From utopia at cs.man.ac.uk Sat Jan 1 09:59:57 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 01 Jan 2011 14:59:57 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getComponentsFromPDBId' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getComponentsFromPDBId' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1108 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 Jan 1 12:49:09 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 01 Jan 2011 17:49:09 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getPDBLigand' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getPDBLigand' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1102 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 Jan 1 18:27:51 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 01 Jan 2011 23:27:51 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1155 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 Jan 1 21:00:15 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 02 Jan 2011 02:00:15 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runLeapFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runLeapFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1146 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 Jan 2 05:47:25 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 02 Jan 2011 10:47:25 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'JACOP/FuncNet' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'JACOP/FuncNet' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/219 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 Jan 2 10:22:53 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 02 Jan 2011 15:22:53 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:genome.imim.es:runDust' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:genome.imim.es:runDust' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1033 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 Jan 2 12:45:52 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 02 Jan 2011 17:45:52 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromGenericSequenceCollectionToFASTA' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromGenericSequenceCollectionToFASTA' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/773 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 Jan 3 11:13:53 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 03 Jan 2011 16:13:53 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'The ELM Resource Structure Filter' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'The ELM Resource Structure Filter' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1620 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Jan 5 20:30:58 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 06 Jan 2011 01:30:58 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:searchOrGuessSymbolIdFromInput' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:searchOrGuessSymbolIdFromInput' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1082 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jan 7 19:28:12 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 00:28:12 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS skipredundant' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS skipredundant' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/522 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jan 7 21:41:20 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 02:41:20 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS ehmmsearch' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS ehmmsearch' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1714 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 Jan 8 00:08:49 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 05:08:49 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS coderet' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS coderet' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/625 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 Jan 8 00:11:11 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 05:11:11 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS helixturnhelix' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS helixturnhelix' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/633 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 Jan 8 00:16:11 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 05:16:11 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS needle' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS needle' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/432 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 Jan 8 00:31:32 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 05:31:32 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS scopparse' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS scopparse' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1832 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 Jan 8 00:13:36 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 05:13:36 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS hmoment' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS hmoment' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/635 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 Jan 8 01:38:27 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 06:38:27 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS fconsense' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS fconsense' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1748 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 Jan 8 01:40:47 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 06:40:47 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS plotcon' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS plotcon' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/448 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 Jan 8 01:43:05 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 06:43:05 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS prettyplot' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS prettyplot' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/450 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 Jan 8 01:45:26 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 06:45:26 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS showalign' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS showalign' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/452 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 Jan 8 01:47:43 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 06:47:43 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS frestboot' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS frestboot' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1806 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 Jan 8 01:50:05 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 06:50:05 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS frestdist' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS frestdist' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1808 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 Jan 8 01:52:20 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 06:52:20 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS frestml' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS frestml' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1810 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 Jan 8 01:54:43 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 06:54:43 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS fseqbootall' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS fseqbootall' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1812 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 Jan 8 01:56:52 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 06:56:52 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS fseqboot' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS fseqboot' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1814 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 Jan 8 01:58:56 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 06:58:56 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS tranalign' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS tranalign' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/454 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 Jan 8 02:01:11 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 07:01:11 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS topo' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS topo' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1820 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 Jan 8 02:03:29 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 07:03:29 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS sigscan' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS sigscan' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1826 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 Jan 8 02:05:49 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 07:05:49 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS ememe' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS ememe' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1828 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 Jan 8 02:07:47 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 07:07:47 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS cathparse' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS cathparse' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1830 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 Jan 8 02:12:30 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 07:12:30 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS ssematch' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS ssematch' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1834 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 Jan 8 02:14:49 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 07:14:49 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS showseq' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS showseq' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/468 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 Jan 8 02:17:06 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 07:17:06 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS sixpack' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS sixpack' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/470 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 Jan 8 02:19:23 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 07:19:23 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS cai' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS cai' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/540 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 Jan 8 02:21:40 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 07:21:40 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS chips' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS chips' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/542 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 Jan 8 02:23:58 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 07:23:58 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS dan' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS dan' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/554 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 Jan 8 02:26:15 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 07:26:15 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS isochore' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS isochore' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/558 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 Jan 8 02:28:35 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 07:28:35 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS sirna' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS sirna' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/560 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 Jan 8 02:30:51 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 07:30:51 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS wordcount' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS wordcount' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/562 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 Jan 8 02:33:07 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 07:33:07 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS geecee' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS geecee' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/568 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 Jan 8 03:06:37 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 08:06:37 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS garnier' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS garnier' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/631 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 Jan 8 03:06:43 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 08:06:43 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS garnier' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS garnier' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/631 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 Jan 8 13:29:15 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 18:29:15 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS ehmmalign' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS ehmmalign' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1698 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 Jan 8 15:10:37 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 Jan 2011 20:10:37 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS jaspscan' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS jaspscan' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/620 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 Jan 8 21:14:40 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 09 Jan 2011 02:14:40 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'CODA (using CATH domains)' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'CODA (using CATH domains)' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/146 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 Jan 9 01:21:45 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 09 Jan 2011 06:21:45 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS fpromlk' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS fpromlk' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1798 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 Jan 9 06:10:41 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 09 Jan 2011 11:10:41 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS restrict' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS restrict' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/616 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 Jan 9 12:51:08 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 09 Jan 2011 17:51:08 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS mwfilter' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS mwfilter' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/647 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 Jan 10 00:25:17 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 10 Jan 2011 05:25:17 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS fpromlk' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS fpromlk' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1798 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Jan 10 20:58:03 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 11 Jan 2011 01:58:03 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS mwfilter' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS mwfilter' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/647 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jan 11 12:27:07 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 11 Jan 2011 17:27:07 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS restrict' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS restrict' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/616 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jan 11 20:08:07 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 12 Jan 2011 01:08:07 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:fromPrankToSLR' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:fromPrankToSLR' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1094 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Jan 13 09:20:27 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 13 Jan 2011 14:20:27 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS ssematch' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS ssematch' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1834 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Thu Jan 13 10:44:17 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 13 Jan 2011 15:44:17 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-526) Generate statistics for the BioCatalogue Annual Report In-Reply-To: <3044374.544.1289913209214.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23363743.24.1294933457190.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-526?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-526. ------------------------------------- Resolution: Responded Report has been submitted with stats. > Generate statistics for the BioCatalogue Annual Report > ------------------------------------------------------ > > Key: BIOCAT-526 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-526 > Project: BioCatalogue > Issue Type: Task > Components: Data > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Generate various statistics for the BioCatalogue annual report. Check with Carole what the specific graphs/tables needed are. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Thu Jan 13 10:59:16 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 13 Jan 2011 15:59:16 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS jaspscan' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS jaspscan' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/620 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Jan 13 16:21:49 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 13 Jan 2011 21:21:49 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'CODA (using CATH domains)' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'CODA (using CATH domains)' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/146 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jan 14 00:02:49 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 14 Jan 2011 05:02:49 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS sirna' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS sirna' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/560 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jan 14 01:08:51 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 14 Jan 2011 06:08:51 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS ehmmalign' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS ehmmalign' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1698 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jan 14 13:49:59 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 14 Jan 2011 18:49:59 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:computeCorrelationsFromMD_TrajectoryCRD' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:computeCorrelationsFromMD_TrajectoryCRD' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1151 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jan 14 20:50:53 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 15 Jan 2011 01:50:53 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getGROMACS_MD_StructureFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getGROMACS_MD_StructureFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1163 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jan 14 20:55:48 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 15 Jan 2011 01:55:48 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runBrownianMDFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runBrownianMDFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1117 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 Jan 15 01:15:09 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 15 Jan 2011 06:15:09 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS frestml' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS frestml' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1810 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Jan 15 01:20:13 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 15 Jan 2011 06:20:13 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS frestdist' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS frestdist' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1808 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Jan 15 05:35:25 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 15 Jan 2011 10:35:25 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:searchPdbForCa' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:searchPdbForCa' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1116 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 Jan 16 11:30:07 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 16 Jan 2011 16:30:07 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS isochore' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS isochore' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/558 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Jan 17 05:55:22 2011 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 17 Jan 2011 10:55:22 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS plotcon' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS plotcon' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/448 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From jits at cs.man.ac.uk Mon Jan 17 09:02:38 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 17 Jan 2011 14:02:38 +0000 Subject: [BioCatalogue-developers] Service monitoring Message-ID: <4D344BFE.7020701@cs.man.ac.uk> Hi Steve, Could you remove the biocatalogue-developers at rubyforge.org email address from the Embrace service monitoring emails please? Cheers, Jits From issues at mygrid.org.uk Mon Jan 17 09:33:17 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 17 Jan 2011 14:33:17 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-556) Change "From" email address of error/exception emails Message-ID: <16814454.147.1295274797044.JavaMail.jira@rosalind.cs.man.ac.uk> Change "From" email address of error/exception emails ----------------------------------------------------- Key: BIOCAT-556 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-556 Project: BioCatalogue Issue Type: Task Reporter: Jiten Bhagat Assignee: Eric Nzuobontane Fix For: 2010-12 Currently, all error/exception emails from the main app are sent using the *biocatalogue-developers at rubyforge.org* email address in the "From" field. This should be changed to *contact at biocatalogue.org*. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From ytanoh at cs.man.ac.uk Tue Jan 18 06:46:19 2011 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 18 Jan 2011 11:46:19 +0000 Subject: [BioCatalogue-developers] last mass curator app Message-ID: Hi Jits, The last mass curator app, I'm using is here: http://dl.dropbox.com/u/1449587/Mass%20Curator%20-%200.1.zip Franck -- ?"Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From jits at cs.man.ac.uk Tue Jan 18 08:17:17 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 18 Jan 2011 13:17:17 +0000 Subject: [BioCatalogue-developers] last mass curator app In-Reply-To: References: Message-ID: <4D3592DD.3080206@cs.man.ac.uk> Thanks Franck! I'll take a look for the final release. And thanks for testing it! Jits On 18/01/11 11:46, Franck Tanoh wrote: > Hi Jits, > > The last mass curator app, I'm using is here: > http://dl.dropbox.com/u/1449587/Mass%20Curator%20-%200.1.zip > > Franck > From issues at mygrid.org.uk Wed Jan 19 09:01:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 19 Jan 2011 14:01:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-431) Update copyright date in footer to 2008-2010 In-Reply-To: <31361560.7125.1278402615439.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23017770.58.1295445669497.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-431?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16389#comment-16389 ] Eric Nzuobontane commented on BIOCAT-431: ----------------------------------------- This should be done for the next release. On the front page we still have 2008-2009! > Update copyright date in footer to 2008-2010 > -------------------------------------------- > > Key: BIOCAT-431 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-431 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Wed Jan 19 10:09:16 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 19 Jan 2011 10:09:16 -0500 (EST) Subject: [BioCatalogue-developers] [2335] trunk/app/views/layouts/_footer.html.erb: Updated copyright date in footer Message-ID: <20110119150916.34F4018582EE@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jan 19 10:14:09 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 19 Jan 2011 15:14:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-431) Update copyright date in footer to 2008-2010 In-Reply-To: <31361560.7125.1278402615439.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4591252.59.1295450049419.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-431?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-431. --------------------------------- Fix Version/s: 2011-02 Resolution: Fixed Done! > Update copyright date in footer to 2008-2010 > -------------------------------------------- > > Key: BIOCAT-431 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-431 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 2011-02 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jan 19 10:14:11 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 19 Jan 2011 15:14:11 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-431) Update copyright date in footer to 2008-2010 In-Reply-To: <31361560.7125.1278402615439.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11055783.60.1295450051802.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-431?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16391#comment-16391 ] Jiten Bhagat commented on BIOCAT-431: ------------------------------------- Updated to: "2008 - 2011" > Update copyright date in footer to 2008-2010 > -------------------------------------------- > > Key: BIOCAT-431 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-431 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 2011-02 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jan 19 10:14:13 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 19 Jan 2011 15:14:13 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-431) Update copyright date in footer to 2008-2010 In-Reply-To: <31361560.7125.1278402615439.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29730627.61.1295450053342.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-431?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-431. ------------------------------- > Update copyright date in footer to 2008-2010 > -------------------------------------------- > > Key: BIOCAT-431 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-431 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 2011-02 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 21 09:34:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 Jan 2011 14:34:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-52) Write server update script Message-ID: <31813119.88.1295620449438.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-52?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-52 started by Eric Nzuobontane. > Write server update script > -------------------------- > > Key: BIOCAT-52 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-52 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Write a script for the server update process. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 21 09:34:10 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 Jan 2011 14:34:10 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-52) Write server update script Message-ID: <13536651.89.1295620450854.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-52?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-52 started by Eric Nzuobontane. > Write server update script > -------------------------- > > Key: BIOCAT-52 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-52 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Write a script for the server update process. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 21 09:34:12 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 Jan 2011 14:34:12 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-52) Write server update script Message-ID: <15579756.90.1295620452430.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-52?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-52 stopped by Eric Nzuobontane. > Write server update script > -------------------------- > > Key: BIOCAT-52 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-52 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Write a script for the server update process. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 21 10:31:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 Jan 2011 15:31:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-302) Add an example to the test script documentation on the wiki Message-ID: <27641337.96.1295623869400.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-302?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-302. ------------------------------------- Resolution: Implemented > Add an example to the test script documentation on the wiki > ----------------------------------------------------------- > > Key: BIOCAT-302 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-302 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Environment: wiki > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Provided some examples of test clients that can be submitted against web services in BioCatalogue. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 21 10:35:10 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 Jan 2011 15:35:10 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-546) Investigate biomart returned email In-Reply-To: <26177817.210.1290679912908.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16254420.98.1295624110420.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-546?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-546. ------------------------------------- Resolution: Fixed > Investigate biomart returned email > ---------------------------------- > > Key: BIOCAT-546 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-546 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > There was an issue delivering the email to Biomart account email. The user email may no longer be valid. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 21 10:35:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 Jan 2011 15:35:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-546) Investigate biomart returned email In-Reply-To: <26177817.210.1290679912908.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17539635.97.1295624109405.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-546?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16400#comment-16400 ] Eric Nzuobontane commented on BIOCAT-546: ----------------------------------------- Correct contact for biomart has now been established.[junjun.zhang [at] oicr.on.ca] > Investigate biomart returned email > ---------------------------------- > > Key: BIOCAT-546 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-546 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > There was an issue delivering the email to Biomart account email. The user email may no longer be valid. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 21 10:35:11 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 Jan 2011 15:35:11 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-541) Documentation url annotations to should be validated to valid URLs. In-Reply-To: <27694451.101.1290180832809.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6796640.99.1295624111354.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-541?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-541 stopped by Eric Nzuobontane. > Documentation url annotations to should be validated to valid URLs. > -------------------------------------------------------------------- > > Key: BIOCAT-541 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-541 > Project: BioCatalogue > Issue Type: Task > Components: Data > Environment: UI > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > At the moment, any string is accepted as a documentation URL. This should be validated to a URL to improve the data quality -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 21 10:35:12 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 Jan 2011 15:35:12 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-546) Investigate biomart returned email In-Reply-To: <26177817.210.1290679912908.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25227422.100.1295624112350.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-546?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-546 stopped by Eric Nzuobontane. > Investigate biomart returned email > ---------------------------------- > > Key: BIOCAT-546 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-546 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > There was an issue delivering the email to Biomart account email. The user email may no longer be valid. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 21 10:37:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 Jan 2011 15:37:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-541) Documentation url annotations to should be validated to valid URLs. In-Reply-To: <27694451.101.1290180832809.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22134241.101.1295624229372.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-541?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-541. ------------------------------------- Resolution: Fixed > Documentation url annotations to should be validated to valid URLs. > -------------------------------------------------------------------- > > Key: BIOCAT-541 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-541 > Project: BioCatalogue > Issue Type: Task > Components: Data > Environment: UI > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > At the moment, any string is accepted as a documentation URL. This should be validated to a URL to improve the data quality -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 21 11:34:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 Jan 2011 16:34:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-507) Soap service show(hmtl format) should redirect to the parent service In-Reply-To: <28972168.10334.1288264995363.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15142681.102.1295627649398.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-507?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-507. ------------------------------------- Resolution: Implemented > Soap service show(hmtl format) should redirect to the parent service > -------------------------------------------------------------------- > > Key: BIOCAT-507 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-507 > Project: BioCatalogue > Issue Type: Refinement > Components: Web Interface > Environment: RoR, UI > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Rather than return an error page, soap service show should redirect to the parent service. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 21 11:36:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 Jan 2011 16:36:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-479) Change the queries that do count to use the ActiveRecord count method In-Reply-To: <33188271.9868.1285671315305.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13503254.103.1295627769383.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-479?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-479. ------------------------------------- Resolution: Fixed > Change the queries that do count to use the ActiveRecord count method > --------------------------------------------------------------------- > > Key: BIOCAT-479 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-479 > Project: BioCatalogue > Issue Type: Task > Components: Performance / Optimisations > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Use the ActiveRecord count method instead of loading records in memory to count. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Fri Jan 21 12:12:29 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 21 Jan 2011 17:12:29 +0000 Subject: [BioCatalogue-developers] Moving to GitHub Message-ID: <4D39BE7D.6090706@cs.man.ac.uk> Hello, After the next release, I want to look to moving the source code to GitHub (thus moving from SVN to Git). This is part of the process of moving to a more "open development" model and separating out the software vs the service. So I suspect that part of moving it will be (possibly) renaming the product itself. Jits From issues at mygrid.org.uk Fri Jan 21 12:18:10 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 Jan 2011 17:18:10 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-541) Documentation url annotations to should be validated to valid URLs. In-Reply-To: <27694451.101.1290180832809.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31503110.105.1295630290945.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-541?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16401#comment-16401 ] Jiten Bhagat commented on BIOCAT-541: ------------------------------------- The current way it's done is too rudimentary. Can we try and use something like this: https://github.com/perfectline/validates_url, although that is for rails 3 specifically. I've also seen some proper regular expressions around that can verify URLs. > Documentation url annotations to should be validated to valid URLs. > -------------------------------------------------------------------- > > Key: BIOCAT-541 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-541 > Project: BioCatalogue > Issue Type: Task > Components: Data > Environment: UI > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > At the moment, any string is accepted as a documentation URL. This should be validated to a URL to improve the data quality -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 21 12:21:09 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 Jan 2011 17:21:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-541) Documentation url annotations to should be validated to valid URLs. In-Reply-To: <27694451.101.1290180832809.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31586413.106.1295630469379.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-541?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16402#comment-16402 ] Jiten Bhagat commented on BIOCAT-541: ------------------------------------- Ahh, ignore comment above. I see that "URI::regexp(%w(http https)" is used, which makes sense. Only thing - might want to enable other protocols there, like FTP. > Documentation url annotations to should be validated to valid URLs. > -------------------------------------------------------------------- > > Key: BIOCAT-541 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-541 > Project: BioCatalogue > Issue Type: Task > Components: Data > Environment: UI > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > At the moment, any string is accepted as a documentation URL. This should be validated to a URL to improve the data quality -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 21 12:40:09 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 Jan 2011 17:40:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-557) Implement a JSON API for component definitions Message-ID: <16710196.108.1295631609372.JavaMail.jira@rosalind.cs.man.ac.uk> Implement a JSON API for component definitions ---------------------------------------------- Key: BIOCAT-557 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-557 Project: BioCatalogue Issue Type: New Feature Components: REST API Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Blocker Fix For: 2011-02 In order to link with the Taverna next gen workbench, the WCL needs to expose component definitions in a JSON format as described here: http://www.mygrid.org.uk/dev/wiki/display/TNG/Workflow+Components Therefore, the app needs to expose a JSON API that provides these component definitions. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 21 12:42:09 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 Jan 2011 17:42:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-558) Implement to_json method for Component model Message-ID: <25353945.109.1295631729394.JavaMail.jira@rosalind.cs.man.ac.uk> Implement to_json method for Component model -------------------------------------------- Key: BIOCAT-558 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-558 Project: BioCatalogue Issue Type: Sub-task Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 2011-02 In order to produce the JSON output, need to implement a to_json method in the Component model that outputs the relevant JSON format (as described here: http://www.mygrid.org.uk/dev/wiki/display/TNG/Workflow+Components). -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jan 24 05:03:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 24 Jan 2011 10:03:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-541) Documentation url annotations to should be validated to valid URLs. In-Reply-To: <27694451.101.1290180832809.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25072625.120.1295863389495.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-541?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16404#comment-16404 ] Eric Nzuobontane commented on BIOCAT-541: ----------------------------------------- There is always room to improve the code, even change it completely or revert it if a "too rudimentary" implementation does not help. Let us see if people are asking for those other protocols. > Documentation url annotations to should be validated to valid URLs. > -------------------------------------------------------------------- > > Key: BIOCAT-541 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-541 > Project: BioCatalogue > Issue Type: Task > Components: Data > Environment: UI > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > At the moment, any string is accepted as a documentation URL. This should be validated to a URL to improve the data quality -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon Jan 24 06:31:45 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 Jan 2011 06:31:45 -0500 (EST) Subject: [BioCatalogue-developers] [2336] trunk/config: Added pre-initializer configuation file and moved cronolog configuration to the file (config/preinitializer.rb) Message-ID: <20110124113145.50FDB167831B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jan 24 06:45:53 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 Jan 2011 06:45:53 -0500 (EST) Subject: [BioCatalogue-developers] [2337] trunk: removed legacy scripts in application root directory Message-ID: <20110124114553.C717D1858356@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Mon Jan 24 07:04:45 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 24 Jan 2011 12:04:45 +0000 Subject: [BioCatalogue-developers] [2336] trunk/config: Added pre-initializer configuation file and moved cronolog configuration to the file (config/preinitializer.rb) In-Reply-To: <20110124113145.50FDB167831B@rubyforge.org> References: <20110124113145.50FDB167831B@rubyforge.org> Message-ID: <4D3D6ADD.2090606@cs.man.ac.uk> Hi, What's the purpose of this change? Jits On 24/01/11 11:31, noreply at rubyforge.org wrote: > > Revision > 2336 > Author > ebontane > Date > 2011-01-24 06:31:44 -0500 (Mon, 24 Jan 2011) > > > Log Message > > Added pre-initializer configuation file and moved cronolog configuration to the file (config/preinitializer.rb) > > > Modified Paths > > * trunk/config/boot.rb <#trunkconfigbootrb> > * trunk/config/environment.rb <#trunkconfigenvironmentrb> > * trunk/config/environments/production.rb > <#trunkconfigenvironmentsproductionrb> > > > Added Paths > > * trunk/config/preinitializer.rb.pre <#trunkconfigpreinitializerrbpre> > > > Property Changed > > * trunk/config/ <#trunkconfig> > > > Diff > > > Property changes: trunk/config > > > Modified: svn:ignore > > biocat_local.rb solr.yml memcache.yml hold_routes.rb > mongrel_cluster.yml + database.yml biocat_local.rb solr.yml > memcache.yml hold_routes.rb mongrel_cluster.yml preinitializer.rb > > > Modified: trunk/config/boot.rb (2335 => 2336) > > > --- trunk/config/boot.rb 2011-01-19 15:09:15 UTC (rev 2335) > +++ trunk/config/boot.rb 2011-01-24 11:31:44 UTC (rev 2336) > @@ -25,7 +25,7 @@ > end > > def preinitialize > - load(preinitializer_path) if File.exist?(preinitializer_path) > + load(preinitializer_path) #if File.exist?(preinitializer_path) > end > > def preinitializer_path > > > Modified: trunk/config/environment.rb (2335 => 2336) > > > --- trunk/config/environment.rb 2011-01-19 15:09:15 UTC (rev 2335) > +++ trunk/config/environment.rb 2011-01-24 11:31:44 UTC (rev 2336) > @@ -26,7 +26,7 @@ > # config.gem "hpricot", :version => '0.6', :source => "http://code.whytheluckystiff.net" > # config.gem "aws-s3", :lib => "aws/s3" > config.gem 'disqus', :version => '1.0.1' > - config.gem 'soap4r', :version => '1.5.8' > + #config.gem 'soap4r', :version => '1.5.8' > config.gem 'mperham-memcache-client', :version => '>= 1.7.4', :lib => 'memcache', :source => "http://gems.github.com" > config.gem 'onyx-cache-money', :version => '>= 0.2.6.1', :lib => 'cache_money', :source => "http://gems.github.com" > config.gem 'geokit', :version => '>= 1.3.2' > @@ -86,8 +86,20 @@ > > # Activate observers that should always be running > config.active_record.observers = :annotation_observer > + > + # Use cronolog for log rotation in production > + # ROTATE_LOGS& CRONOLOG_PARAMS constants > + # are set in config/preinitializer.rb > + # By default log rotation is switched off > + if ROTATE_LOGS&& CRONOLOG_PARAMS > + config.logger = Logger.new(IO.popen( CRONOLOG_PARAMS, "w" )) > + config.logger.level = Logger::DEBUG > + end > + > end > > + > + > # Code to handle the issue of unintential file descriptor sharing in Phusion Passenger. > # Ref: http://www.modrails.com/documentation/Users%20guide.html#_example_1_memcached_connection_sharing_harmful > # and: http://info.michael-simons.eu/2009/03/23/phusion-passenger-and-memcache-client-revisited/ > > > Modified: trunk/config/environments/production.rb (2335 => 2336) > > > --- trunk/config/environments/production.rb 2011-01-19 15:09:15 UTC (rev 2335) > +++ trunk/config/environments/production.rb 2011-01-24 11:31:44 UTC (rev 2336) > @@ -9,13 +9,13 @@ > > # Use cronolog for log rotation in production > # Set ROTATE_LOGS=false to turn off log rotation. > -ROTATE_LOGS = false > -cronolog_params = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" > +#ROTATE_LOGS = false > +#cronolog_params = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" > > -if ROTATE_LOGS > - config.logger = Logger.new(IO.popen( cronolog_params, "w" )) > - config.logger.level = Logger::INFO > -end > +#if ROTATE_LOGS&& CRONOLOG_PARAMS > +# config.logger = Logger.new(IO.popen( CRONOLOG_PARAMS, "w" )) > +# config.logger.level = Logger::INFO > +#end > > # Full error reports are disabled and caching is turned on > config.action_controller.consider_all_requests_local = false > > > Added: trunk/config/preinitializer.rb.pre (0 => 2336) > > > --- trunk/config/preinitializer.rb.pre (rev 0) > +++ trunk/config/preinitializer.rb.pre 2011-01-24 11:31:44 UTC (rev 2336) > @@ -0,0 +1,10 @@ > +#Configurations needed before the app init > + > +# Logs rotation > +# > +# Set this to true to rotate the logs > +ROTATE_LOGS = false > +# > +# Set the rotation parameters > +# Example CRONOLOG_PARAMS = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" > +CRONOLOG_PARAMS = nil > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Mon Jan 24 08:12:10 2011 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 24 Jan 2011 13:12:10 +0000 Subject: [BioCatalogue-developers] [2336] trunk/config: Added pre-initializer configuation file and moved cronolog configuration to the file (config/preinitializer.rb) In-Reply-To: <4D3D6ADD.2090606@cs.man.ac.uk> References: <20110124113145.50FDB167831B@rubyforge.org> <4D3D6ADD.2090606@cs.man.ac.uk> Message-ID: <4D3D7AAA.5050101@ebi.ac.uk> The purpose of this change is it make it clearer(especially to the non-developers that will be running the application here) that this file needs some local configuration like the rest of the pre- files. Otherwise they will have to know that they need to edit environment files. At the moment, environments/production.rb is edited on the server for log rotation settings. Eric On 24/01/2011 12:04, Jiten Bhagat wrote: > Hi, > > What's the purpose of this change? > > Jits > > > > On 24/01/11 11:31, noreply at rubyforge.org wrote: >> >> Revision >> 2336 >> Author >> ebontane >> Date >> 2011-01-24 06:31:44 -0500 (Mon, 24 Jan 2011) >> >> >> Log Message >> >> Added pre-initializer configuation file and moved cronolog configuration to the file (config/preinitializer.rb) >> >> >> Modified Paths >> >> * trunk/config/boot.rb <#trunkconfigbootrb> >> * trunk/config/environment.rb <#trunkconfigenvironmentrb> >> * trunk/config/environments/production.rb >> <#trunkconfigenvironmentsproductionrb> >> >> >> Added Paths >> >> * trunk/config/preinitializer.rb.pre >> <#trunkconfigpreinitializerrbpre> >> >> >> Property Changed >> >> * trunk/config/ <#trunkconfig> >> >> >> Diff >> >> >> Property changes: trunk/config >> >> >> Modified: svn:ignore >> >> biocat_local.rb solr.yml memcache.yml hold_routes.rb >> mongrel_cluster.yml + database.yml biocat_local.rb solr.yml >> memcache.yml hold_routes.rb mongrel_cluster.yml preinitializer.rb >> >> >> Modified: trunk/config/boot.rb (2335 => 2336) >> >> >> --- trunk/config/boot.rb 2011-01-19 15:09:15 UTC (rev 2335) >> +++ trunk/config/boot.rb 2011-01-24 11:31:44 UTC (rev 2336) >> @@ -25,7 +25,7 @@ >> end >> >> def preinitialize >> - load(preinitializer_path) if File.exist?(preinitializer_path) >> + load(preinitializer_path) #if File.exist?(preinitializer_path) >> end >> >> def preinitializer_path >> >> >> Modified: trunk/config/environment.rb (2335 => 2336) >> >> >> --- trunk/config/environment.rb 2011-01-19 15:09:15 UTC (rev 2335) >> +++ trunk/config/environment.rb 2011-01-24 11:31:44 UTC (rev 2336) >> @@ -26,7 +26,7 @@ >> # config.gem "hpricot", :version => '0.6', :source => "http://code.whytheluckystiff.net" >> # config.gem "aws-s3", :lib => "aws/s3" >> config.gem 'disqus', :version => '1.0.1' >> - config.gem 'soap4r', :version => '1.5.8' >> + #config.gem 'soap4r', :version => '1.5.8' >> config.gem 'mperham-memcache-client', :version => '>= 1.7.4', :lib => 'memcache', :source => "http://gems.github.com" >> config.gem 'onyx-cache-money', :version => '>= 0.2.6.1', :lib => 'cache_money', :source => "http://gems.github.com" >> config.gem 'geokit', :version => '>= 1.3.2' >> @@ -86,8 +86,20 @@ >> >> # Activate observers that should always be running >> config.active_record.observers = :annotation_observer >> + >> + # Use cronolog for log rotation in production >> + # ROTATE_LOGS& CRONOLOG_PARAMS constants >> + # are set in config/preinitializer.rb >> + # By default log rotation is switched off >> + if ROTATE_LOGS&& CRONOLOG_PARAMS >> + config.logger = Logger.new(IO.popen( CRONOLOG_PARAMS, "w" )) >> + config.logger.level = Logger::DEBUG >> + end >> + >> end >> >> + >> + >> # Code to handle the issue of unintential file descriptor sharing in Phusion Passenger. >> # Ref:http://www.modrails.com/documentation/Users%20guide.html#_example_1_memcached_connection_sharing_harmful >> # and:http://info.michael-simons.eu/2009/03/23/phusion-passenger-and-memcache-client-revisited/ >> >> >> Modified: trunk/config/environments/production.rb (2335 => 2336) >> >> >> --- trunk/config/environments/production.rb 2011-01-19 15:09:15 UTC (rev 2335) >> +++ trunk/config/environments/production.rb 2011-01-24 11:31:44 UTC (rev 2336) >> @@ -9,13 +9,13 @@ >> >> # Use cronolog for log rotation in production >> # Set ROTATE_LOGS=false to turn off log rotation. >> -ROTATE_LOGS = false >> -cronolog_params = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" >> +#ROTATE_LOGS = false >> +#cronolog_params = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" >> >> -if ROTATE_LOGS >> - config.logger = Logger.new(IO.popen( cronolog_params, "w" )) >> - config.logger.level = Logger::INFO >> -end >> +#if ROTATE_LOGS&& CRONOLOG_PARAMS >> +# config.logger = Logger.new(IO.popen( CRONOLOG_PARAMS, "w" )) >> +# config.logger.level = Logger::INFO >> +#end >> >> # Full error reports are disabled and caching is turned on >> config.action_controller.consider_all_requests_local = false >> >> >> Added: trunk/config/preinitializer.rb.pre (0 => 2336) >> >> >> --- trunk/config/preinitializer.rb.pre (rev 0) >> +++ trunk/config/preinitializer.rb.pre 2011-01-24 11:31:44 UTC (rev 2336) >> @@ -0,0 +1,10 @@ >> +#Configurations needed before the app init >> + >> +# Logs rotation >> +# >> +# Set this to true to rotate the logs >> +ROTATE_LOGS = false >> +# >> +# Set the rotation parameters >> +# Example CRONOLOG_PARAMS = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" >> +CRONOLOG_PARAMS = nil >> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Mon Jan 24 08:38:38 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 24 Jan 2011 13:38:38 +0000 Subject: [BioCatalogue-developers] [2336] trunk/config: Added pre-initializer configuation file and moved cronolog configuration to the file (config/preinitializer.rb) In-Reply-To: <4D3D7AAA.5050101@ebi.ac.uk> References: <20110124113145.50FDB167831B@rubyforge.org> <4D3D6ADD.2090606@cs.man.ac.uk> <4D3D7AAA.5050101@ebi.ac.uk> Message-ID: <4D3D80DE.9030400@cs.man.ac.uk> Hi Eric, Thanks for the explanation. The intention makes a lot of sense! My concerns are: 1. The boot.rb file, which is the one generated by Rails, has been modified. Looks like you commented out an 'if' check? This might affect the app boot process as I assume the 'if' check was there for a very specific reason. 2. CRONOLOG specific stuff has been added to the environment.rb file, which seems to make it a dependency now (as in, those constants must exist in order for the app to start up). Will this break things for other environments that don't have chronolog set up? Jits On 24/01/11 13:12, Eric Nzuobontane wrote: > The purpose of this change is it make it clearer(especially to the > non-developers that will be running the application here) that this > file needs some local configuration like the rest of the pre- files. > Otherwise they will have to know that they need to edit environment > files. At the moment, environments/production.rb is edited on the > server for log rotation settings. > > Eric > > > On 24/01/2011 12:04, Jiten Bhagat wrote: >> Hi, >> >> What's the purpose of this change? >> >> Jits >> >> >> >> On 24/01/11 11:31, noreply at rubyforge.org wrote: >>> >>> Revision >>> 2336 >>> Author >>> ebontane >>> Date >>> 2011-01-24 06:31:44 -0500 (Mon, 24 Jan 2011) >>> >>> >>> Log Message >>> >>> Added pre-initializer configuation file and moved cronolog configuration to the file (config/preinitializer.rb) >>> >>> >>> Modified Paths >>> >>> * trunk/config/boot.rb <#trunkconfigbootrb> >>> * trunk/config/environment.rb <#trunkconfigenvironmentrb> >>> * trunk/config/environments/production.rb >>> <#trunkconfigenvironmentsproductionrb> >>> >>> >>> Added Paths >>> >>> * trunk/config/preinitializer.rb.pre >>> <#trunkconfigpreinitializerrbpre> >>> >>> >>> Property Changed >>> >>> * trunk/config/ <#trunkconfig> >>> >>> >>> Diff >>> >>> >>> Property changes: trunk/config >>> >>> >>> Modified: svn:ignore >>> >>> biocat_local.rb solr.yml memcache.yml hold_routes.rb >>> mongrel_cluster.yml + database.yml biocat_local.rb solr.yml >>> memcache.yml hold_routes.rb mongrel_cluster.yml preinitializer.rb >>> >>> >>> Modified: trunk/config/boot.rb (2335 => 2336) >>> >>> >>> --- trunk/config/boot.rb 2011-01-19 15:09:15 UTC (rev 2335) >>> +++ trunk/config/boot.rb 2011-01-24 11:31:44 UTC (rev 2336) >>> @@ -25,7 +25,7 @@ >>> end >>> >>> def preinitialize >>> - load(preinitializer_path) if File.exist?(preinitializer_path) >>> + load(preinitializer_path) #if File.exist?(preinitializer_path) >>> end >>> >>> def preinitializer_path >>> >>> >>> Modified: trunk/config/environment.rb (2335 => 2336) >>> >>> >>> --- trunk/config/environment.rb 2011-01-19 15:09:15 UTC (rev 2335) >>> +++ trunk/config/environment.rb 2011-01-24 11:31:44 UTC (rev 2336) >>> @@ -26,7 +26,7 @@ >>> # config.gem "hpricot", :version => '0.6', :source => "http://code.whytheluckystiff.net" >>> # config.gem "aws-s3", :lib => "aws/s3" >>> config.gem 'disqus', :version => '1.0.1' >>> - config.gem 'soap4r', :version => '1.5.8' >>> + #config.gem 'soap4r', :version => '1.5.8' >>> config.gem 'mperham-memcache-client', :version => '>= 1.7.4', :lib => 'memcache', :source => "http://gems.github.com" >>> config.gem 'onyx-cache-money', :version => '>= 0.2.6.1', :lib => 'cache_money', :source => "http://gems.github.com" >>> config.gem 'geokit', :version => '>= 1.3.2' >>> @@ -86,8 +86,20 @@ >>> >>> # Activate observers that should always be running >>> config.active_record.observers = :annotation_observer >>> + >>> + # Use cronolog for log rotation in production >>> + # ROTATE_LOGS& CRONOLOG_PARAMS constants >>> + # are set in config/preinitializer.rb >>> + # By default log rotation is switched off >>> + if ROTATE_LOGS&& CRONOLOG_PARAMS >>> + config.logger = Logger.new(IO.popen( CRONOLOG_PARAMS, "w" )) >>> + config.logger.level = Logger::DEBUG >>> + end >>> + >>> end >>> >>> + >>> + >>> # Code to handle the issue of unintential file descriptor sharing in Phusion Passenger. >>> # Ref:http://www.modrails.com/documentation/Users%20guide.html#_example_1_memcached_connection_sharing_harmful >>> # and:http://info.michael-simons.eu/2009/03/23/phusion-passenger-and-memcache-client-revisited/ >>> >>> >>> Modified: trunk/config/environments/production.rb (2335 => 2336) >>> >>> >>> --- trunk/config/environments/production.rb 2011-01-19 15:09:15 UTC (rev 2335) >>> +++ trunk/config/environments/production.rb 2011-01-24 11:31:44 UTC (rev 2336) >>> @@ -9,13 +9,13 @@ >>> >>> # Use cronolog for log rotation in production >>> # Set ROTATE_LOGS=false to turn off log rotation. >>> -ROTATE_LOGS = false >>> -cronolog_params = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" >>> +#ROTATE_LOGS = false >>> +#cronolog_params = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" >>> >>> -if ROTATE_LOGS >>> - config.logger = Logger.new(IO.popen( cronolog_params, "w" )) >>> - config.logger.level = Logger::INFO >>> -end >>> +#if ROTATE_LOGS&& CRONOLOG_PARAMS >>> +# config.logger = Logger.new(IO.popen( CRONOLOG_PARAMS, "w" )) >>> +# config.logger.level = Logger::INFO >>> +#end >>> >>> # Full error reports are disabled and caching is turned on >>> config.action_controller.consider_all_requests_local = false >>> >>> >>> Added: trunk/config/preinitializer.rb.pre (0 => 2336) >>> >>> >>> --- trunk/config/preinitializer.rb.pre (rev 0) >>> +++ trunk/config/preinitializer.rb.pre 2011-01-24 11:31:44 UTC (rev 2336) >>> @@ -0,0 +1,10 @@ >>> +#Configurations needed before the app init >>> + >>> +# Logs rotation >>> +# >>> +# Set this to true to rotate the logs >>> +ROTATE_LOGS = false >>> +# >>> +# Set the rotation parameters >>> +# Example CRONOLOG_PARAMS = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" >>> +CRONOLOG_PARAMS = nil >>> >>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel : +44 1223 492654 > email :ericnzuo at ebi.ac.uk > ================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jan 24 08:43:09 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 24 Jan 2011 13:43:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-541) Documentation url annotations to should be validated to valid URLs. In-Reply-To: <27694451.101.1290180832809.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30705924.122.1295876589451.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-541?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16406#comment-16406 ] Jiten Bhagat commented on BIOCAT-541: ------------------------------------- Makes sense Eric. Thanks. > Documentation url annotations to should be validated to valid URLs. > -------------------------------------------------------------------- > > Key: BIOCAT-541 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-541 > Project: BioCatalogue > Issue Type: Task > Components: Data > Environment: UI > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > At the moment, any string is accepted as a documentation URL. This should be validated to a URL to improve the data quality -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Mon Jan 24 08:48:29 2011 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 24 Jan 2011 13:48:29 +0000 Subject: [BioCatalogue-developers] [2336] trunk/config: Added pre-initializer configuation file and moved cronolog configuration to the file (config/preinitializer.rb) In-Reply-To: <4D3D80DE.9030400@cs.man.ac.uk> References: <20110124113145.50FDB167831B@rubyforge.org> <4D3D6ADD.2090606@cs.man.ac.uk> <4D3D7AAA.5050101@ebi.ac.uk> <4D3D80DE.9030400@cs.man.ac.uk> Message-ID: <4D3D832D.20506@ebi.ac.uk> On 24/01/2011 13:38, Jiten Bhagat wrote: > Hi Eric, > > Thanks for the explanation. The intention makes a lot of sense! > > My concerns are: > > 1. The boot.rb file, which is the one generated by Rails, has been > modified. Looks like you commented out an 'if' check? This might > affect the app boot process as I assume the 'if' check was there for a > very specific reason. Yes this will affect the boot process. Previously rails boot would continue with or without this file. I made this file a requirement and provided defaults that should work for all environments. > > 2. CRONOLOG specific stuff has been added to the environment.rb file, > which seems to make it a dependency now (as in, those constants must > exist in order for the app to start up). Will this break things for > other environments that don't have chronolog set up? If the file pre-initializer.rb file exists with the defaults in pre-initializer.rb.pre then it should work. The default is that cronolog will not be used. Given the possible size of the logs, I think that reminding user about the log rotation is a good idea. Eric > > > > On 24/01/11 13:12, Eric Nzuobontane wrote: >> The purpose of this change is it make it clearer(especially to the >> non-developers that will be running the application here) that this >> file needs some local configuration like the rest of the pre- files. >> Otherwise they will have to know that they need to edit environment >> files. At the moment, environments/production.rb is edited on the >> server for log rotation settings. >> >> Eric >> >> >> On 24/01/2011 12:04, Jiten Bhagat wrote: >>> Hi, >>> >>> What's the purpose of this change? >>> >>> Jits >>> >>> >>> >>> On 24/01/11 11:31, noreply at rubyforge.org wrote: >>>> >>>> Revision >>>> 2336 >>>> Author >>>> ebontane >>>> Date >>>> 2011-01-24 06:31:44 -0500 (Mon, 24 Jan 2011) >>>> >>>> >>>> Log Message >>>> >>>> Added pre-initializer configuation file and moved cronolog configuration to the file (config/preinitializer.rb) >>>> >>>> >>>> Modified Paths >>>> >>>> * trunk/config/boot.rb <#trunkconfigbootrb> >>>> * trunk/config/environment.rb <#trunkconfigenvironmentrb> >>>> * trunk/config/environments/production.rb >>>> <#trunkconfigenvironmentsproductionrb> >>>> >>>> >>>> Added Paths >>>> >>>> * trunk/config/preinitializer.rb.pre >>>> <#trunkconfigpreinitializerrbpre> >>>> >>>> >>>> Property Changed >>>> >>>> * trunk/config/ <#trunkconfig> >>>> >>>> >>>> Diff >>>> >>>> >>>> Property changes: trunk/config >>>> >>>> >>>> Modified: svn:ignore >>>> >>>> biocat_local.rb solr.yml memcache.yml hold_routes.rb >>>> mongrel_cluster.yml + database.yml biocat_local.rb solr.yml >>>> memcache.yml hold_routes.rb mongrel_cluster.yml preinitializer.rb >>>> >>>> >>>> Modified: trunk/config/boot.rb (2335 => 2336) >>>> >>>> >>>> --- trunk/config/boot.rb 2011-01-19 15:09:15 UTC (rev 2335) >>>> +++ trunk/config/boot.rb 2011-01-24 11:31:44 UTC (rev 2336) >>>> @@ -25,7 +25,7 @@ >>>> end >>>> >>>> def preinitialize >>>> - load(preinitializer_path) if File.exist?(preinitializer_path) >>>> + load(preinitializer_path) #if File.exist?(preinitializer_path) >>>> end >>>> >>>> def preinitializer_path >>>> >>>> >>>> Modified: trunk/config/environment.rb (2335 => 2336) >>>> >>>> >>>> --- trunk/config/environment.rb 2011-01-19 15:09:15 UTC (rev 2335) >>>> +++ trunk/config/environment.rb 2011-01-24 11:31:44 UTC (rev 2336) >>>> @@ -26,7 +26,7 @@ >>>> # config.gem "hpricot", :version => '0.6', :source => "http://code.whytheluckystiff.net" >>>> # config.gem "aws-s3", :lib => "aws/s3" >>>> config.gem 'disqus', :version => '1.0.1' >>>> - config.gem 'soap4r', :version => '1.5.8' >>>> + #config.gem 'soap4r', :version => '1.5.8' >>>> config.gem 'mperham-memcache-client', :version => '>= 1.7.4', :lib => 'memcache', :source => "http://gems.github.com" >>>> config.gem 'onyx-cache-money', :version => '>= 0.2.6.1', :lib => 'cache_money', :source => "http://gems.github.com" >>>> config.gem 'geokit', :version => '>= 1.3.2' >>>> @@ -86,8 +86,20 @@ >>>> >>>> # Activate observers that should always be running >>>> config.active_record.observers = :annotation_observer >>>> + >>>> + # Use cronolog for log rotation in production >>>> + # ROTATE_LOGS& CRONOLOG_PARAMS constants >>>> + # are set in config/preinitializer.rb >>>> + # By default log rotation is switched off >>>> + if ROTATE_LOGS&& CRONOLOG_PARAMS >>>> + config.logger = Logger.new(IO.popen( CRONOLOG_PARAMS, "w" )) >>>> + config.logger.level = Logger::DEBUG >>>> + end >>>> + >>>> end >>>> >>>> + >>>> + >>>> # Code to handle the issue of unintential file descriptor sharing in Phusion Passenger. >>>> # Ref:http://www.modrails.com/documentation/Users%20guide.html#_example_1_memcached_connection_sharing_harmful >>>> # and:http://info.michael-simons.eu/2009/03/23/phusion-passenger-and-memcache-client-revisited/ >>>> >>>> >>>> Modified: trunk/config/environments/production.rb (2335 => >>>> 2336) >>>> >>>> >>>> --- trunk/config/environments/production.rb 2011-01-19 15:09:15 UTC (rev 2335) >>>> +++ trunk/config/environments/production.rb 2011-01-24 11:31:44 UTC (rev 2336) >>>> @@ -9,13 +9,13 @@ >>>> >>>> # Use cronolog for log rotation in production >>>> # Set ROTATE_LOGS=false to turn off log rotation. >>>> -ROTATE_LOGS = false >>>> -cronolog_params = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" >>>> +#ROTATE_LOGS = false >>>> +#cronolog_params = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" >>>> >>>> -if ROTATE_LOGS >>>> - config.logger = Logger.new(IO.popen( cronolog_params, "w" )) >>>> - config.logger.level = Logger::INFO >>>> -end >>>> +#if ROTATE_LOGS&& CRONOLOG_PARAMS >>>> +# config.logger = Logger.new(IO.popen( CRONOLOG_PARAMS, "w" )) >>>> +# config.logger.level = Logger::INFO >>>> +#end >>>> >>>> # Full error reports are disabled and caching is turned on >>>> config.action_controller.consider_all_requests_local = false >>>> >>>> >>>> Added: trunk/config/preinitializer.rb.pre (0 => 2336) >>>> >>>> >>>> --- trunk/config/preinitializer.rb.pre (rev 0) >>>> +++ trunk/config/preinitializer.rb.pre 2011-01-24 11:31:44 UTC (rev 2336) >>>> @@ -0,0 +1,10 @@ >>>> +#Configurations needed before the app init >>>> + >>>> +# Logs rotation >>>> +# >>>> +# Set this to true to rotate the logs >>>> +ROTATE_LOGS = false >>>> +# >>>> +# Set the rotation parameters >>>> +# Example CRONOLOG_PARAMS = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" >>>> +CRONOLOG_PARAMS = nil >>>> >>>> >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email :ericnzuo at ebi.ac.uk >> ================================== > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Mon Jan 24 09:10:21 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 24 Jan 2011 14:10:21 +0000 Subject: [BioCatalogue-developers] [2336] trunk/config: Added pre-initializer configuation file and moved cronolog configuration to the file (config/preinitializer.rb) In-Reply-To: <4D3D832D.20506@ebi.ac.uk> References: <20110124113145.50FDB167831B@rubyforge.org> <4D3D6ADD.2090606@cs.man.ac.uk> <4D3D7AAA.5050101@ebi.ac.uk> <4D3D80DE.9030400@cs.man.ac.uk> <4D3D832D.20506@ebi.ac.uk> Message-ID: <4D3D884D.5060205@cs.man.ac.uk> Hi Eric, OK, cool. Please could you update the installation instructions to mention this. I will update my local environment and report any issues. Jits On 24/01/11 13:48, Eric Nzuobontane wrote: > On 24/01/2011 13:38, Jiten Bhagat wrote: >> Hi Eric, >> >> Thanks for the explanation. The intention makes a lot of sense! >> >> My concerns are: >> >> 1. The boot.rb file, which is the one generated by Rails, has been >> modified. Looks like you commented out an 'if' check? This might >> affect the app boot process as I assume the 'if' check was there for >> a very specific reason. > Yes this will affect the boot process. Previously rails boot would > continue with or without this file. I made this file a requirement and > provided defaults that should work for all environments. >> >> 2. CRONOLOG specific stuff has been added to the environment.rb file, >> which seems to make it a dependency now (as in, those constants must >> exist in order for the app to start up). Will this break things for >> other environments that don't have chronolog set up? > If the file pre-initializer.rb file exists with the defaults in > pre-initializer.rb.pre then it should work. The default is that > cronolog will not be used. > Given the possible size of the logs, I think that reminding user about > the log rotation is a good idea. > > Eric >> >> >> >> On 24/01/11 13:12, Eric Nzuobontane wrote: >>> The purpose of this change is it make it clearer(especially to the >>> non-developers that will be running the application here) that this >>> file needs some local configuration like the rest of the pre- files. >>> Otherwise they will have to know that they need to edit environment >>> files. At the moment, environments/production.rb is edited on the >>> server for log rotation settings. >>> >>> Eric >>> >>> >>> On 24/01/2011 12:04, Jiten Bhagat wrote: >>>> Hi, >>>> >>>> What's the purpose of this change? >>>> >>>> Jits >>>> >>>> >>>> >>>> On 24/01/11 11:31, noreply at rubyforge.org wrote: >>>>> >>>>> Revision >>>>> 2336 >>>>> Author >>>>> ebontane >>>>> Date >>>>> 2011-01-24 06:31:44 -0500 (Mon, 24 Jan 2011) >>>>> >>>>> >>>>> Log Message >>>>> >>>>> Added pre-initializer configuation file and moved cronolog configuration to the file (config/preinitializer.rb) >>>>> >>>>> >>>>> Modified Paths >>>>> >>>>> * trunk/config/boot.rb <#trunkconfigbootrb> >>>>> * trunk/config/environment.rb <#trunkconfigenvironmentrb> >>>>> * trunk/config/environments/production.rb >>>>> <#trunkconfigenvironmentsproductionrb> >>>>> >>>>> >>>>> Added Paths >>>>> >>>>> * trunk/config/preinitializer.rb.pre >>>>> <#trunkconfigpreinitializerrbpre> >>>>> >>>>> >>>>> Property Changed >>>>> >>>>> * trunk/config/ <#trunkconfig> >>>>> >>>>> >>>>> Diff >>>>> >>>>> >>>>> Property changes: trunk/config >>>>> >>>>> >>>>> Modified: svn:ignore >>>>> >>>>> biocat_local.rb solr.yml memcache.yml hold_routes.rb >>>>> mongrel_cluster.yml + database.yml biocat_local.rb solr.yml >>>>> memcache.yml hold_routes.rb mongrel_cluster.yml preinitializer.rb >>>>> >>>>> >>>>> Modified: trunk/config/boot.rb (2335 => 2336) >>>>> >>>>> >>>>> --- trunk/config/boot.rb 2011-01-19 15:09:15 UTC (rev 2335) >>>>> +++ trunk/config/boot.rb 2011-01-24 11:31:44 UTC (rev 2336) >>>>> @@ -25,7 +25,7 @@ >>>>> end >>>>> >>>>> def preinitialize >>>>> - load(preinitializer_path) if File.exist?(preinitializer_path) >>>>> + load(preinitializer_path) #if File.exist?(preinitializer_path) >>>>> end >>>>> >>>>> def preinitializer_path >>>>> >>>>> >>>>> Modified: trunk/config/environment.rb (2335 => 2336) >>>>> >>>>> >>>>> --- trunk/config/environment.rb 2011-01-19 15:09:15 UTC (rev 2335) >>>>> +++ trunk/config/environment.rb 2011-01-24 11:31:44 UTC (rev 2336) >>>>> @@ -26,7 +26,7 @@ >>>>> # config.gem "hpricot", :version => '0.6', :source => "http://code.whytheluckystiff.net" >>>>> # config.gem "aws-s3", :lib => "aws/s3" >>>>> config.gem 'disqus', :version => '1.0.1' >>>>> - config.gem 'soap4r', :version => '1.5.8' >>>>> + #config.gem 'soap4r', :version => '1.5.8' >>>>> config.gem 'mperham-memcache-client', :version => '>= 1.7.4', :lib => 'memcache', :source => "http://gems.github.com" >>>>> config.gem 'onyx-cache-money', :version => '>= 0.2.6.1', :lib => 'cache_money', :source => "http://gems.github.com" >>>>> config.gem 'geokit', :version => '>= 1.3.2' >>>>> @@ -86,8 +86,20 @@ >>>>> >>>>> # Activate observers that should always be running >>>>> config.active_record.observers = :annotation_observer >>>>> + >>>>> + # Use cronolog for log rotation in production >>>>> + # ROTATE_LOGS& CRONOLOG_PARAMS constants >>>>> + # are set in config/preinitializer.rb >>>>> + # By default log rotation is switched off >>>>> + if ROTATE_LOGS&& CRONOLOG_PARAMS >>>>> + config.logger = Logger.new(IO.popen( CRONOLOG_PARAMS, "w" )) >>>>> + config.logger.level = Logger::DEBUG >>>>> + end >>>>> + >>>>> end >>>>> >>>>> + >>>>> + >>>>> # Code to handle the issue of unintential file descriptor sharing in Phusion Passenger. >>>>> # Ref:http://www.modrails.com/documentation/Users%20guide.html#_example_1_memcached_connection_sharing_harmful >>>>> # and:http://info.michael-simons.eu/2009/03/23/phusion-passenger-and-memcache-client-revisited/ >>>>> >>>>> >>>>> Modified: trunk/config/environments/production.rb (2335 => >>>>> 2336) >>>>> >>>>> >>>>> --- trunk/config/environments/production.rb 2011-01-19 15:09:15 UTC (rev 2335) >>>>> +++ trunk/config/environments/production.rb 2011-01-24 11:31:44 UTC (rev 2336) >>>>> @@ -9,13 +9,13 @@ >>>>> >>>>> # Use cronolog for log rotation in production >>>>> # Set ROTATE_LOGS=false to turn off log rotation. >>>>> -ROTATE_LOGS = false >>>>> -cronolog_params = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" >>>>> +#ROTATE_LOGS = false >>>>> +#cronolog_params = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" >>>>> >>>>> -if ROTATE_LOGS >>>>> - config.logger = Logger.new(IO.popen( cronolog_params, "w" )) >>>>> - config.logger.level = Logger::INFO >>>>> -end >>>>> +#if ROTATE_LOGS&& CRONOLOG_PARAMS >>>>> +# config.logger = Logger.new(IO.popen( CRONOLOG_PARAMS, "w" )) >>>>> +# config.logger.level = Logger::INFO >>>>> +#end >>>>> >>>>> # Full error reports are disabled and caching is turned on >>>>> config.action_controller.consider_all_requests_local = false >>>>> >>>>> >>>>> Added: trunk/config/preinitializer.rb.pre (0 => 2336) >>>>> >>>>> >>>>> --- trunk/config/preinitializer.rb.pre (rev 0) >>>>> +++ trunk/config/preinitializer.rb.pre 2011-01-24 11:31:44 UTC (rev 2336) >>>>> @@ -0,0 +1,10 @@ >>>>> +#Configurations needed before the app init >>>>> + >>>>> +# Logs rotation >>>>> +# >>>>> +# Set this to true to rotate the logs >>>>> +ROTATE_LOGS = false >>>>> +# >>>>> +# Set the rotation parameters >>>>> +# Example CRONOLOG_PARAMS = "/my/server/cronolog /my/application/file/log/production.log.%Y%m%d" >>>>> +CRONOLOG_PARAMS = nil >>>>> >>>>> >>>>> _______________________________________________ >>>>> BioCatalogue-developers mailing list >>>>> BioCatalogue-developers at rubyforge.org >>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>> >>>> >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >>> >>> -- >>> Eric Nzuobontane >>> ================================== >>> European Bioinformatics Institute >>> Wellcome Trust Genome Campus >>> Hinxton, Cambridge >>> CB10 1SD >>> United Kingdom >>> >>> Tel : +44 1223 492654 >>> email :ericnzuo at ebi.ac.uk >>> ================================== >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel : +44 1223 492654 > email :ericnzuo at ebi.ac.uk > ================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jan 24 10:21:44 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 Jan 2011 10:21:44 -0500 (EST) Subject: [BioCatalogue-developers] [2338] trunk/public/robots.txt: Stop bots from accessing application. Message-ID: <20110124152144.4DE731858317@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Jan 25 09:40:30 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 Jan 2011 09:40:30 -0500 (EST) Subject: [BioCatalogue-developers] [2339] trunk/public/robots.txt: updated robot access control file. Message-ID: <20110125144030.BEB42185838D@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jan 25 12:11:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 25 Jan 2011 17:11:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-560) Assign ibcp.fr services in BioCatalogue to Christophe Message-ID: <20906238.146.1295975469376.JavaMail.jira@rosalind.cs.man.ac.uk> Assign ibcp.fr services in BioCatalogue to Christophe ----------------------------------------------------- Key: BIOCAT-560 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-560 Project: BioCatalogue Issue Type: Task Reporter: Eric Nzuobontane Assignee: Jiten Bhagat Christelle Eloto left the christophe's team at ibcp, so her services need to be assigned to Christophe. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Wed Jan 26 06:42:45 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 26 Jan 2011 06:42:45 -0500 (EST) Subject: [BioCatalogue-developers] [2340] trunk/public/robots.txt: update to robot.txt file Message-ID: <20110126114245.3AE0918583C9@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jan 26 06:45:07 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 26 Jan 2011 06:45:07 -0500 (EST) Subject: [BioCatalogue-developers] [2341] trunk/app/mailers: mailer for sending some info to members Message-ID: <20110126114507.CDF521678324@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jan 26 06:46:25 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 26 Jan 2011 06:46:25 -0500 (EST) Subject: [BioCatalogue-developers] [2342] trunk/lib/bio_catalogue/jobs/member_info_email.rb: background job to send a message to members Message-ID: <20110126114625.B058A1678324@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jan 26 06:47:51 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 26 Jan 2011 06:47:51 -0500 (EST) Subject: [BioCatalogue-developers] [2343] trunk/lib/tasks/update_service_annotation_levels.rake: minor (debug) update to task Message-ID: <20110126114752.11AE218583C9@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jan 26 06:59:39 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 26 Jan 2011 06:59:39 -0500 (EST) Subject: [BioCatalogue-developers] [2344] trunk/script/biocatalogue: scripts moved from application base directory and on-off to send a message to all members Message-ID: <20110126115939.2E3B81678324@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jan 26 09:12:52 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 26 Jan 2011 09:12:52 -0500 (EST) Subject: [BioCatalogue-developers] [2345] trunk/app/views/service_responsibles/_listing.html.erb: some UI fixes for notification listings Message-ID: <20110126141252.438B718583C1@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jan 26 09:28:44 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 26 Jan 2011 09:28:44 -0500 (EST) Subject: [BioCatalogue-developers] [2346] trunk/app/models/service.rb: helper methods to service and call to create service responsible Message-ID: <20110126142845.0B00318583CC@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jan 27 04:53:14 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 27 Jan 2011 09:53:14 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-560) Assign ibcp.fr services in BioCatalogue to Christophe In-Reply-To: <20906238.146.1295975469376.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22460958.171.1296121994371.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-560?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-560. ------------------------------------- Resolution: Fixed > Assign ibcp.fr services in BioCatalogue to Christophe > ----------------------------------------------------- > > Key: BIOCAT-560 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-560 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > Christelle Eloto left the christophe's team at ibcp, so her services need to be assigned to Christophe. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jan 27 04:53:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 27 Jan 2011 09:53:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-560) Assign ibcp.fr services in BioCatalogue to Christophe In-Reply-To: <20906238.146.1295975469376.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15678308.170.1296121989822.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-560?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16415#comment-16415 ] Eric Nzuobontane commented on BIOCAT-560: ----------------------------------------- Done > Assign ibcp.fr services in BioCatalogue to Christophe > ----------------------------------------------------- > > Key: BIOCAT-560 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-560 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > Christelle Eloto left the christophe's team at ibcp, so her services need to be assigned to Christophe. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jan 27 06:35:10 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 27 Jan 2011 11:35:10 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-561) Update the public facing BioCatalogue Roadmap Message-ID: <5092817.172.1296128110712.JavaMail.jira@rosalind.cs.man.ac.uk> Update the public facing BioCatalogue Roadmap --------------------------------------------- Key: BIOCAT-561 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-561 Project: BioCatalogue Issue Type: Task Reporter: Eric Nzuobontane Assignee: Jiten Bhagat The BioCatalogue Roadmap needs to be updated with the 2011 plans. Current roadmap is for 2010! -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Jan 27 07:54:23 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 Jan 2011 07:54:23 -0500 (EST) Subject: [BioCatalogue-developers] [2347] trunk/app/models: fixes to monitoring Message-ID: <20110127125423.A3D151858267@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jan 27 11:19:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 27 Jan 2011 16:19:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-540) Move to using Bundler to handle gem dependencies In-Reply-To: <18008377.73.1290164217231.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27628641.177.1296145149558.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-540?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16418#comment-16418 ] Eric Nzuobontane commented on BIOCAT-540: ----------------------------------------- When the BioCatalogue moves to a new infrastructure at EBI, it would be good to get it to use bundler as well. > Move to using Bundler to handle gem dependencies > ------------------------------------------------ > > Key: BIOCAT-540 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-540 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase, Server Management > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 2011-02 > > > Stuart has successfully and easily moved to using Bundler (http://gembundler.com/) for managing gem dependencies in Sysmo-SEEK. > We should look to do the same as it makes managing gem dependencies much easier. Also, Rails 3 uses Bundler by default. > Stuart's email to the e-lab-hackers list: > {quote} > Hi, > Last week I mentioned that in SEEK I switched over to Bundler. The only thing I need to check is that it worked with passenger, and I've now confirmed this works without any problems or additional effort. > To switch to using bundler, I simply followed the instructions at http://gembundler.com/rails23.html . The only extra things I found I needed to do was define some gems that weren't already defined in my environment.rb, and also in a couple of places I seemed to need to add a require 'xxx' . My functional tests picked all of these up. > Overall it took me about 2hrs altogether, and much of this time was spent testing and waiting for gems to download. > The only downside I've found and not yet solved is that it doesn't work very happily with RadRails 2, so I can currently no longer run the application and debug within the IDE. > Switching to Bundler for SEEK is a big advantage, because as other projects are now starting to use SEEK it makes the installation much simpler. It also means that I no longer need to maintain the installation instructions whenever I add or remove gems, or change versions. > Stuart. > {quote} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jan 28 10:16:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 28 Jan 2011 15:16:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-562) Make the default listing of services in BioCatalogue configurable Message-ID: <653900.189.1296227769402.JavaMail.jira@rosalind.cs.man.ac.uk> Make the default listing of services in BioCatalogue configurable ----------------------------------------------------------------- Key: BIOCAT-562 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-562 Project: BioCatalogue Issue Type: Task Components: Web Interface Affects Versions: 2011-02 Reporter: Eric Nzuobontane Assignee: Jiten Bhagat The current default listing is grid. This is fine for listing with a considerable number of entries. However, for a few entries, like when starting a new catalogue, the grid view might not be the most appropriate. Allowing the default listing setting to be configurable would help. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jan 31 04:11:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 31 Jan 2011 09:11:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-29) Review code to ensure messages are logged appropriately Message-ID: <13007626.192.1296465069666.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-29?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-29. ------------------------------------ Resolution: No longer relevant > Review code to ensure messages are logged appropriately > ------------------------------------------------------- > > Key: BIOCAT-29 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-29 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Priority: Minor > > Ensure messages are logged and severity levels are appropriately assigned -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jan 31 04:13:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 31 Jan 2011 09:13:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-556) Change "From" email address of error/exception emails In-Reply-To: <16814454.147.1295274797044.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11347454.193.1296465189427.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-556?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16424#comment-16424 ] Eric Nzuobontane commented on BIOCAT-556: ----------------------------------------- Done on the live site. Needed for new installations as well. > Change "From" email address of error/exception emails > ----------------------------------------------------- > > Key: BIOCAT-556 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-556 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > Fix For: 2011-02 > > > Currently, all error/exception emails from the main app are sent using the *biocatalogue-developers at rubyforge.org* email address in the "From" field. This should be changed to *contact at biocatalogue.org*. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon Jan 31 04:36:33 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 31 Jan 2011 04:36:33 -0500 (EST) Subject: [BioCatalogue-developers] [2348] trunk/app/views/home/index.html.erb: Minor fix Message-ID: <20110131093633.F1CA21858361@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jan 31 05:17:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 31 Jan 2011 10:17:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-563) Make the job worker script configurable. Add ability for it to be started for both environments[production and development] Message-ID: <2954379.194.1296469029445.JavaMail.jira@rosalind.cs.man.ac.uk> Make the job worker script configurable. Add ability for it to be started for both environments[production and development] --------------------------------------------------------------------------------------------------------------------------- Key: BIOCAT-563 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-563 Project: BioCatalogue Issue Type: Task Reporter: Eric Nzuobontane Assignee: Jiten Bhagat The current job worker script only runs in production mode. It should be possible to run it in development mode as well. This is needed during development. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jan 31 07:37:09 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 31 Jan 2011 12:37:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-564) Set up new sandbox server Message-ID: <14703282.195.1296477429427.JavaMail.jira@rosalind.cs.man.ac.uk> Set up new sandbox server ------------------------- Key: BIOCAT-564 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-564 Project: BioCatalogue Issue Type: Task Components: Server Management Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 2011-02 Set up, and migrate to, a new sandbox server for http://sandbox.biocatalogue.org -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon Jan 31 08:23:59 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 31 Jan 2011 08:23:59 -0500 (EST) Subject: [BioCatalogue-developers] [2349] trunk/script/biocatalogue: shell scripts for launching some [rake] tasks. Message-ID: <20110131132359.75ADC1678324@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jan 31 08:30:11 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 31 Jan 2011 13:30:11 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-565) Move shell scripts for launching cron jobs into repository In-Reply-To: <9599295.196.1296480609416.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15892056.197.1296480611138.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-565?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-565 started by Eric Nzuobontane. > Move shell scripts for launching cron jobs into repository > ---------------------------------------------------------- > > Key: BIOCAT-565 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-565 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Remove any local configs in the various cron scripts and add them to repository -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jan 31 08:30:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 31 Jan 2011 13:30:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-565) Move shell scripts for launching cron jobs into repository Message-ID: <9599295.196.1296480609416.JavaMail.jira@rosalind.cs.man.ac.uk> Move shell scripts for launching cron jobs into repository ---------------------------------------------------------- Key: BIOCAT-565 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-565 Project: BioCatalogue Issue Type: Sub-task Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Remove any local configs in the various cron scripts and add them to repository -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jan 31 10:57:21 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 31 Jan 2011 15:57:21 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-498) Create a listing(index) page for all service tests In-Reply-To: <7834499.9954.1286441415341.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13474533.205.1296489441550.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-498?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-498. ------------------------------------- Resolution: Fixed > Create a listing(index) page for all service tests > -------------------------------------------------- > > Key: BIOCAT-498 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-498 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > The listing of service test will enable an easy navigation for monitoring purposes. At the moment, it is hard going through the service to get to the service test especially when one has to look at a number of tests -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jan 31 10:59:09 2011 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 31 Jan 2011 15:59:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-549) cleanup the application directory In-Reply-To: <11485269.313.1291218592822.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9918681.207.1296489549366.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-549?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-549. ------------------------------------- Resolution: No longer relevant > cleanup the application directory > --------------------------------- > > Key: BIOCAT-549 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-549 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > remove all redundant files and folders in the codebase -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira