From utopia at cs.man.ac.uk Sun Aug 1 00:10:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 01 Aug 2010 05:10:06 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runCExonic' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runCExonic' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1098 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Mon Aug 2 09:51:11 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 2 Aug 2010 09:51:11 -0400 (EDT) Subject: [BioCatalogue-developers] [2166] branches/rest-api-updates: - updated /service_providers/ {id} to include the hostnames associated with the specified service provider Message-ID: <20100802135111.874AD1678317@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Aug 4 10:49:20 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 04 Aug 2010 15:49:20 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'phosphoELMdb' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'phosphoELMdb' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/115 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Aug 4 10:53:34 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 04 Aug 2010 15:53:34 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:textQueryOMIM' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:textQueryOMIM' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1061 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Wed Aug 4 10:54:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 4 Aug 2010 15:54:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-450) Update functional tests Message-ID: <16071792.7950.1280933655385.JavaMail.jira@rosalind.cs.man.ac.uk> Update functional tests ----------------------- Key: BIOCAT-450 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-450 Project: BioCatalogue Issue Type: Task Components: Misc Codebase 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 utopia at cs.man.ac.uk Wed Aug 4 11:02:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 04 Aug 2010 16:02:33 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'phosphoELMdb' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'phosphoELMdb' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/115 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Aug 5 03:16:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 05 Aug 2010 08:16:06 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS topo' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS topo' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1820 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Aug 5 03:26:35 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 05 Aug 2010 08:26:35 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getSymbolInteractions' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getSymbolInteractions' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1088 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Aug 5 03:31:59 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 05 Aug 2010 08:31:59 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runLeapFromAMBER_MD_Structure' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runLeapFromAMBER_MD_Structure' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1182 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Aug 5 03:34:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 05 Aug 2010 08:34:10 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getMaskTrajectoryFromMD_Trajectory' changed to Passed 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 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1148 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Thu Aug 5 09:12:48 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 5 Aug 2010 09:12:48 -0400 (EDT) Subject: [BioCatalogue-developers] [2167] trunk/test/functional: - updated the functional tests that were failing to make them pass ( for now) Message-ID: <20100805131248.976D61858378@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Aug 5 11:07:52 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 5 Aug 2010 11:07:52 -0400 (EDT) Subject: [BioCatalogue-developers] [2168] branches/rest-api-updates: - pulled in changes from trunk to make functional tests pass Message-ID: <20100805150752.E923D185838A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Aug 5 11:27:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 5 Aug 2010 11:27:14 -0400 (EDT) Subject: [BioCatalogue-developers] [2169] branches/rest-api-updates/script/biocatalogue/api/tests/ json_test_helper.rb: Fix for unsupported method Hash#first on some versions of Ruby. Message-ID: <20100805152715.094841858379@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Aug 6 03:00:18 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 06 Aug 2010 08:00:18 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getSymbolInteractionsXML' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getSymbolInteractionsXML' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1087 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Aug 6 05:42:25 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 06 Aug 2010 10:42:25 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:fromXYDataTextToArrayFloat' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:fromXYDataTextToArrayFloat' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1059 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Aug 6 06:15:30 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 6 Aug 2010 06:15:30 -0400 (EDT) Subject: [BioCatalogue-developers] [2170] branches/rest-api-updates: REST API work: bringing the schema up to date with the new REST Services endpoints and other changes . Message-ID: <20100806101530.E88F4185837E@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Aug 6 09:00:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 6 Aug 2010 09:00:07 -0400 (EDT) Subject: [BioCatalogue-developers] [2171] branches/rest-api-updates/public/2009/xml/rest/schema-v1.xsd: REST API work: minor update to the XML schema. Message-ID: <20100806130008.221621858395@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Aug 6 09:05:50 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 6 Aug 2010 09:05:50 -0400 (EDT) Subject: [BioCatalogue-developers] [2172] branches/rest-api-updates/public/2009/xml/rest/schema-v1.xsd: REST API work: updated schema for RestMethod to further break down the " inputs" and "outputs" into sub-collection of "parameters" and " representations". Message-ID: <20100806130551.1214B18583A0@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Aug 6 09:39:02 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 06 Aug 2010 14:39:02 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:parseAccessibilityFromPHDText' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:parseAccessibilityFromPHDText' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1110 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Aug 6 11:24:27 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 6 Aug 2010 11:24:27 -0400 (EDT) Subject: [BioCatalogue-developers] [2173] branches/rest-api-updates/public/2009/xml/rest/schema-v1.xsd: REST API work: fixes for some nested collections. Message-ID: <20100806152428.325681858366@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Aug 6 13:25:55 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 06 Aug 2010 18:25:55 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:solvateStructureWithLigandsFromPDBText' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:solvateStructureWithLigandsFromPDBText' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1180 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Aug 6 13:25:51 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 06 Aug 2010 18:25:51 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getPropertySequenceFromFeatureAASequence' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getPropertySequenceFromFeatureAASequence' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1167 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Aug 6 13:42:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 6 Aug 2010 13:42:07 -0400 (EDT) Subject: [BioCatalogue-developers] [2174] branches/rest-api-updates: - updated the REST API to match the XML Schema Message-ID: <20100806174208.2D75C1678318@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Aug 6 18:49:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 06 Aug 2010 23:49:33 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:www.cnb.uam.es:getStatisticalLog' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:www.cnb.uam.es:getStatisticalLog' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1027 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Aug 7 05:23:51 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 07 Aug 2010 10:23:51 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runTTSFinder' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runTTSFinder' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1104 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Aug 7 19:09:35 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 08 Aug 2010 00:09:35 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runNCBITBlastxXML' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runNCBITBlastxXML' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/847 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Mon Aug 9 10:01:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 9 Aug 2010 10:01:42 -0400 (EDT) Subject: [BioCatalogue-developers] [2175] branches/rest-api-updates/app/views: - updated /service_provider/ {id} Message-ID: <20100809140143.113F31858367@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Aug 9 10:09:01 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 9 Aug 2010 10:09:01 -0400 (EDT) Subject: [BioCatalogue-developers] [2176] branches/rest-api-updates/app/views/service_providers/api/_hostnames .xml.builder: - updated /service_provider/{id} Message-ID: <20100809140901.D3E401678319@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Aug 9 10:10:53 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 9 Aug 2010 10:10:53 -0400 (EDT) Subject: [BioCatalogue-developers] [2177] branches/rest-api-updates/app/views/service_provider_hostnames/api/: removed a folder that was not needed anymore Message-ID: <20100809141053.BD50D185838A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Aug 9 10:17:52 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 9 Aug 2010 10:17:52 -0400 (EDT) Subject: [BioCatalogue-developers] [2178] branches/rest-api-updates/public/2009/xml/rest/schema-v1.xsd: REST API work: updates and fixes to XML schema for latest work. Message-ID: <20100809141752.420C01678319@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Mon Aug 9 14:29:58 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 09 Aug 2010 19:29:58 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:cleanStructureFromPDBText' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:cleanStructureFromPDBText' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1142 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Aug 9 16:48:55 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 09 Aug 2010 21:48:55 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getStructureFromMD_Trajectory' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getStructureFromMD_Trajectory' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1165 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Aug 9 17:53:05 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 09 Aug 2010 22:53:05 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parsePropertySequenceFromPMUTText' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parsePropertySequenceFromPMUTText' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/998 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Aug 9 19:21:47 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 10 Aug 2010 00:21:47 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parsePropertySequenceFromFSOLVText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parsePropertySequenceFromFSOLVText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/992 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 Aug 10 09:48:02 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 10 Aug 2010 14:48:02 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runPrank' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runPrank' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1095 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 Aug 10 15:26:51 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 10 Aug 2010 20:26:51 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runDiscreteMDFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runDiscreteMDFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1119 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 Aug 10 21:03:49 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 11 Aug 2010 02:03:49 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:genome.imim.es:runDustCollection' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:genome.imim.es:runDustCollection' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1032 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Aug 11 01:05:45 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 11 Aug 2010 06:05:45 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runUnusualPhysicalProperties' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runUnusualPhysicalProperties' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1015 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 Aug 11 06:53:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 11 Aug 2010 11:53:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-451) Update the models to include #associated_service as well as other methods to improve performance Message-ID: <25831151.8036.1281523995361.JavaMail.jira@rosalind.cs.man.ac.uk> 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 Wed Aug 11 06:56:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 11 Aug 2010 11:56:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-452) Implement a filter for RestMethod Message-ID: <8021914.8037.1281524175308.JavaMail.jira@rosalind.cs.man.ac.uk> Implement a filter for RestMethod --------------------------------- Key: BIOCAT-452 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-452 Project: BioCatalogue Issue Type: Task Components: REST API, REST Services Support Reporter: Mannie Tagarira Assignee: Mannie Tagarira 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 Wed Aug 11 06:58:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 11 Aug 2010 11:58:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-453) Implement functionality to allow users to save their favourite search filters Message-ID: <11270692.8038.1281524295332.JavaMail.jira@rosalind.cs.man.ac.uk> Implement functionality to allow users to save their favourite search filters ----------------------------------------------------------------------------- Key: BIOCAT-453 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-453 Project: BioCatalogue Issue Type: Task Components: REST API 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 Wed Aug 11 06:58:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 11 Aug 2010 11:58:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-453) Implement functionality to allow users to save their favourite search filters In-Reply-To: <11270692.8038.1281524295332.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31043554.8039.1281524296904.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-453?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15686#action_15686 ] Mannie Tagarira commented on BIOCAT-453: ---------------------------------------- The main use case for this will be Sergey's BioCatalogue plugin in Taverna > Implement functionality to allow users to save their favourite search filters > ----------------------------------------------------------------------------- > > Key: BIOCAT-453 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-453 > Project: BioCatalogue > Issue Type: Task > Components: REST API > 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 Wed Aug 11 07:00:48 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 11 Aug 2010 07:00:48 -0400 (EDT) Subject: [BioCatalogue-developers] [2179] branches/rest-api-updates/app: - made some API optimisations Message-ID: <20100811110049.1843A1858363@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 11 08:04:17 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 11 Aug 2010 08:04:17 -0400 (EDT) Subject: [BioCatalogue-developers] [2180] branches/rest-api-updates: - bug fix for the ClientApplication model which made the "callback url" mandatory Message-ID: <20100811120417.313641678319@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 11 08:43:45 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 11 Aug 2010 08:43:45 -0400 (EDT) Subject: [BioCatalogue-developers] [2181] trunk: Merged 2133:2180 of Mannie's rest-api-updates branch. Message-ID: <20100811124346.00A51167831B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 11 09:11:40 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 11 Aug 2010 09:11:40 -0400 (EDT) Subject: [BioCatalogue-developers] [2182] trunk: - a few changes to the ssl_requirement to allow :all ( to ssl_require all actions) Message-ID: <20100811131140.4B6A3185836F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 11 09:15:48 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 11 Aug 2010 09:15:48 -0400 (EDT) Subject: [BioCatalogue-developers] [2183] trunk/vendor/plugins/ssl_requirement/lib/ssl_requirement.rb: - bug fix for the ssl_requirement module Message-ID: <20100811131548.9C067185836F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 11 10:31:36 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 11 Aug 2010 10:31:36 -0400 (EDT) Subject: [BioCatalogue-developers] [2184] trunk/app/models/rest_method.rb: Index more fields (into search) for the RestMethod model. Message-ID: <20100811143136.B3D1C1858373@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 11 10:39:03 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 11 Aug 2010 10:39:03 -0400 (EDT) Subject: [BioCatalogue-developers] [2185] trunk/app/views/rest_methods: - added result item for RestMethods Message-ID: <20100811143903.A35531858370@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 11 10:43:53 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 11 Aug 2010 10:43:53 -0400 (EDT) Subject: [BioCatalogue-developers] [2186] trunk: REST API work: Enabled RestMethod resources (aka " REST Endpoints") to show up properly in the search endpoint. Message-ID: <20100811144354.0A5481858371@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 11 11:43:51 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 11 Aug 2010 11:43:51 -0400 (EDT) Subject: [BioCatalogue-developers] [2187] trunk: Added caching to the search process. Message-ID: <20100811154351.C8B70185831A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 11 11:44:16 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 11 Aug 2010 11:44:16 -0400 (EDT) Subject: [BioCatalogue-developers] [2188] trunk/lib/bio_catalogue/search.rb: Minor update to documentation Message-ID: <20100811154416.76517185831A@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Aug 12 11:01:27 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 12 Aug 2010 16:01:27 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runNormalModeAnalysisFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runNormalModeAnalysisFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1118 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Thu Aug 12 11:20:56 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 12 Aug 2010 11:20:56 -0400 (EDT) Subject: [BioCatalogue-developers] [2189] trunk: - updated the rest api json indexes to show some information about the contained resources e .g. Message-ID: <20100812152056.70F96185839B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Aug 12 12:02:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 12 Aug 2010 12:02:47 -0400 (EDT) Subject: [BioCatalogue-developers] [2190] trunk/app/controllers: - ssl_allowed cleanup Message-ID: <20100812160247.7C8CF1858363@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Aug 12 13:28:16 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 12 Aug 2010 13:28:16 -0400 (EDT) Subject: [BioCatalogue-developers] [2191] trunk/app/controllers: - added sort_by "name" for /users, / service_providers, /rest_methods, and /soap_operations Message-ID: <20100812172816.61A1A19782CD@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Aug 13 17:42:20 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 13 Aug 2010 22:42:20 +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 utopia at cs.man.ac.uk Sun Aug 15 06:30:08 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 15 Aug 2010 11:30:08 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runCExonic' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runCExonic' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1098 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Aug 16 06:26:02 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 16 Aug 2010 11:26:02 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getSnapshotFromMD_Trajectory' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getSnapshotFromMD_Trajectory' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1135 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Aug 16 06:32:39 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 16 Aug 2010 11:32:39 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runNCBITBlastxXML' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runNCBITBlastxXML' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/847 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 Mon Aug 16 06:39:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 16 Aug 2010 06:39:14 -0400 (EDT) Subject: [BioCatalogue-developers] [2192] trunk/lib/bio_catalogue: - bug fix for the RestMethods filter which meant that (in the returned xml) would be empty Message-ID: <20100816103914.A5A0C19782D4@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Aug 16 06:42:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 16 Aug 2010 11:42:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-454) Help Tod Jackson setup test script monitoring for Emory web services registry Message-ID: <16007019.8060.1281955335307.JavaMail.jira@rosalind.cs.man.ac.uk> Help Tod Jackson setup test script monitoring for Emory web services registry ----------------------------------------------------------------------------- Key: BIOCAT-454 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-454 Project: BioCatalogue Issue Type: Task Components: Service Monitoring Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Help Tod Jackson setup a test script execution environment for the Emory web services registry. Use the process of setup to enhance the protocol and potability of the test script execution setup. -- 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 Mon Aug 16 06:43:57 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 16 Aug 2010 11:43:57 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:loadPersistentFile' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:loadPersistentFile' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1114 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Aug 16 07:00:39 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 16 Aug 2010 12:00:39 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:textQueryOMIM' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:textQueryOMIM' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1061 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 Aug 16 07:09:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 16 Aug 2010 12:09:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-455) Add XML support for the submission of annotations and services via the API Message-ID: <31779577.8064.1281956955306.JavaMail.jira@rosalind.cs.man.ac.uk> Add XML support for the submission of annotations and services via the API -------------------------------------------------------------------------- Key: BIOCAT-455 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-455 Project: BioCatalogue Issue Type: Improvement 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 noreply at rubyforge.org Mon Aug 16 08:52:41 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 16 Aug 2010 08:52:41 -0400 (EDT) Subject: [BioCatalogue-developers] [2193] trunk: - added filtering for ServiceProviders (query based) Message-ID: <20100816125241.87AFD19782D4@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Mon Aug 16 22:31:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 17 Aug 2010 03:31:06 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getLindemannFromPCZ' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getLindemannFromPCZ' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1171 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 Tue Aug 17 04:29:50 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 17 Aug 2010 09:29:50 +0100 Subject: [BioCatalogue-developers] Write API Message-ID: <4C6A487E.8030408@ebi.ac.uk> Hi Guys, I had a chat yesterday with Mannie and he seems to be making good progress with the API. I understood from him that he has implemented json support for submission of services via the api. This is great as it lays the basis for the submission of other pieces via the API as well. I just want to mention that if there is anything you think I could do to help with the API work, please let me know. I know there is always lots to do and I understand Jits is working on other projects. 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 Aug 17 04:41:58 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 17 Aug 2010 04:41:58 -0400 (EDT) Subject: [BioCatalogue-developers] [2194] trunk/script/biocatalogue/api/tests: - updated the API test for the newly added filters and the updated JSON indexes Message-ID: <20100817084158.DD1A719783BC@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue Aug 17 08:49:37 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 17 Aug 2010 13:49:37 +0100 Subject: [BioCatalogue-developers] Write API In-Reply-To: <4C6A487E.8030408@ebi.ac.uk> References: <4C6A487E.8030408@ebi.ac.uk> Message-ID: <4C6A8561.203@cs.man.ac.uk> Hi Eric, Yeap, Mannie and I have made good progress with the write API; I did the bulk annotations API a while back and Mannie has done service submissions and OAuth support (as well as much more read API stuff). However, we are still ironing things out and making this "production ready", which could take a little while. I'm hoping that as soon as you're back in September you and Mannie can go ahead with a release. Thanks for the offer of help. At the moment there's nothing that comes to mind but we'll let you know if there is. Otherwise, please could you carry on with the stuff you were doing before? (did you merge this into trunk yet) We can add this to the release in September. Cheers, Jits Eric Nzuobontane wrote: > Hi Guys, > > I had a chat yesterday with Mannie and he seems to be making good > progress with the API. I understood from him that he has implemented > json support for submission of services via the api. This is great as > it lays the basis for the submission of other pieces via the API as > well. I just want to mention that if there is anything you think I > could do to help with the API work, please let me know. I know there > is always lots to do and I understand Jits is working on other projects. > > cheers, > > Eric > > From noreply at rubyforge.org Tue Aug 17 08:58:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 17 Aug 2010 08:58:09 -0400 (EDT) Subject: [BioCatalogue-developers] [2195] trunk/public/2009/xml/rest/schema-v1.xsd: REST API work: updated schema to take into account latest work on filtering on Users, ServiceProviders and RestMethods. Message-ID: <20100817125809.C9E73185838A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Aug 17 11:50:15 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 17 Aug 2010 11:50:15 -0400 (EDT) Subject: [BioCatalogue-developers] [2196] trunk/vendor/embrace_scripts/README: added read me file to the test harness to help in setting it up Message-ID: <20100817155015.A9A541858351@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Aug 17 12:56:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 17 Aug 2010 12:56:14 -0400 (EDT) Subject: [BioCatalogue-developers] [2197] trunk: - removed OAuth specific layout Message-ID: <20100817165615.24D7519782DB@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Aug 18 09:53:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 18 Aug 2010 14:53:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-456) Potentially optimise the BioCatalogue::Util::display_name method Message-ID: <2178224.8102.1282139595466.JavaMail.jira@rosalind.cs.man.ac.uk> Potentially optimise the BioCatalogue::Util::display_name method ---------------------------------------------------------------- Key: BIOCAT-456 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-456 Project: BioCatalogue Issue Type: Improvement Components: Performance / Optimisations Reporter: Jiten Bhagat Assignee: Jiten Bhagat Currently, the BioCatalogue::Util::display_name method helper method (which is used everywhere to show display names of objects) makes heavy use of eval(). This is a potential performance hog, so look to optimise this and move away from using eval. -- 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 Aug 18 10:19:19 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 18 Aug 2010 10:19:19 -0400 (EDT) Subject: [BioCatalogue-developers] [2198] trunk/public/2009/xml/rest/schema-v1.xsd: REST API work: Updated schema for new field addition to RestMethod. Message-ID: <20100818141919.8D0DF185836B@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Aug 18 10:24:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 18 Aug 2010 15:24:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-457) Implement new custom "lean" JSON API endpoints for the Services, SoapOperations, RestMethods, Users and ServiceProviders indexes Message-ID: <30233473.8103.1282141455310.JavaMail.jira@rosalind.cs.man.ac.uk> Implement new custom "lean" JSON API endpoints for the Services, SoapOperations, RestMethods, Users and ServiceProviders indexes -------------------------------------------------------------------------------------------------------------------------------- Key: BIOCAT-457 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-457 Project: BioCatalogue Issue Type: New Feature Components: REST API Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical New API required with much slimmer results AND with no paging (so full results)! JSON based; Need new content type... application/biocat-lean+json .bljson This idea came about from a requirement from Sergey's BioCatalogue plugin for Taverna. So this API will be trialled with the plugin to start with. -- 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 Aug 18 10:58:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 18 Aug 2010 10:58:14 -0400 (EDT) Subject: [BioCatalogue-developers] [2199] trunk: [BIOCAT-457] Initial implmentation of the custom "lean" API ( JSON based). Message-ID: <20100818145815.2286D1858375@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Aug 18 11:06:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 18 Aug 2010 16:06:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-457) Implement new custom "lean" JSON API endpoints for the Services, SoapOperations, RestMethods, Users and ServiceProviders indexes In-Reply-To: <30233473.8103.1282141455310.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <33817.8104.1282143975349.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-457?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10435 ] Jiten Bhagat logged work on BIOCAT-457: --------------------------------------- Author: Jiten Bhagat Created on: 2010-08-18 16:04 Start Date: 2010-08-18 13:15 Worklog Time Spent: 2 hours, 30 minutes Work Description: Initial implementation done. Now need performance optimisations! Issue Time Tracking ------------------- Remaining Estimate: 3 hours, 30 minutes (was: 6 hours) Time Spent: 2 hours, 30 minutes > Implement new custom "lean" JSON API endpoints for the Services, SoapOperations, RestMethods, Users and ServiceProviders indexes > -------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-457 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-457 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Original Estimate: 6 hours > Time Spent: 2 hours, 30 minutes > Remaining Estimate: 3 hours, 30 minutes > > New API required with much slimmer results AND with no paging (so full results)! > JSON based; Need new content type... > application/biocat-lean+json > .bljson > This idea came about from a requirement from Sergey's BioCatalogue plugin for Taverna. So this API will be trialled with the plugin to start with. -- 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 Aug 18 11:54:30 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 18 Aug 2010 11:54:30 -0400 (EDT) Subject: [BioCatalogue-developers] [2200] trunk/vendor/embrace_scripts/src: added logging to make debugging much easier Message-ID: <20100818155430.D67FB1858376@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 18 11:56:18 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 18 Aug 2010 11:56:18 -0400 (EDT) Subject: [BioCatalogue-developers] [2201] trunk/vendor/embrace_scripts/README: minor changes to readme file Message-ID: <20100818155618.8356E185836B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 18 12:29:12 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 18 Aug 2010 12:29:12 -0400 (EDT) Subject: [BioCatalogue-developers] [2202] trunk: REST API work: more work on the custom "lean" JSON API: Message-ID: <20100818162912.F13031858354@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 18 12:39:21 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 18 Aug 2010 12:39:21 -0400 (EDT) Subject: [BioCatalogue-developers] [2203] trunk/script/biocatalogue/api/tests/bljson_test_helper.rb: REST API work: more work on the custom "lean" JSON API: Message-ID: <20100818163921.A2DEC1858376@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Aug 18 13:00:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 18 Aug 2010 18:00:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-456) Potentially optimise the BioCatalogue::Util::display_name method In-Reply-To: <2178224.8102.1282139595466.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28755451.8109.1282150815577.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-456?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15714#action_15714 ] Jiten Bhagat commented on BIOCAT-456: ------------------------------------- Some profiling reveals that the current use of eval() is not causing any significant slow downs (for lists of objects up to ~15K). Therefore we don't need to think about optimising this just yet. > Potentially optimise the BioCatalogue::Util::display_name method > ---------------------------------------------------------------- > > Key: BIOCAT-456 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-456 > Project: BioCatalogue > Issue Type: Improvement > Components: Performance / Optimisations > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Remaining Estimate: 2 hours > > Currently, the BioCatalogue::Util::display_name method helper method (which is used everywhere to show display names of objects) makes heavy use of eval(). This is a potential performance hog, so look to optimise this and move away from using eval. -- 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 Aug 18 13:00:18 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 18 Aug 2010 18:00:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-456) Potentially optimise the BioCatalogue::Util::display_name method In-Reply-To: <2178224.8102.1282139595466.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27087097.8111.1282150818472.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-456?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10436 ] Jiten Bhagat logged work on BIOCAT-456: --------------------------------------- Author: Jiten Bhagat Created on: 2010-08-18 17:59 Start Date: 2010-08-18 16:58 Worklog Time Spent: 30 minutes Work Description: Did some profiling Issue Time Tracking ------------------- Remaining Estimate: 1 hour, 30 minutes (was: 2 hours) Time Spent: 30 minutes > Potentially optimise the BioCatalogue::Util::display_name method > ---------------------------------------------------------------- > > Key: BIOCAT-456 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-456 > Project: BioCatalogue > Issue Type: Improvement > Components: Performance / Optimisations > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Original Estimate: 2 hours > Time Spent: 30 minutes > Remaining Estimate: 1 hour, 30 minutes > > Currently, the BioCatalogue::Util::display_name method helper method (which is used everywhere to show display names of objects) makes heavy use of eval(). This is a potential performance hog, so look to optimise this and move away from using eval. -- 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 Aug 18 13:00:22 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 18 Aug 2010 18:00:22 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-457) Implement new custom "lean" JSON API endpoints for the Services, SoapOperations, RestMethods, Users and ServiceProviders indexes In-Reply-To: <30233473.8103.1282141455310.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12480701.8113.1282150822120.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-457?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-457. --------------------------------- Resolution: Implemented > Implement new custom "lean" JSON API endpoints for the Services, SoapOperations, RestMethods, Users and ServiceProviders indexes > -------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-457 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-457 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Original Estimate: 6 hours > Time Spent: 4 hours, 30 minutes > Remaining Estimate: 1 hour, 30 minutes > > New API required with much slimmer results AND with no paging (so full results)! > JSON based; Need new content type... > application/biocat-lean+json > .bljson > This idea came about from a requirement from Sergey's BioCatalogue plugin for Taverna. So this API will be trialled with the plugin to start with. -- 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 Aug 18 13:00:19 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 18 Aug 2010 18:00:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-457) Implement new custom "lean" JSON API endpoints for the Services, SoapOperations, RestMethods, Users and ServiceProviders indexes In-Reply-To: <30233473.8103.1282141455310.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30779740.8112.1282150819552.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-457?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10437 ] Jiten Bhagat logged work on BIOCAT-457: --------------------------------------- Author: Jiten Bhagat Created on: 2010-08-18 17:59 Start Date: 2010-08-18 15:59 Worklog Time Spent: 2 hours Work Description: More work carried to optimise performance, and also to write tests. Issue Time Tracking ------------------- Remaining Estimate: 1 hour, 30 minutes (was: 3 hours, 30 minutes) Time Spent: 4 hours, 30 minutes (was: 2 hours, 30 minutes) > Implement new custom "lean" JSON API endpoints for the Services, SoapOperations, RestMethods, Users and ServiceProviders indexes > -------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-457 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-457 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Original Estimate: 6 hours > Time Spent: 4 hours, 30 minutes > Remaining Estimate: 1 hour, 30 minutes > > New API required with much slimmer results AND with no paging (so full results)! > JSON based; Need new content type... > application/biocat-lean+json > .bljson > This idea came about from a requirement from Sergey's BioCatalogue plugin for Taverna. So this API will be trialled with the plugin to start with. -- 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 Aug 18 13:00:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 18 Aug 2010 18:00:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-456) Potentially optimise the BioCatalogue::Util::display_name method In-Reply-To: <2178224.8102.1282139595466.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8568553.8110.1282150817407.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-456?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-456: -------------------------------- Priority: Minor (was: Major) > Potentially optimise the BioCatalogue::Util::display_name method > ---------------------------------------------------------------- > > Key: BIOCAT-456 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-456 > Project: BioCatalogue > Issue Type: Improvement > Components: Performance / Optimisations > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Original Estimate: 2 hours > Remaining Estimate: 2 hours > > Currently, the BioCatalogue::Util::display_name method helper method (which is used everywhere to show display names of objects) makes heavy use of eval(). This is a potential performance hog, so look to optimise this and move away from using eval. -- 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 Thu Aug 19 05:25:09 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 19 Aug 2010 10:25:09 +0100 Subject: [BioCatalogue-developers] Database Encoding Issues In-Reply-To: References: Message-ID: <4C6CF875.8050406@cs.man.ac.uk> Note that: - the database is storing it "correctly" (i.e.: not losing any information, just that it's a different encoding then what it should be). - but the Rails app expects things in UTF-8 usually, so displaying it in the UI (and API) causes it to mess up due to a disjointedness in the encodings. - interestingly, PHPMyAdmin displays it correctly, probably because it is not assuming the encoding and instead working with the database's encoding (we could simulate something like with String#mb_chars in Rails, but...) So, there is the bigger issue of the database being an encoding that is not modern enough and different to what is expected in Rails; I remember we had those issues a while back when people were trying to submit content with non-english characters and it kept failing in the database due to a "swedish collation/encoding" issue. I may be wrong though; this could be a Ruby issue (I know that Ruby has recently been criticised a lot for how it handles encodings of strings). This is something VERY IMPORTANT to look into, please. Jits Mannie Tagarira wrote: > Hi Eric, > > 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... > > Regards, > Mannie > > From ericnzuo at ebi.ac.uk Thu Aug 19 05:52:48 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 19 Aug 2010 10:52:48 +0100 Subject: [BioCatalogue-developers] Database Encoding Issues In-Reply-To: <4C6CF875.8050406@cs.man.ac.uk> References: <4C6CF875.8050406@cs.man.ac.uk> Message-ID: <4C6CFEF0.6080906@ebi.ac.uk> Like I mentioned earlier, the default encoding for mysql which we are using for most tables is latin1. I believe this can be changed and should be changed to utf-8, which would make it consistent with rails expectations as well. This should apply to the db engine as well except there is a special reason for using myISAM tables, I would expect all tables to use innodb engine. Eric Jiten Bhagat wrote: > Note that: > - the database is storing it "correctly" (i.e.: not losing any > information, just that it's a different encoding then what it should be). > - but the Rails app expects things in UTF-8 usually, so displaying it in > the UI (and API) causes it to mess up due to a disjointedness in the > encodings. > - interestingly, PHPMyAdmin displays it correctly, probably because it > is not assuming the encoding and instead working with the database's > encoding (we could simulate something like with String#mb_chars in > Rails, but...) > > So, there is the bigger issue of the database being an encoding that is > not modern enough and different to what is expected in Rails; I remember > we had those issues a while back when people were trying to submit > content with non-english characters and it kept failing in the database > due to a "swedish collation/encoding" issue. > > I may be wrong though; this could be a Ruby issue (I know that Ruby has > recently been criticised a lot for how it handles encodings of strings). > > This is something VERY IMPORTANT to look into, please. > > Jits > > > > Mannie Tagarira wrote: > >> Hi Eric, >> >> 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... >> >> Regards, >> Mannie >> >> >> -- 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 embedded and charset-unspecified text was scrubbed... Name: biocat_db_encoding.txt URL: From issues at mygrid.org.uk Thu Aug 19 06:06:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 19 Aug 2010 11:06:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-458) Investigate biocatalogue db encoding problems and fix any inconsistencies with the rails application Message-ID: <27122381.8114.1282212375444.JavaMail.jira@rosalind.cs.man.ac.uk> 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 Thu Aug 19 06:06:19 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 19 Aug 2010 11:06:19 +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: <4920848.8115.1282212379441.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=15715#action_15715 ] Eric Nzuobontane commented on BIOCAT-458: ----------------------------------------- >From Jits: Note that: - the database is storing it "correctly" (i.e.: not losing any information, just that it's a different encoding then what it should be). - but the Rails app expects things in UTF-8 usually, so displaying it in the UI (and API) causes it to mess up due to a disjointedness in the encodings. - interestingly, PHPMyAdmin displays it correctly, probably because it is not assuming the encoding and instead working with the database's encoding (we could simulate something like with String#mb_chars in Rails, but...) So, there is the bigger issue of the database being an encoding that is not modern enough and different to what is expected in Rails; I remember we had those issues a while back when people were trying to submit content with non-english characters and it kept failing in the database due to a "swedish collation/encoding" issue. I may be wrong though; this could be a Ruby issue (I know that Ruby has recently been criticised a lot for how it handles encodings of strings). This is something VERY IMPORTANT to look into, please. > 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 Thu Aug 19 06:12:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 19 Aug 2010 11:12:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-454) Help Tod Jackson setup test script monitoring for Emory web services registry In-Reply-To: <16007019.8060.1281955335307.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26164335.8116.1282212735333.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-454?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-454. ------------------------------------- Resolution: Fixed The main issue here was a misunderstanding of the what the term "executable" meant at test submission point. Also, there was no information on where to look for clues of any apparent problems. A README file has therefore been created in the test harness package to give the user more information on how to setup the test script execution machine. > Help Tod Jackson setup test script monitoring for Emory web services registry > ----------------------------------------------------------------------------- > > Key: BIOCAT-454 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-454 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Help Tod Jackson setup a test script execution environment for the Emory web services registry. Use the process of setup to enhance the protocol and potability of the test script execution setup. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Thu Aug 19 06:33:24 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 19 Aug 2010 11:33:24 +0100 Subject: [BioCatalogue-developers] jira question Message-ID: <4C6D0874.8090509@ebi.ac.uk> Hi Jits, Is there a way to create tickets in Jira via email? So sending email to given email will create an issue in jira. 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 Thu Aug 19 07:13:50 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 19 Aug 2010 07:13:50 -0400 (EDT) Subject: [BioCatalogue-developers] [2204] trunk: REST API work: renamed the custom "lean" JSON API to "lite". Message-ID: <20100819111351.1EBA31858386@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Aug 19 07:18:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 19 Aug 2010 12:18:15 +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: <18142829.8117.1282216695320.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=15717#action_15717 ] Eric Nzuobontane commented on BIOCAT-458: ----------------------------------------- there are suggestions on how this can be done. http://dev.mysql.com/doc/refman/5.0/en/alter-table.html But as this concerns data, it has to be done very carefully. > 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 jits at cs.man.ac.uk Thu Aug 19 07:23:27 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 19 Aug 2010 12:23:27 +0100 Subject: [BioCatalogue-developers] jira question In-Reply-To: <4C6D0874.8090509@ebi.ac.uk> References: <4C6D0874.8090509@ebi.ac.uk> Message-ID: <4C6D142F.4050102@cs.man.ac.uk> Hi Eric, Good question! I think there should be... I'll take a closer look after lunch. Cheers, Jits Eric Nzuobontane wrote: > Hi Jits, > > Is there a way to create tickets in Jira via email? So sending email > to given email will create an issue in jira. > > Eric > From noreply at rubyforge.org Thu Aug 19 08:33:15 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 19 Aug 2010 08:33:15 -0400 (EDT) Subject: [BioCatalogue-developers] [2205] trunk: - added the foundation for saved searches Message-ID: <20100819123315.33ED01858383@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu Aug 19 08:37:42 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 19 Aug 2010 13:37:42 +0100 Subject: [BioCatalogue-developers] jira question In-Reply-To: <4C6D142F.4050102@cs.man.ac.uk> References: <4C6D0874.8090509@ebi.ac.uk> <4C6D142F.4050102@cs.man.ac.uk> Message-ID: <4C6D2596.8000707@cs.man.ac.uk> Seems like this can be done... http://confluence.atlassian.com/display/JIRA/Creating+Issues+and+Comments+from+Email ... but it requires a fair bit of setting up, and access to password(s). Jits Jiten Bhagat wrote: > Hi Eric, > > Good question! > > I think there should be... I'll take a closer look after lunch. > > Cheers, > Jits > > > Eric Nzuobontane wrote: > >> Hi Jits, >> >> Is there a way to create tickets in Jira via email? So sending email >> to given email will create an issue in jira. >> >> Eric >> >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From ericnzuo at ebi.ac.uk Thu Aug 19 08:41:14 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 19 Aug 2010 13:41:14 +0100 Subject: [BioCatalogue-developers] jira question In-Reply-To: <4C6D2596.8000707@cs.man.ac.uk> References: <4C6D0874.8090509@ebi.ac.uk> <4C6D142F.4050102@cs.man.ac.uk> <4C6D2596.8000707@cs.man.ac.uk> Message-ID: <4C6D266A.5000807@ebi.ac.uk> OK, just something I thought might be nice to have but not really an issue. Eric Jiten Bhagat wrote: > Seems like this can be done... > > http://confluence.atlassian.com/display/JIRA/Creating+Issues+and+Comments+from+Email > > ... but it requires a fair bit of setting up, and access to password(s). > > Jits > > > Jiten Bhagat wrote: > >> Hi Eric, >> >> Good question! >> >> I think there should be... I'll take a closer look after lunch. >> >> Cheers, >> Jits >> >> >> Eric Nzuobontane wrote: >> >> >>> Hi Jits, >>> >>> Is there a way to create tickets in Jira via email? So sending email >>> to given email will create an issue in jira. >>> >>> Eric >>> >>> >>> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Thu Aug 19 09:05:34 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 19 Aug 2010 09:05:34 -0400 (EDT) Subject: [BioCatalogue-developers] [2206] trunk/public/2009/xml/rest/schema-v1.xsd: REST API work: new schema for SavedSearches. Message-ID: <20100819130534.803A119783B7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Aug 19 09:22:29 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 19 Aug 2010 09:22:29 -0400 (EDT) Subject: [BioCatalogue-developers] [2207] trunk/public/2009/xml/rest/schema-v1.xsd: REST API work: tweaks to the schema for SavedSearch. Message-ID: <20100819132229.B0A7819783C6@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu Aug 19 09:28:16 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 19 Aug 2010 14:28:16 +0100 Subject: [BioCatalogue-developers] jira question In-Reply-To: <4C6D266A.5000807@ebi.ac.uk> References: <4C6D0874.8090509@ebi.ac.uk> <4C6D142F.4050102@cs.man.ac.uk> <4C6D2596.8000707@cs.man.ac.uk> <4C6D266A.5000807@ebi.ac.uk> Message-ID: <4C6D3170.6080902@cs.man.ac.uk> Yeah, let's keep this in mind. Maybe we could have all emails sent to the contact at biocatalogue.org be created as issues in JIRA, in the future. Jits Eric Nzuobontane wrote: > OK, just something I thought might be nice to have but not really an > issue. > > Eric > > > Jiten Bhagat wrote: >> Seems like this can be done... >> >> http://confluence.atlassian.com/display/JIRA/Creating+Issues+and+Comments+from+Email >> >> >> ... but it requires a fair bit of setting up, and access to password(s). >> >> Jits >> >> >> Jiten Bhagat wrote: >> >>> Hi Eric, >>> >>> Good question! >>> >>> I think there should be... I'll take a closer look after lunch. >>> >>> Cheers, >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>> >>>> Hi Jits, >>>> >>>> Is there a way to create tickets in Jira via email? So sending email >>>> to given email will create an issue in jira. >>>> >>>> Eric >>>> >>>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> > > From ericnzuo at ebi.ac.uk Thu Aug 19 09:31:38 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 19 Aug 2010 14:31:38 +0100 Subject: [BioCatalogue-developers] jira question In-Reply-To: <4C6D3170.6080902@cs.man.ac.uk> References: <4C6D0874.8090509@ebi.ac.uk> <4C6D142F.4050102@cs.man.ac.uk> <4C6D2596.8000707@cs.man.ac.uk> <4C6D266A.5000807@ebi.ac.uk> <4C6D3170.6080902@cs.man.ac.uk> Message-ID: <4C6D323A.8040808@ebi.ac.uk> Yeah, I thought about that. But then again if someone attacks our contact form for example, then they would be hitting our tracking system as well. Just a thought! Eric Jiten Bhagat wrote: > Yeah, let's keep this in mind. > > Maybe we could have all emails sent to the contact at biocatalogue.org be > created as issues in JIRA, in the future. > > Jits > > > > Eric Nzuobontane wrote: > >> OK, just something I thought might be nice to have but not really an >> issue. >> >> Eric >> >> >> Jiten Bhagat wrote: >> >>> Seems like this can be done... >>> >>> http://confluence.atlassian.com/display/JIRA/Creating+Issues+and+Comments+from+Email >>> >>> >>> ... but it requires a fair bit of setting up, and access to password(s). >>> >>> Jits >>> >>> >>> Jiten Bhagat wrote: >>> >>> >>>> Hi Eric, >>>> >>>> Good question! >>>> >>>> I think there should be... I'll take a closer look after lunch. >>>> >>>> Cheers, >>>> Jits >>>> >>>> >>>> Eric Nzuobontane wrote: >>>> >>>> >>>>> Hi Jits, >>>>> >>>>> Is there a way to create tickets in Jira via email? So sending email >>>>> to given email will create an issue in jira. >>>>> >>>>> Eric >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>> >>>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Thu Aug 19 10:29:12 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 19 Aug 2010 15:29:12 +0100 Subject: [BioCatalogue-developers] leaving a bit early Message-ID: <4C6D3FB8.2060806@ebi.ac.uk> Hi Guys, I am leaving a bit early today to catch an appointment. I will be online later in the evening if there is anything. cheers -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Thu Aug 19 10:42:20 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 19 Aug 2010 10:42:20 -0400 (EDT) Subject: [BioCatalogue-developers] [2208] trunk/app: - Inform user that submission of soaplab services in done in background Message-ID: <20100819144220.2057219783C5@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Aug 20 06:05:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 11:05:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-104) Inform the user that the soaplab server submission will happen in the background Message-ID: <10034411.8120.1282298715453.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-104?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-104 started by Eric Nzuobontane. > Inform the user that the soaplab server submission will happen in the background > -------------------------------------------------------------------------------- > > Key: BIOCAT-104 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-104 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Submission, Web Interface > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > Priority: Critical > > Paul submitted his soaplab service. When he got back to the browse page the service weren't there like for normal soap service. He then said 'it doesn't work'. Actually it does work. Soaplab submission takes a while and it is processed in the background. The problem is that we don't tell user what is happening...so they expect the submission to be as normal SOAP service. Can we have sensible messages to warn user that their soaplab submission may take longer than usual and we will notify them (e.g by email) when the process is completed? > OR if technically possible, the process need to be made shorter. -- 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 Aug 20 06:07:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 11:07:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-104) Inform the user that the soaplab server submission will happen in the background Message-ID: <15770595.8121.1282298835345.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-104?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15720#action_15720 ] Eric Nzuobontane commented on BIOCAT-104: ----------------------------------------- Added an info message (flash) which informs the User that the process is proceeding and that they need to wait a while to see the services. > Inform the user that the soaplab server submission will happen in the background > -------------------------------------------------------------------------------- > > Key: BIOCAT-104 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-104 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Submission, Web Interface > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > Priority: Critical > > Paul submitted his soaplab service. When he got back to the browse page the service weren't there like for normal soap service. He then said 'it doesn't work'. Actually it does work. Soaplab submission takes a while and it is processed in the background. The problem is that we don't tell user what is happening...so they expect the submission to be as normal SOAP service. Can we have sensible messages to warn user that their soaplab submission may take longer than usual and we will notify them (e.g by email) when the process is completed? > OR if technically possible, the process need to be made shorter. -- 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 Aug 20 06:09:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 11:09:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-104) Inform the user that the soaplab server submission will happen in the background Message-ID: <15008652.8122.1282298955342.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-104?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-104 stopped by Eric Nzuobontane. > Inform the user that the soaplab server submission will happen in the background > -------------------------------------------------------------------------------- > > Key: BIOCAT-104 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-104 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Submission, Web Interface > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > Priority: Critical > > Paul submitted his soaplab service. When he got back to the browse page the service weren't there like for normal soap service. He then said 'it doesn't work'. Actually it does work. Soaplab submission takes a while and it is processed in the background. The problem is that we don't tell user what is happening...so they expect the submission to be as normal SOAP service. Can we have sensible messages to warn user that their soaplab submission may take longer than usual and we will notify them (e.g by email) when the process is completed? > OR if technically possible, the process need to be made shorter. -- 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 Aug 20 06:09:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 11:09:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-104) Inform the user that the soaplab server submission will happen in the background Message-ID: <8492768.8123.1282298956291.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-104?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-104 started by Eric Nzuobontane. > Inform the user that the soaplab server submission will happen in the background > -------------------------------------------------------------------------------- > > Key: BIOCAT-104 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-104 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Submission, Web Interface > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > Priority: Critical > > Paul submitted his soaplab service. When he got back to the browse page the service weren't there like for normal soap service. He then said 'it doesn't work'. Actually it does work. Soaplab submission takes a while and it is processed in the background. The problem is that we don't tell user what is happening...so they expect the submission to be as normal SOAP service. Can we have sensible messages to warn user that their soaplab submission may take longer than usual and we will notify them (e.g by email) when the process is completed? > OR if technically possible, the process need to be made shorter. -- 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 Aug 20 06:11:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 11:11:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-104) Inform the user that the soaplab server submission will happen in the background Message-ID: <1473544.8124.1282299075333.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-104?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-104. ------------------------------------- Original Estimate: 1 hour Remaining Estimate: 1 hour Resolution: Implemented Added a flash message which tell informs the user that the submissions of the services is being done in the background and that they need to come back later. > Inform the user that the soaplab server submission will happen in the background > -------------------------------------------------------------------------------- > > Key: BIOCAT-104 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-104 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Submission, Web Interface > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > Priority: Critical > Original Estimate: 1 hour > Remaining Estimate: 1 hour > > Paul submitted his soaplab service. When he got back to the browse page the service weren't there like for normal soap service. He then said 'it doesn't work'. Actually it does work. Soaplab submission takes a while and it is processed in the background. The problem is that we don't tell user what is happening...so they expect the submission to be as normal SOAP service. Can we have sensible messages to warn user that their soaplab submission may take longer than usual and we will notify them (e.g by email) when the process is completed? > OR if technically possible, the process need to be made shorter. -- 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 Aug 20 06:14:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 11:14:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-123) Get the reliability profile of a service Message-ID: <23596167.8125.1282299255313.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-123?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15722#action_15722 ] Eric Nzuobontane commented on BIOCAT-123: ----------------------------------------- This task needs some clarification. We already have license information and all that in the service profile and I do not see how we get usage statistics. I am not sure if anything needs to be done on this task. > Get the reliability profile of a service > ---------------------------------------- > > Key: BIOCAT-123 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-123 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard, Service Monitoring, Web Interface > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > > From the 20Q's, Q3 - > "What is the reliability profile of service X?", "Can I see the usage history of service X?", "who is the provider?", "is it free?" > - Each service should have a profile (reliability, history of use, free, licenses etc) -- This message is automatically generated by JIRA. - 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 Aug 20 06:20:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 11:20:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-210) Setup cron job to reindex on a regular basis Message-ID: <331185.8126.1282299615313.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-210?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15723#action_15723 ] Eric Nzuobontane commented on BIOCAT-210: ----------------------------------------- Experience shows that rake solr index can fail for different reasons. So like Alan said, it would not be a good idea to setup a cron for run solr. However, there should be a schedule for regular manual reindexing of the application. > Setup cron job to reindex on a regular basis > -------------------------------------------- > > Key: BIOCAT-210 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-210 > Project: BioCatalogue > Issue Type: Task > Components: Search / Filtering / Browsing, Server Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > the cron job would make the sure the index is fairly up to date -- This message is automatically generated by JIRA. - 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 Aug 20 06:34:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 20 Aug 2010 11:34:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-210) Setup cron job to reindex on a regular basis Message-ID: <7502782.8127.1282300455315.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-210?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15724#action_15724 ] Jiten Bhagat commented on BIOCAT-210: ------------------------------------- Note that Alan didn't make all those comments; those are the comments imported from the previous RubyForge tasks list and since Alan carried out the import it automatically assigned his name to everything. > Setup cron job to reindex on a regular basis > -------------------------------------------- > > Key: BIOCAT-210 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-210 > Project: BioCatalogue > Issue Type: Task > Components: Search / Filtering / Browsing, Server Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > the cron job would make the sure the index is fairly up to date -- This message is automatically generated by JIRA. - 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 Aug 20 06:37:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 20 Aug 2010 11:37:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-210) Setup cron job to reindex on a regular basis Message-ID: <15420178.8128.1282300635314.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-210?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15725#action_15725 ] Jiten Bhagat commented on BIOCAT-210: ------------------------------------- Eric Nzuobontane added a comment - 2010-08-20 11:18 > Experience shows that rake solr index can fail for different reasons. So like Alan said, it would not be a good idea to setup a cron for run solr. However, there should be a schedule for regular manual reindexing of the application. Note that since the original comment(s), I have significantly modified the solr:reindex task by: - optimising the batching of docs to index, - adding sleeps so that Solr is given some breathing space (as it is Solr that causes this process to fail, when it is overloaded). This is to provide more reliability during the solr:reindex task. It would be very useful to know if any recent manual reindexing has failed, and if so, any hints as to the failure / error messages. > Setup cron job to reindex on a regular basis > -------------------------------------------- > > Key: BIOCAT-210 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-210 > Project: BioCatalogue > Issue Type: Task > Components: Search / Filtering / Browsing, Server Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > the cron job would make the sure the index is fairly up to date -- This message is automatically generated by JIRA. - 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 Aug 20 06:40:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 20 Aug 2010 11:40:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-210) Setup cron job to reindex on a regular basis Message-ID: <10443364.8129.1282300815344.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-210?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15725#action_15725 ] Jiten Bhagat edited comment on BIOCAT-210 at 20/08/10 11:39: ------------------------------------------------------------- {quote} *Eric Nzuobontane added a comment - 2010-08-20 11:18* Experience shows that rake solr index can fail for different reasons. So like Alan said, it would not be a good idea to setup a cron for run solr. However, there should be a schedule for regular manual reindexing of the application. {quote} Note that since the original comment(s), I have significantly modified the solr:reindex task by: - optimising the batching of docs to index, - adding sleeps so that Solr is given some breathing space (as it is Solr that causes this process to fail, when it is overloaded). This is to provide more reliability during the solr:reindex task. It would be very useful to know if any recent manual reindexing has failed, and if so, any hints as to the failure / error messages. was (Author: jbhagat): Eric Nzuobontane added a comment - 2010-08-20 11:18 > Experience shows that rake solr index can fail for different reasons. So like Alan said, it would not be a good idea to setup a cron for run solr. However, there should be a schedule for regular manual reindexing of the application. Note that since the original comment(s), I have significantly modified the solr:reindex task by: - optimising the batching of docs to index, - adding sleeps so that Solr is given some breathing space (as it is Solr that causes this process to fail, when it is overloaded). This is to provide more reliability during the solr:reindex task. It would be very useful to know if any recent manual reindexing has failed, and if so, any hints as to the failure / error messages. > Setup cron job to reindex on a regular basis > -------------------------------------------- > > Key: BIOCAT-210 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-210 > Project: BioCatalogue > Issue Type: Task > Components: Search / Filtering / Browsing, Server Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > the cron job would make the sure the index is fairly up to date -- This message is automatically generated by JIRA. - 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 Aug 20 09:13:28 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 20 Aug 2010 09:13:28 -0400 (EDT) Subject: [BioCatalogue-developers] [2209] trunk/lib/bio_catalogue/api/bljson.rb: Cleanup Message-ID: <20100820131328.7442A185837B@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Aug 20 09:25:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 14:25:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-256) For monitoring tab - add "monitored since" Message-ID: <22199643.8130.1282310715392.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-256?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-256. ------------------------------------- Resolution: Implemented This has been implemented and already in production. > For monitoring tab - add "monitored since" > ------------------------------------------ > > Key: BIOCAT-256 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-256 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > > Add "Monitored since: xxx" for each of the individual monitoring types in the monitoring tab so people know when this service has been monitored since. > Also possibly in the tooltip that comes up on hover. -- 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 Aug 20 09:28:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 14:28:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-340) For failing tests(checks) indicate for how long they have been failing In-Reply-To: <9779773.478.1274086997118.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9761166.8131.1282310895333.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-340?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15727#action_15727 ] Eric Nzuobontane commented on BIOCAT-340: ----------------------------------------- For failing test, you can now hover over the status icon and see since when it has been failing. This is already in production. > For failing tests(checks) indicate for how long they have been failing > ---------------------------------------------------------------------- > > Key: BIOCAT-340 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-340 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Show in the UI how long a particular test/check has been failing. -- 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 Aug 20 09:30:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 14:30:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-340) For failing tests(checks) indicate for how long they have been failing In-Reply-To: <9779773.478.1274086997118.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3225675.8132.1282311015310.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-340?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-340. ------------------------------------- Resolution: Implemented > For failing tests(checks) indicate for how long they have been failing > ---------------------------------------------------------------------- > > Key: BIOCAT-340 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-340 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Show in the UI how long a particular test/check has been failing. -- 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 Aug 20 09:34:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 14:34:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-277) Test Harness and wrapper port Message-ID: <2866676.8133.1282311255339.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-277?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15728#action_15728 ] Eric Nzuobontane commented on BIOCAT-277: ----------------------------------------- The original embrace harness and wrapper scripts were completely re-written and functionality extended to include execution of soapUI scripts. This is already in production and also being used by the Emory Registry instance. > Test Harness and wrapper port > ----------------------------- > > Key: BIOCAT-277 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-277 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Examine and possibly port the test harness and wrapper from the embrace services registry -- 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 Aug 20 09:34:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 14:34:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-277) Test Harness and wrapper port Message-ID: <29072718.8134.1282311257199.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-277?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-277. ------------------------------------- Resolution: Implemented > Test Harness and wrapper port > ----------------------------- > > Key: BIOCAT-277 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-277 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Examine and possibly port the test harness and wrapper from the embrace services registry -- 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 Aug 20 09:43:53 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 20 Aug 2010 09:43:53 -0400 (EDT) Subject: [BioCatalogue-developers] [2210] trunk/public/2009/xml/rest/schema-v1.xsd: REST API work: schema cleanup Message-ID: <20100820134353.36CD7177994B@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Aug 20 10:47:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 15:47:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-341) Possibility to harvest soaplab service description during submission In-Reply-To: <9661112.503.1274111116993.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27281714.8135.1282315635342.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-341?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15729#action_15729 ] Eric Nzuobontane commented on BIOCAT-341: ----------------------------------------- As part of the registration process, the description of the services from the soaplab server are also harvested. These are shown in the service profile as "Details(from server)" > Possibility to harvest soaplab service description during submission > -------------------------------------------------------------------- > > Key: BIOCAT-341 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-341 > Project: BioCatalogue > Issue Type: Task > Components: Content Acquisition, Service Submission > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > Priority: Critical > > We need to automatically harvest annotation for soaplab service during submission. -- 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 Aug 20 10:47:20 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 15:47:20 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-341) Possibility to harvest soaplab service description during submission In-Reply-To: <9661112.503.1274111116993.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29642800.8136.1282315640289.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-341?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-341. ------------------------------------- Resolution: Implemented > Possibility to harvest soaplab service description during submission > -------------------------------------------------------------------- > > Key: BIOCAT-341 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-341 > Project: BioCatalogue > Issue Type: Task > Components: Content Acquisition, Service Submission > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > Priority: Critical > > We need to automatically harvest annotation for soaplab service during submission. -- 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 Aug 20 11:13:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 16:13:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-344) Update soaplab services descriptions by calling the describe method In-Reply-To: <7031632.523.1274179577000.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25084845.8137.1282317195322.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-344?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-344. ------------------------------------- Resolution: Implemented > Update soaplab services descriptions by calling the describe method > ------------------------------------------------------------------- > > Key: BIOCAT-344 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-344 > Project: BioCatalogue > Issue Type: Task > Components: Content Acquisition > Environment: SAOP, Soaplab, soapclients > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > Call the describe method for the soaplab services and add the content to the service description -- 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 Aug 20 11:44:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 16:44:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-338) fix rake task to check wsdl parsing In-Reply-To: <31790990.448.1273851557004.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10023332.8138.1282319055327.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-338?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15730#action_15730 ] Eric Nzuobontane commented on BIOCAT-338: ----------------------------------------- Now this can be passed a command line argument(no of wsdls to check) and takes into account the wsdl refactoring. > fix rake task to check wsdl parsing > ----------------------------------- > > Key: BIOCAT-338 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-338 > Project: BioCatalogue > Issue Type: Bug > Components: Misc Codebase > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Fix the rake task which checks whether WSDLs parse and make it configurable. -- 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 Aug 20 11:44:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 20 Aug 2010 16:44:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-338) fix rake task to check wsdl parsing In-Reply-To: <31790990.448.1273851557004.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27200327.8139.1282319057663.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-338?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-338. ------------------------------------- Resolution: Fixed > fix rake task to check wsdl parsing > ----------------------------------- > > Key: BIOCAT-338 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-338 > Project: BioCatalogue > Issue Type: Bug > Components: Misc Codebase > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Fix the rake task which checks whether WSDLs parse and make it configurable. -- 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 Sun Aug 22 17:15:41 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 22 Aug 2010 22:15:41 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getPDBLigandStructure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getPDBLigandStructure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1103 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 Mon Aug 23 04:47:27 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 23 Aug 2010 04:47:27 -0400 (EDT) Subject: [BioCatalogue-developers] [2211] trunk: - delete associated services when soaplab server is deleted Message-ID: <20100823084727.4DDAE185835A@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Aug 23 04:55:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 23 Aug 2010 09:55:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-357) Add helper text to test script submission UI In-Reply-To: <24301496.1660.1274950337144.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17581695.8141.1282553715297.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-357?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-357. ------------------------------------- Resolution: Fixed This is now done and available in production. See "About TestScripts" link in the monitoring tab > Add helper text to test script submission UI > -------------------------------------------- > > Key: BIOCAT-357 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-357 > Project: BioCatalogue > Issue Type: Refinement > Components: Web Interface > Environment: RoR > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Priority: Minor > > Add some helper text to explain what test scripts are and how they are used in BioCatalogue, in the same spirit of 'about soaplab helper text' -- 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 Aug 23 04:57:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 23 Aug 2010 09:57:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-304) Investigate twittering failure on live site Message-ID: <12159886.8143.1282553835567.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-304?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15732#action_15732 ] Eric Nzuobontane commented on BIOCAT-304: ----------------------------------------- The reason for twitting problems is because the application server is behind a proxy > Investigate twittering failure on live site > ------------------------------------------- > > Key: BIOCAT-304 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-304 > Project: BioCatalogue > Issue Type: Bug > Components: Server Management > Environment: RoR > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Priority: Minor > > Tweets fail to be created/sent from the live site to the biocatalogue twitter account. -- This message is automatically generated by JIRA. - 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 Aug 23 04:59:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 23 Aug 2010 09:59:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-446) Anyone responsible for a service( this includes : submitter, other responsibles, curators and admins) should be able to enable/disable tests on the service In-Reply-To: <16685674.7582.1279881141133.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18283102.8144.1282553955359.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-446?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-446 started by Eric Nzuobontane. > Anyone responsible for a service( this includes : submitter, other responsibles, curators and admins) should be able to enable/disable tests on the service > ----------------------------------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-446 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-446 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > At the moment, only admins are able to enable/disable tests. This should be extended to anyone responsible for the service -- 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 Aug 23 04:59:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 23 Aug 2010 09:59:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-446) Anyone responsible for a service( this includes : submitter, other responsibles, curators and admins) should be able to enable/disable tests on the service In-Reply-To: <16685674.7582.1279881141133.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11474600.8145.1282553956408.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-446?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane updated BIOCAT-446: ------------------------------------ Original Estimate: 4 hours Remaining Estimate: 4 hours > Anyone responsible for a service( this includes : submitter, other responsibles, curators and admins) should be able to enable/disable tests on the service > ----------------------------------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-446 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-446 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > At the moment, only admins are able to enable/disable tests. This should be extended to anyone responsible for the service -- 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 Aug 23 04:55:19 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 23 Aug 2010 09:55:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-304) Investigate twittering failure on live site Message-ID: <15282734.8142.1282553719970.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-304?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14874#action_14874 ] Eric Nzuobontane edited comment on BIOCAT-304 at 23/08/10 09:54: ----------------------------------------------------------------- Tested creating tweets from the server using curl with proxy option which works. A tweet was sent to BioCatalogue using this approach. Thu May 06 10:03:06 +0000 2010 13478973979 A service test changed status from FAILED to PASSED. See http://www.biocatalogue.org/services/2513 <a href="http://apiwiki.twitter.com/" rel="nofollow">API</a> false false 49449269 BioCatalogue biocatalogue United Kingdom The Life Science Web Services Registry http://a1.twimg.com/profile_images/275352856/biocatalogue_cog_normal.png http://www.biocatalogue.org false 51 9ae4e8 000000 0000ff e0ff92 87bc44 5 Sun Jun 21 22:23:10 +0000 2009 0 0 London http://s.twimg.com/a/1273086425/images/themes/theme1/bg.png false false false false false 98 en false was (Author: eric): Tested creating tweets from the server using curl with proxy option which works. A tweet was sent to BioCatalogue using this mean. Thu May 06 10:03:06 +0000 2010 13478973979 A service test changed status from FAILED to PASSED. See http://www.biocatalogue.org/services/2513 <a href="http://apiwiki.twitter.com/" rel="nofollow">API</a> false false 49449269 BioCatalogue biocatalogue United Kingdom The Life Science Web Services Registry http://a1.twimg.com/profile_images/275352856/biocatalogue_cog_normal.png http://www.biocatalogue.org false 51 9ae4e8 000000 0000ff e0ff92 87bc44 5 Sun Jun 21 22:23:10 +0000 2009 0 0 London http://s.twimg.com/a/1273086425/images/themes/theme1/bg.png false false false false false 98 en false > Investigate twittering failure on live site > ------------------------------------------- > > Key: BIOCAT-304 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-304 > Project: BioCatalogue > Issue Type: Bug > Components: Server Management > Environment: RoR > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Priority: Minor > > Tweets fail to be created/sent from the live site to the biocatalogue twitter account. -- This message is automatically generated by JIRA. - 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 Aug 23 05:08:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 23 Aug 2010 10:08:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-300) Notify Curator when test script is submitted Message-ID: <11811836.8146.1282554495336.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-300?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15733#action_15733 ] Eric Nzuobontane commented on BIOCAT-300: ----------------------------------------- Those subscribed to notification for from the registry( usually admins and curators) are now notified when a test is disabled. > Notify Curator when test script is submitted > --------------------------------------------- > > Key: BIOCAT-300 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-300 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > Test scripts are disabled by default on submission. This requires the curation to go on the catalogue and enable them. We therefore need a notification mechanism to inform the curator when test scripts are uploaded -- 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 Aug 23 05:08:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 23 Aug 2010 10:08:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-300) Notify Curator when test script is submitted Message-ID: <31037050.8147.1282554496403.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-300?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-300. ------------------------------------- Resolution: Implemented > Notify Curator when test script is submitted > --------------------------------------------- > > Key: BIOCAT-300 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-300 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > Test scripts are disabled by default on submission. This requires the curation to go on the catalogue and enable them. We therefore need a notification mechanism to inform the curator when test scripts are uploaded -- 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 Aug 23 05:24:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 23 Aug 2010 10:24:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-376) Automatically parse the description within the text returned by the soaplab 'describe' methods. Soaplab services will then have a description assigned by 'the BioCatalogue agent' Message-ID: <15780263.8148.1282555455324.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-376?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-376. ------------------------------------- Resolution: Implemented This is a duplicate task which has already been resolved. Soaplab service descriptions from server are now automatically parsed. > Automatically parse the description within the text returned by the soaplab 'describe' methods. Soaplab services will then have a description assigned by 'the BioCatalogue agent' > ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-376 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-376 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > > Discussion on SKYPE: > [10/06/2010 15:17:42] Franck Tanoh: i actually started to parse some description from the list of junk from the soaplab server http://test.biocatalogue.org/services/2157 > [10/06/2010 15:18:33] Franck Tanoh: so the description is there but just bury in load of other things > [10/06/2010 15:18:35] Jiten Bhagat: we should be able to set the description field from that > [10/06/2010 15:18:45] Jiten Bhagat: we should be able to automatically parse it out! > [10/06/2010 15:18:53] Jiten Bhagat: as we store it in a structured way > [10/06/2010 15:18:58] Franck Tanoh: that's will be ace > [10/06/2010 15:20:13] Jiten Bhagat: franck, can yu please add a task for parsing the description field from the soaplab details, and assign it to eric > [10/06/2010 15:21:14] Eric Nzuobontane: But this will be done only in the case that there is no description from wsdl -- 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 Aug 23 05:26:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 23 Aug 2010 10:26:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-430) Re-factor the service monitoring view to bring in line with the improved view of the soap operations In-Reply-To: <31922042.7080.1278139815362.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20074217.8149.1282555575337.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-430?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-430. ------------------------------------- Resolution: Implemented New few no follows the pattern for the 'new soap operations' view > Re-factor the service monitoring view to bring in line with the improved view of the soap operations > ----------------------------------------------------------------------------------------------------- > > Key: BIOCAT-430 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-430 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > The monitoring view needs to be refactored in order to make it more user friendly. Similar to the soap operations tab, the monitoring view should list the service test with just some important data exposed with the possibility of drilling down to individual operations. -- 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 Aug 23 06:04:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 23 Aug 2010 11:04:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-445) Upgrade main packages/libraries use by BioCatalogue In-Reply-To: <3176667.7559.1279796355366.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5555976.8150.1282557855313.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-445?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15736#action_15736 ] Eric Nzuobontane commented on BIOCAT-445: ----------------------------------------- Request has been made to system administrators for consideration. Waiting for feedback... > Upgrade main packages/libraries use by BioCatalogue > --------------------------------------------------- > > Key: BIOCAT-445 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-445 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > It is desirable for performance and other reasons, to update the following libraries used by BioCatalogue > * MySQL - Server version: 5.0.41-log MySQL Community Server (GPL) > * Solr - 1.3.0 694707 - grantingersoll - 2008-09-12 11 > * Ruby - 1.8.5 > * passenger-2.2.2 > * PHP -5.1.6 > The desired versions are : > * MySQL - 5.1 > * Solr - 1.4.1 > * Ruby - 1.8.6 or 1.8.7 > * passenger - 2.2.15 > * PHP- 5.3 -- 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 Mon Aug 23 07:23:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 23 Aug 2010 07:23:08 -0400 (EDT) Subject: [BioCatalogue-developers] [2212] trunk: - updated the models to have 2 distinct methods for use with the JSON API: #to_json and #to_inline_json Message-ID: <20100823112308.D7A0C1858368@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Aug 23 07:52:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 23 Aug 2010 12:52:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-348) Create release notes for new code base deployment In-Reply-To: <13638682.569.1274264416998.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4993921.8151.1282564335319.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-348?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-348. ------------------------------------- Resolution: Fixed > Create release notes for new code base deployment > ------------------------------------------------- > > Key: BIOCAT-348 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-348 > Project: BioCatalogue > Issue Type: Sub-task > Components: Wiki > Environment: Wiki > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 2 hours > Remaining Estimate: 2 hours > > Create a page for release instructions, testing script and major features for the release -- 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 Aug 23 07:54:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 23 Aug 2010 12:54:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-360) Add the requester (name) and possible role of approver in responsibility request approval mail In-Reply-To: <24185522.1673.1274973617031.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30457142.8152.1282564455310.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-360?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-360. ------------------------------------- Resolution: Implemented > Add the requester (name) and possible role of approver in responsibility request approval mail > ---------------------------------------------------------------------------------------------- > > Key: BIOCAT-360 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-360 > Project: BioCatalogue > Issue Type: Refinement > Components: User Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 2 hours > Remaining Estimate: 2 hours > > Add the name of the person that made the request and the to the confirmation mail on approval/turn down -- 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 Aug 23 07:56:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 23 Aug 2010 12:56:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Reopened: (BIOCAT-360) Add the requester (name) and possible role of approver in responsibility request approval mail In-Reply-To: <24185522.1673.1274973617031.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7052154.8153.1282564575340.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-360?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reopened BIOCAT-360: ------------------------------------- requester name has been implemented but not role. > Add the requester (name) and possible role of approver in responsibility request approval mail > ---------------------------------------------------------------------------------------------- > > Key: BIOCAT-360 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-360 > Project: BioCatalogue > Issue Type: Refinement > Components: User Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 2 hours > Remaining Estimate: 2 hours > > Add the name of the person that made the request and the to the confirmation mail on approval/turn down -- 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 Mon Aug 23 12:16:11 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 23 Aug 2010 12:16:11 -0400 (EDT) Subject: [BioCatalogue-developers] [2213] trunk: - cleanups for POST /rest_services and POST /soap_services Message-ID: <20100823161611.C75631858363@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Aug 24 05:16:44 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 24 Aug 2010 05:16:44 -0400 (EDT) Subject: [BioCatalogue-developers] [2214] trunk/app: - all users responsible for a service should be able to enable/ disable tests. Message-ID: <20100824091644.C06161858379@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Aug 24 05:20:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 24 Aug 2010 10:20:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-446) Anyone responsible for a service( this includes : submitter, other responsibles, curators and admins) should be able to enable/disable tests on the service In-Reply-To: <16685674.7582.1279881141133.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18495314.8154.1282641615423.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-446?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-446. ------------------------------------- Resolution: Fixed All responsibles are now able to activate and deactivate tests on services > Anyone responsible for a service( this includes : submitter, other responsibles, curators and admins) should be able to enable/disable tests on the service > ----------------------------------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-446 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-446 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > At the moment, only admins are able to enable/disable tests. This should be extended to anyone responsible for the service -- 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 Aug 24 05:31:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 24 Aug 2010 10:31:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-377) update soaplab services descriptions by calling the describe method on submit of soaplab server Message-ID: <30298103.8155.1282642275316.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-377?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-377. ------------------------------------- Resolution: Fixed > update soaplab services descriptions by calling the describe method on submit of soaplab server > ----------------------------------------------------------------------------------------------- > > Key: BIOCAT-377 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-377 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Add the update of the descriptions from soaplab as part the soaplab server submission -- 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 Aug 24 09:08:59 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 24 Aug 2010 09:08:59 -0400 (EDT) Subject: [BioCatalogue-developers] [2215] trunk: - bug fixes for /saved_search/{id} and /users/{id}/ saved_searches.json Message-ID: <20100824130900.1A918185838C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Aug 24 11:23:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 24 Aug 2010 11:23:14 -0400 (EDT) Subject: [BioCatalogue-developers] [2216] trunk: - updated mine? so that it does not automatically assume false for api_requests Message-ID: <20100824152314.51DBD1858361@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Aug 24 13:20:27 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 24 Aug 2010 18:20:27 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'metabolicgraphconstruction' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'metabolicgraphconstruction' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/2814 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 Aug 24 23:41:24 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 24 Aug 2010 23:41:24 -0400 (EDT) Subject: [BioCatalogue-developers] [2217] trunk/public/2009/xml/rest/schema-v1.xsd: REST API work: added various things to schema: Message-ID: <20100825034124.B7E9C1858368@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Aug 25 03:38:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 25 Aug 2010 08:38:28 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'metabolicgraphconstruction' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'metabolicgraphconstruction' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/2814 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Aug 25 06:12:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 25 Aug 2010 06:12:08 -0400 (EDT) Subject: [BioCatalogue-developers] [2218] trunk: - updated the api to match the schema Message-ID: <20100825101208.430E6177993F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 25 07:09:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 25 Aug 2010 07:09:07 -0400 (EDT) Subject: [BioCatalogue-developers] [2219] trunk/public/2009/xml/rest/schema-v1.xsd: REST API work: fix to the User - made it into a ResourceLink. Message-ID: <20100825110907.34AD5177993F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 25 09:28:15 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 25 Aug 2010 09:28:15 -0400 (EDT) Subject: [BioCatalogue-developers] [2220] trunk/app/controllers/users_controller.rb: - removed users that not been activated from /users (JSON + XML) Message-ID: <20100825132815.A697A1858375@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 25 10:08:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 25 Aug 2010 10:08:47 -0400 (EDT) Subject: [BioCatalogue-developers] [2221] trunk: - bug fixes: Message-ID: <20100825140847.3CEB41858367@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Aug 25 10:47:38 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 25 Aug 2010 10:47:38 -0400 (EDT) Subject: [BioCatalogue-developers] [2222] trunk/lib/bio_catalogue: - merged BioCatalogue::Filtering::Services. validate_item and BioCatalogue::Filtering::RestMethods. validate_item into BioCatalogue::Util. validate_as_rest_input_output_else_true Message-ID: <20100825144738.9A622185838E@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Aug 25 12:01:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 25 Aug 2010 17:01:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-459) Implement lookup functionality for REST Methods Message-ID: <32920953.8161.1282752075507.JavaMail.jira@rosalind.cs.man.ac.uk> Implement lookup functionality for REST Methods ----------------------------------------------- Key: BIOCAT-459 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-459 Project: BioCatalogue Issue Type: Task Components: Misc Codebase, REST API Reporter: Mannie Tagarira Assignee: Jiten Bhagat Consider this email snippet: The BioCatalogue plugin in Taverna would try to do a lookup (via the use of /lookup?...) for a REST Method entry in the main catalogue based on a URL template. This template could be, for demonstrative purposes, "http://example.com?service=ONE&method={METHOD}". The BioCatalogue could have some REST Services registered based on the following list of base URLs: - "http://example.com?service=ONE" - "http://example.com?service=TWO" - "http://example.com?service=THREE" At first glance this looks doable; then you start to think about cases where the user might enter the following templates: - "http://example.com?service={SERVICE}&method={METHOD}&x={X}&y=Y&z=Z" - "http://example.com/{API_VERSION}/rest/{database}/{id}?x={X}&y=Y" - "http://example.com/{API_VERSION}/rest?x={X}&y=Y" - and many other permutations The BioCatalogue currently has no way of knowing what the base URL of the user provided template is, so this will have to be "intelligently" derived. This would involve getting all the services that have a base URL that contains the hostname of the provided template, "example.com" in this case. For each of these services, check that it is possible to create a template that matches the one provided by the user; the use of different combinations of required and optional parameters available is probable. This could result in long waiting times depending on the number of services matching the hostname, and the number of query (and template) parameters in the template being passed in; think DDBJ! - "http://xml.nig.ac.jp/rest/Invoke?service={service}&method={method}&accession={accession}&..." After intelligently filtering these services and REST methods in a "maintainable, manageable, and actually possible to squat bugs in the future" manner, which I'm sure is possible by the way, i am fairly certain that it will not always return *one and only one* REST method; again, think DDBJ! -- 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 Aug 25 12:01:22 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 25 Aug 2010 17:01:22 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-452) Implement a filter for RestMethod In-Reply-To: <8021914.8037.1281524175308.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27591598.8163.1282752082117.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-452?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-452. ------------------------------------ Resolution: Implemented > Implement a filter for RestMethod > --------------------------------- > > Key: BIOCAT-452 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-452 > Project: BioCatalogue > Issue Type: Task > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > 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 Wed Aug 25 12:01:21 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 25 Aug 2010 17:01:21 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-448) Integrate OAuth into the application In-Reply-To: <4348614.7764.1280398395360.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10056286.8162.1282752081160.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-448?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-448. ------------------------------------ Resolution: Fixed > Integrate OAuth into the application > ------------------------------------ > > Key: BIOCAT-448 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-448 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > 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 Wed Aug 25 12:03:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 25 Aug 2010 17:03:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-452) Implement a filter for RestMethod In-Reply-To: <8021914.8037.1281524175308.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27236816.8164.1282752195351.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-452?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-452. ---------------------------------- > Implement a filter for RestMethod > --------------------------------- > > Key: BIOCAT-452 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-452 > Project: BioCatalogue > Issue Type: Task > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > 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 Wed Aug 25 12:03:25 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 25 Aug 2010 17:03:25 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-453) Implement functionality to allow users to save their favourite search filters In-Reply-To: <11270692.8038.1281524295332.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30870123.8165.1282752205069.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-453?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-453. ------------------------------------ Resolution: Implemented > Implement functionality to allow users to save their favourite search filters > ----------------------------------------------------------------------------- > > Key: BIOCAT-453 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-453 > Project: BioCatalogue > Issue Type: Task > Components: REST API > 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 Wed Aug 25 12:05:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 25 Aug 2010 17:05:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-460) Document updates to the API Message-ID: <6899755.8166.1282752315321.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 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 utopia at cs.man.ac.uk Sat Aug 28 13:58:30 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 28 Aug 2010 18:58:30 +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 Sat Aug 28 15:52:16 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 28 Aug 2010 20:52:16 +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 utopia at cs.man.ac.uk Sun Aug 29 06:56:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 29 Aug 2010 11:56:28 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getRelatedSymbols' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getRelatedSymbols' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1081 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 MAILER-DAEMON at ebi.ac.uk Sun Aug 29 12:14:04 2010 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Sun, 29 Aug 2010 17:14:04 +0100 Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201008291614.o7TGE4kw026540@spike.ebi.ac.uk> The original message was received at Sun, 29 Aug 2010 17:13:53 +0100 from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 This message contains a virus (Exploit.E107).) ----- Transcript of session follows ----- ... while talking to mx0.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: Sun, 29 Aug 2010 17:13:53 +0100 Size: 12070 URL: From ytanoh at cs.man.ac.uk Tue Aug 31 09:20:25 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 31 Aug 2010 14:20:25 +0100 Subject: [BioCatalogue-developers] back Message-ID: Hi guys, I'm back from my holidays and going through my load of emails. If there are anything urgent you want me to take a look, pls let me know. Cheers, Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Aug 31 09:33:30 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 31 Aug 2010 09:33:30 -0400 (EDT) Subject: [BioCatalogue-developers] [2223] trunk/public/2009/xml/rest/schema-v1.xsd: REST API work: Added < httpMethodType> to RestMethod. Message-ID: <20100831133330.24B521858356@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Aug 31 10:04:19 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 31 Aug 2010 10:04:19 -0400 (EDT) Subject: [BioCatalogue-developers] [2224] trunk: - added RestMethod#prefered_description and RestMethod:: SUPPORTED_HTTP_METHODS Message-ID: <20100831140419.AC6261858356@rubyforge.org> An HTML attachment was scrubbed... URL: