858368@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Sep 29 06:29:59 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Sep 2010 06:29:59 -0400 (EDT) Subject: [BioCatalogue-developers] [2255] trunk/db/migrate/ 20100928132446_remove_hidden_field_from_service_test.rb: fix migration class Message-ID: <20100929102959.2FAC1177994B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Sep 29 07:04:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Sep 2010 07:04:22 -0400 (EDT) Subject: [BioCatalogue-developers] [2256] trunk: Minor fixes Message-ID: <20100929110422.B37231858379@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Sep 29 09:03:06 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Sep 2010 09:03:06 -0400 (EDT) Subject: [BioCatalogue-developers] [2257] trunk/app/models/test_result.rb: minor fixes to decouple test result create and pre/post processing Message-ID: <20100929130306.70D4B177994B@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Sep 29 09:20:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 29 Sep 2010 14:20:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-481) Actually allow users to delete test scripts only, not URL monitors. In-Reply-To: <18563836.9870.1285672335308.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8723324.9894.1285766415375.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-481?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15994#action_15994 ] Eric Nzuobontane commented on BIOCAT-481: ----------------------------------------- Even admins should not be deleting url monitors. They should just be disable if it is so required. > Actually allow users to delete test scripts only, not URL monitors. > -------------------------------------------------------------------- > > Key: BIOCAT-481 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-481 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Deleting test scripts would completely remove their history from BioCatalogue as well. The history of the script is longer relevant to the service if the test itself is not longer relevant, so it is not necessary to keep it. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Sep 29 09:20:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 29 Sep 2010 14:20:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-481) Actually allow users to delete test scripts only, not URL monitors. In-Reply-To: <18563836.9870.1285672335308.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8233200.9895.1285766417679.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-481?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-481. ------------------------------------- Resolution: Fixed Now fixed and in trunk > Actually allow users to delete test scripts only, not URL monitors. > -------------------------------------------------------------------- > > Key: BIOCAT-481 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-481 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Deleting test scripts would completely remove their history from BioCatalogue as well. The history of the script is longer relevant to the service if the test itself is not longer relevant, so it is not necessary to keep it. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Sep 29 09:22:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 29 Sep 2010 14:22:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-472) Submitters(responsibles) should be able to remove their uploaded tests In-Reply-To: <9613162.9376.1284717435488.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12638386.9896.1285766535318.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-472?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-472. ------------------------------------- Resolution: Fixed > Submitters(responsibles) should be able to remove their uploaded tests > ---------------------------------------------------------------------- > > Key: BIOCAT-472 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-472 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Users should be given the possibility to remove their own tests. Removing test however would mean that all the monitoring data associated with that test would be lost as well. At the moment, the policy has been to disable tests rather than to remove them. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Sep 29 09:24:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 29 Sep 2010 14:24:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-483) Monitoring should only send status updates to humans, not virtual submitters like registries. In-Reply-To: <17780554.9880.1285683495310.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18993969.9897.1285766655309.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-483?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-483. ------------------------------------- Resolution: Fixed Fixed > Monitoring should only send status updates to humans, not virtual submitters like registries. > --------------------------------------------------------------------------------------------- > > Key: BIOCAT-483 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-483 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > The monitoring piece should only send mail to humans and the sending of mail and the submission of test results should be decoupled. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Sep 29 09:46:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 29 Sep 2010 14:46:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-486) Write up the requirements for the annotation level feature on the wiki page Message-ID: <31626901.9901.1285767975304.JavaMail.jira@rosalind.cs.man.ac.uk> Write up the requirements for the annotation level feature on the wiki page --------------------------------------------------------------------------- Key: BIOCAT-486 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-486 Project: BioCatalogue Issue Type: Task Components: Wiki Environment: Wiki Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Add the Requirements & documentation for the annotation level feature to the existing wiki page. http://www.biocatalogue.org/wiki/doku.php?id=development:software_development:annotation_models -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Sep 29 12:26:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 29 Sep 2010 17:26:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-487) Exception generated by linked_data handler Message-ID: <18811203.9902.1285777575311.JavaMail.jira@rosalind.cs.man.ac.uk> Exception generated by linked_data handler ------------------------------------------ Key: BIOCAT-487 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-487 Project: BioCatalogue Issue Type: Task Components: REST API Reporter: Eric Nzuobontane Assignee: Jiten Bhagat LinkedDataHandler metal app... Intial URL: /services/10 undefined method `to_sym' for nil:NilClass /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/app/metal/linked_data_handler.rb:86:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/app/metal/linked_data_handler.rb:43:in `call' /usr/lib/ruby/1.8/benchmark.rb:293:in `measure' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/app/metal/linked_data_handler.rb:41:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/railties/lib/rails/rack/metal.rb:44:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/railties/lib/rails/rack/metal.rb:43:in `each' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/railties/lib/rails/rack/metal.rb:43:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in `cache' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in `cache' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `synchronize' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in `call' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in `safe_fork' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in `start' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in `start' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Sep 29 12:28:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 29 Sep 2010 17:28:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-487) Exception generated by linked_data handler In-Reply-To: <18811203.9902.1285777575311.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26458572.9903.1285777695325.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-487?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane updated BIOCAT-487: ------------------------------------ Description: LinkedDataHandler metal app... Intial URL: /services/10 undefined method `to_sym' for nil:NilClass /rails/biocatalogue/app/metal/linked_data_handler.rb:86:in `call' rails/biocatalogue/app/metal/linked_data_handler.rb:43:in `call' lib/ruby/1.8/benchmark.rb:293:in `measure' was: LinkedDataHandler metal app... Intial URL: /services/10 undefined method `to_sym' for nil:NilClass /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/app/metal/linked_data_handler.rb:86:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/app/metal/linked_data_handler.rb:43:in `call' /usr/lib/ruby/1.8/benchmark.rb:293:in `measure' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/app/metal/linked_data_handler.rb:41:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/railties/lib/rails/rack/metal.rb:44:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/railties/lib/rails/rack/metal.rb:43:in `each' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/railties/lib/rails/rack/metal.rb:43:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in `cache' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in `cache' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `synchronize' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' /net/nas11a/vol1/alien-www/html/test_biocatalogue/rails/biocatalogue/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in `call' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in `safe_fork' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in `start' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in `start' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' /ebi/www/ptest/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 > Exception generated by linked_data handler > ------------------------------------------ > > Key: BIOCAT-487 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-487 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > LinkedDataHandler metal app... > Intial URL: /services/10 > undefined method `to_sym' for nil:NilClass > /rails/biocatalogue/app/metal/linked_data_handler.rb:86:in `call' > rails/biocatalogue/app/metal/linked_data_handler.rb:43:in `call' > lib/ruby/1.8/benchmark.rb:293:in `measure' -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Sep 29 12:40:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 29 Sep 2010 17:40:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-488) Investigate the double rendering error generated by the login controller when ssl is switched on Message-ID: <16949619.9904.1285778415305.JavaMail.jira@rosalind.cs.man.ac.uk> Investigate the double rendering error generated by the login controller when ssl is switched on ------------------------------------------------------------------------------------------------ Key: BIOCAT-488 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-488 Project: BioCatalogue Issue Type: Task Components: Misc Codebase Reporter: Eric Nzuobontane Assignee: Jiten Bhagat Login fails with a double rendering error when ssl is switch on. Preliminary investigation shows that this may be cause by the redirects in "ensure_proper_protocol" method in the vendor/plugins/ssl_requirement/lib/ssl_requirement.rb. Further investigation needed. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Wed Sep 29 14:01:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Sep 2010 14:01:47 -0400 (EDT) Subject: [BioCatalogue-developers] [2258] trunk: Latest work on a new service annotation report script ( unfinished). Message-ID: <20100929180147.CAF1619782D4@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Sep 30 10:29:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 30 Sep 2010 15:29:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-484) Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) In-Reply-To: <20152521.9882.1285684455326.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27198208.9907.1285856955395.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-484: -------------------------------- Original Estimate: 6 hours (was: 4 hours) Remaining Estimate: 6 hours (was: 4 hours) > Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-484 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 6 hours > Remaining Estimate: 6 hours > > Need: > # To take into account REST services > # To take into account the Soaplab descriptions > # To add percentages > # To add more breakdowns -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Sep 30 10:29:19 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 30 Sep 2010 15:29:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-484) Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) In-Reply-To: <20152521.9882.1285684455326.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32381206.9908.1285856959647.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10439 ] Jiten Bhagat logged work on BIOCAT-484: --------------------------------------- Author: Jiten Bhagat Created on: 2010-09-30 15:27 Start Date: 2010-09-29 15:27 Worklog Time Spent: 3 hours Issue Time Tracking ------------------- Remaining Estimate: 3 hours (was: 6 hours) Time Spent: 3 hours > Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-484 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 6 hours > Time Spent: 3 hours > Remaining Estimate: 3 hours > > Need: > # To take into account REST services > # To take into account the Soaplab descriptions > # To add percentages > # To add more breakdowns -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Sep 30 11:06:35 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 30 Sep 2010 11:06:35 -0400 (EDT) Subject: [BioCatalogue-developers] [2259] trunk: Latest work on the service annotation report script. Message-ID: <20100930150636.07A9D1858396@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Sep 30 11:53:45 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 30 Sep 2010 11:53:45 -0400 (EDT) Subject: [BioCatalogue-developers] [2260] trunk/script/biocatalogue: Latest work on the service annotation report script. Message-ID: <20100930155345.75FB71678316@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Sep 30 12:56:00 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 30 Sep 2010 12:56:00 -0400 (EDT) Subject: [BioCatalogue-developers] [2261] trunk/script/biocatalogue/service_annotation_report.rb: Latest work on the service annotation report script. Message-ID: <20100930165600.1DA46197828C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Sep 30 13:03:46 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 30 Sep 2010 13:03:46 -0400 (EDT) Subject: [BioCatalogue-developers] [2262] trunk/script/biocatalogue: Latest work on the service annotation report script. Message-ID: <20100930170346.9D2381858373@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Sep 30 13:05:48 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 30 Sep 2010 13:05:48 -0400 (EDT) Subject: [BioCatalogue-developers] [2263] trunk/script/biocatalogue: Latest work on the service annotation report script. Message-ID: <20100930170548.D019F197828C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Sep 30 16:57:57 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 30 Sep 2010 16:57:57 -0400 (EDT) Subject: [BioCatalogue-developers] [2264] trunk/script/biocatalogue: Latest work on the service annotation report script. Message-ID: <20100930205757.87FBB1858375@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Sep 30 17:04:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 30 Sep 2010 17:04:42 -0400 (EDT) Subject: [BioCatalogue-developers] [2265] trunk/script/biocatalogue/service_annotation_report.rb: Latest work on the service annotation report script. Message-ID: <20100930210442.84FE4177993F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Sep 30 17:16:33 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 30 Sep 2010 17:16:33 -0400 (EDT) Subject: [BioCatalogue-developers] [2266] trunk/script/biocatalogue: Latest work on the service annotation report script. Message-ID: <20100930211633.405821858368@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Sep 30 17:25:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 30 Sep 2010 22:25:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-489) Update stats to take into account archived items Message-ID: <17224897.9910.1285881915438.JavaMail.jira@rosalind.cs.man.ac.uk> Update stats to take into account archived items ------------------------------------------------ Key: BIOCAT-489 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-489 Project: BioCatalogue Issue Type: Improvement Components: Stats Dashboard Reporter: Jiten Bhagat Assignee: Jiten Bhagat So the totals should reflect only unarchived things, and maybe a separate archived count can be shown too. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Sep 30 17:28:12 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 30 Sep 2010 17:28:12 -0400 (EDT) Subject: [BioCatalogue-developers] [2267] trunk/app/models/rest_method.rb: Made the associations in RestMethod aware of the archived status of things . Message-ID: <20100930212812.E6BA9185836B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Sep 30 17:31:17 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 30 Sep 2010 17:31:17 -0400 (EDT) Subject: [BioCatalogue-developers] [2268] trunk/script/biocatalogue: Latest work on the service annotation report script - take into account archived items . Message-ID: <20100930213117.BBB45185836B@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Sep 30 17:25:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 30 Sep 2010 22:25:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-489) Update stats to take into account archived items Message-ID: <17224897.9910.1285881915438.JavaMail.jira@rosalind.cs.man.ac.uk> Update stats to take into account archived items ------------------------------------------------ Key: BIOCAT-489 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-489 Project: BioCatalogue Issue Type: Improvement Components: Stats Dashboard Reporter: Jiten Bhagat Assignee: Jiten Bhagat So the totals should reflect only unarchived things, and maybe a separate archived count can be shown too. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Sep 30 17:52:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 30 Sep 2010 17:52:09 -0400 (EDT) Subject: [BioCatalogue-developers] [2269] trunk/script/biocatalogue/service_annotation_report.rb: Latest work on the service annotation report script - fixes for total counts . Message-ID: <20100930215209.E6C121678316@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Sep 30 17:25:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 30 Sep 2010 22:25:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-489) Update stats to take into account archived items Message-ID: <17224897.9910.1285881915438.JavaMail.jira@rosalind.cs.man.ac.uk> Update stats to take into account archived items ------------------------------------------------ Key: BIOCAT-489 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-489 Project: BioCatalogue Issue Type: Improvement Components: Stats Dashboard Reporter: Jiten Bhagat Assignee: Jiten Bhagat So the totals should reflect only unarchived things, and maybe a separate archived count can be shown too. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Sep 30 18:03:51 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 30 Sep 2010 18:03:51 -0400 (EDT) Subject: [BioCatalogue-developers] [2270] trunk/script/biocatalogue/service_annotation_report.rb: Latest work on the service annotation report script - bugfix. Message-ID: <20100930220351.78214185836C@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Sep 30 18:19:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 30 Sep 2010 23:19:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-484) Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) In-Reply-To: <20152521.9882.1285684455326.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18319496.9913.1285885156485.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-484. ------------------------------- > Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-484 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 6 hours > Time Spent: 1 day, 2 hours > Remaining Estimate: 0 minutes > > Need: > # To take into account REST services > # To take into account the Soaplab descriptions > # To add percentages > # To add more breakdowns -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Sep 30 18:17:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 30 Sep 2010 23:17:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-484) Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) In-Reply-To: <20152521.9882.1285684455326.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1884096.9911.1285885035889.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10440 ] Jiten Bhagat logged work on BIOCAT-484: --------------------------------------- Author: Jiten Bhagat Created on: 2010-09-30 23:15 Start Date: 2010-09-30 10:30 Worklog Time Spent: 7 hours Work Description: Took longer than expected Issue Time Tracking ------------------- Remaining Estimate: 0 minutes (was: 3 hours) Time Spent: 1 day, 2 hours (was: 3 hours) > Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-484 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 6 hours > Time Spent: 1 day, 2 hours > Remaining Estimate: 0 minutes > > Need: > # To take into account REST services > # To take into account the Soaplab descriptions > # To add percentages > # To add more breakdowns -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Sep 30 18:19:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 30 Sep 2010 23:19:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-484) Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) In-Reply-To: <20152521.9882.1285684455326.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10358655.9912.1285885155361.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-484. --------------------------------- Resolution: Implemented Script has been rewritten to output an HTML report with more stats now and taking into account REST service too. > Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-484 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 6 hours > Time Spent: 1 day, 2 hours > Remaining Estimate: 0 minutes > > Need: > # To take into account REST services > # To take into account the Soaplab descriptions > # To add percentages > # To add more breakdowns -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Sep 30 18:19:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 30 Sep 2010 23:19:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-484) Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) In-Reply-To: <20152521.9882.1285684455326.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10358655.9912.1285885155361.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-484. --------------------------------- Resolution: Implemented Script has been rewritten to output an HTML report with more stats now and taking into account REST service too. > Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-484 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 6 hours > Time Spent: 1 day, 2 hours > Remaining Estimate: 0 minutes > > Need: > # To take into account REST services > # To take into account the Soaplab descriptions > # To add percentages > # To add more breakdowns -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Sep 30 18:17:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 30 Sep 2010 23:17:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-484) Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) In-Reply-To: <20152521.9882.1285684455326.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1884096.9911.1285885035889.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10440 ] Jiten Bhagat logged work on BIOCAT-484: --------------------------------------- Author: Jiten Bhagat Created on: 2010-09-30 23:15 Start Date: 2010-09-30 10:30 Worklog Time Spent: 7 hours Work Description: Took longer than expected Issue Time Tracking ------------------- Remaining Estimate: 0 minutes (was: 3 hours) Time Spent: 1 day, 2 hours (was: 3 hours) > Improve the service_annotation_report script for stats generation for Carole's BioIT talk (Sep 2010) > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-484 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-484 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 6 hours > Time Spent: 1 day, 2 hours > Remaining Estimate: 0 minutes > > Need: > # To take into account REST services > # To take into account the Soaplab descriptions > # To add percentages > # To add more breakdowns -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira