From utopia at cs.man.ac.uk Thu Apr 1 01:09:31 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 01 Apr 2010 06:09:31 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossEmowse' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossEmowse' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/813 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 ytanoh at cs.man.ac.uk Thu Apr 1 05:19:20 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 1 Apr 2010 10:19:20 +0100 Subject: [BioCatalogue-developers] REST service example endpoint Message-ID: Hi Mannie, When i select an example endpoint, the biocat automatically insert characters like 'amp' and ';' in the URL making then inaccessible through the biocat. Try to access the example endpoint here: http://test.biocatalogue.org/rest_methods/2 Cheers, Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From utopia at cs.man.ac.uk Thu Apr 1 05:23:26 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 01 Apr 2010 10:23:26 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:showFSOLVonStructure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:showFSOLVonStructure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/993 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 Apr 1 10:07:48 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 01 Apr 2010 15:07:48 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:getPDBFromTransfac' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:getPDBFromTransfac' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1012 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Thu Apr 1 12:55:05 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 1 Apr 2010 12:55:05 -0400 (EDT) Subject: [BioCatalogue-developers] [1807] branches/web-service-ownership: work on services ownership( or service responsibility) Message-ID: <20100401165505.E2DE518582D5@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Apr 1 13:30:08 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 01 Apr 2010 18:30:08 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'SIDDbase' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'SIDDbase' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1692 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 Apr 1 14:18:27 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 01 Apr 2010 19:18:27 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:browseCATHClassification' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:browseCATHClassification' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/885 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 Apr 1 15:28:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 01 Apr 2010 20:28:10 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:fromGenericToNucleotideSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:fromGenericToNucleotideSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/882 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 Apr 1 16:23:03 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 01 Apr 2010 21:23:03 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getCATHHierarchyCodesFromPDBID' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getCATHHierarchyCodesFromPDBID' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/918 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 Apr 1 18:44:42 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 01 Apr 2010 23:44:42 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'GOR IV protein secondary structure prediction (CNRS IBCP)' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'GOR IV protein secondary structure prediction (CNRS IBCP)' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/270 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 Apr 1 22:10:52 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 02 Apr 2010 03:10:52 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossOctanolFromSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossOctanolFromSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/818 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 Apr 2 04:39:30 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 02 Apr 2010 09:39:30 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:parseFeatureAASequenceWithArticle' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:parseFeatureAASequenceWithArticle' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/878 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 Apr 2 11:40:24 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 02 Apr 2010 16:40:24 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromGenericSequenceToFASTA' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromGenericSequenceToFASTA' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/772 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 Apr 2 11:41:03 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 02 Apr 2010 16:41:03 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parseGFFFromFeatureAASequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parseGFFFromFeatureAASequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/985 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 Apr 2 16:42:31 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 02 Apr 2010 21:42:31 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:www.bioinfo.uma.es:getAminoAcidSequenceCollection' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:www.bioinfo.uma.es:getAminoAcidSequenceCollection' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/961 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 Apr 2 18:24:43 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 02 Apr 2010 23:24:43 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runBlast2gene' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runBlast2gene' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/804 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 Apr 3 08:18:29 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 03 Apr 2010 13:18:29 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'NetPhos - Prediction of generic phosphorylation sites in eukaryotic proteins' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'NetPhos - Prediction of generic phosphorylation sites in eukaryotic proteins' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1627 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 Apr 3 09:13:09 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 03 Apr 2010 14:13:09 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToPDB_Collection' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToPDB_Collection' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1126 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Apr 3 15:50:16 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 03 Apr 2010 20:50:16 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getGraphFromTerm' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getGraphFromTerm' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/905 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 Apr 4 03:38:15 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 04 Apr 2010 08:38:15 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'NetGlycate - Prediction of glycation of ? amino groups of lysines in mammalian proteins' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'NetGlycate - Prediction of glycation of ? amino groups of lysines in mammalian proteins' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1630 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 Apr 4 06:21:00 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 04 Apr 2010 11:21:00 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEnsemblIDsFromUniprot' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEnsemblIDsFromUniprot' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/891 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 Apr 4 11:12:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 04 Apr 2010 16:12:28 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'BLAST blastp protein similarity search (CNRS IBCP)' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'BLAST blastp protein similarity search (CNRS IBCP)' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/92 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 Apr 4 15:38:53 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 04 Apr 2010 20:38:53 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getAminoAcidSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getAminoAcidSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/943 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 Apr 4 18:40:17 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 04 Apr 2010 23:40:17 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:translateNucleoSeqToAminoSeq' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:translateNucleoSeqToAminoSeq' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1074 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Apr 5 02:10:18 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 05 Apr 2010 07:10:18 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:pdg.cnb.uam.es:getInteractions' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:pdg.cnb.uam.es:getInteractions' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/749 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 Apr 5 05:30:01 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 05 Apr 2010 10:30:01 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getPDBIdsFromLigandId' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getPDBIdsFromLigandId' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1107 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Apr 5 06:06:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 05 Apr 2010 11:06:10 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:www.cnb.uam.es:fromEMBLToMGI' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:www.cnb.uam.es:fromEMBLToMGI' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/763 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 Apr 5 06:22:35 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 05 Apr 2010 11:22:35 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromMetaAlignmentsToScoreMatrix' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromMetaAlignmentsToScoreMatrix' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/771 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 Apr 5 08:37:50 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 05 Apr 2010 13:37:50 +0100 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 Mon Apr 5 08:45:36 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 05 Apr 2010 13:45:36 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getUniprotIDsFromAccession' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getUniprotIDsFromAccession' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/911 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 Apr 5 09:51:23 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 05 Apr 2010 14:51:23 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getLindemannFromPCZ' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getLindemannFromPCZ' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1171 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Apr 5 11:08:21 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 05 Apr 2010 16:08:21 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMatScanGFFCollection' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMatScanGFFCollection' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/777 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 Apr 5 11:19:38 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 05 Apr 2010 16:19:38 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getFeatureAASequenceFromUniprot' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getFeatureAASequenceFromUniprot' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/887 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 Apr 5 11:36:09 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 05 Apr 2010 16:36:09 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runPs_scanAgainstSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runPs_scanAgainstSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/883 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Mon Apr 5 15:42:32 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 5 Apr 2010 15:42:32 -0400 (EDT) Subject: [BioCatalogue-developers] [1808] trunk/public: rest support UI bug fix; some browsers do not support css3 (background-size) very well Message-ID: <20100405194232.DDD0C1978117@rubyforge.org> An HTML attachment was scrubbed... URL: From mannie.tags at googlemail.com Tue Apr 6 06:43:52 2010 From: mannie.tags at googlemail.com (Mannie Tagarira) Date: Tue, 6 Apr 2010 11:43:52 +0100 Subject: [BioCatalogue-developers] REST service example endpoint In-Reply-To: References: Message-ID: <18FB6675-8A2B-403E-8B12-B99D26A06AF5@gmail.com> Hi Franck, I just thought to let you know that am looking into this :) Thanks, Mannie On 1 Apr 2010, at 10:19, Franck Tanoh wrote: > Hi Mannie, > > When i select an example endpoint, the biocat automatically insert > characters like 'amp' and ';' in the URL making then inaccessible > through the biocat. > Try to access the example endpoint here: > http://test.biocatalogue.org/rest_methods/2 > > Cheers, > Franck > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From ytanoh at cs.man.ac.uk Tue Apr 6 07:34:05 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 6 Apr 2010 12:34:05 +0100 Subject: [BioCatalogue-developers] REST service example endpoint In-Reply-To: <18FB6675-8A2B-403E-8B12-B99D26A06AF5@gmail.com> References: <18FB6675-8A2B-403E-8B12-B99D26A06AF5@gmail.com> Message-ID: Thanks Franck On 6 April 2010 11:43, Mannie Tagarira wrote: > Hi Franck, > > I just thought to let you know that am looking into this :) > > Thanks, > Mannie > > > > On 1 Apr 2010, at 10:19, Franck Tanoh wrote: > >> Hi Mannie, >> >> When i select an example endpoint, the biocat automatically insert >> characters like 'amp' and ';' in the URL making then inaccessible >> through the biocat. >> Try to access the example endpoint here: >> http://test.biocatalogue.org/rest_methods/2 >> >> Cheers, >> Franck >> >> -- >> "Science knows no country, because knowledge belongs to humanity, and >> is the torch which illuminates the world." - Louis Pasteur >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Tue Apr 6 08:45:39 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 6 Apr 2010 08:45:39 -0400 (EDT) Subject: [BioCatalogue-developers] [1809] trunk: Patch for Rails' s auto_link function which overrides the AUTO_LINK_RE regexp constant and the auto_link_url function . Message-ID: <20100406124539.485A718582E7@rubyforge.org> An HTML attachment was scrubbed... URL: From mannie.tags at googlemail.com Tue Apr 6 08:47:18 2010 From: mannie.tags at googlemail.com (Mannie Tagarira) Date: Tue, 6 Apr 2010 13:47:18 +0100 Subject: [BioCatalogue-developers] REST service example endpoint In-Reply-To: References: <18FB6675-8A2B-403E-8B12-B99D26A06AF5@gmail.com> Message-ID: <1A754870-5CEB-4B65-877D-50E1579907AB@gmail.com> The issue has been resolved :) Mannie On 6 Apr 2010, at 12:34, Franck Tanoh wrote: > Thanks > > Franck > > On 6 April 2010 11:43, Mannie Tagarira wrote: >> Hi Franck, >> >> I just thought to let you know that am looking into this :) >> >> Thanks, >> Mannie >> >> >> >> On 1 Apr 2010, at 10:19, Franck Tanoh wrote: >> >>> Hi Mannie, >>> >>> When i select an example endpoint, the biocat automatically insert >>> characters like 'amp' and ';' in the URL making then inaccessible >>> through the biocat. >>> Try to access the example endpoint here: >>> http://test.biocatalogue.org/rest_methods/2 >>> >>> Cheers, >>> Franck >>> >>> -- >>> "Science knows no country, because knowledge belongs to humanity, and >>> is the torch which illuminates the world." - Louis Pasteur >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> > > > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Tue Apr 6 13:03:12 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 6 Apr 2010 13:03:12 -0400 (EDT) Subject: [BioCatalogue-developers] [1810] trunk/public/stylesheets/styles.css: Update last search message box to not take up the whole header. Message-ID: <20100406170312.D45AF18582E3@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue Apr 6 13:13:13 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 06 Apr 2010 18:13:13 +0100 Subject: [BioCatalogue-developers] Update to the live site Message-ID: <4BBB6BA9.7040705@cs.man.ac.uk> Hi Eric, I've made a style update for the "last search" message box based on Franck's suggestion. Please could you update the live site with this? This should only need an svn update and then asset packager rebuild, no server restart. Cheers, Jits From utopia at cs.man.ac.uk Tue Apr 6 16:11:30 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 06 Apr 2010 21:11:30 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossPepstatsFromSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossPepstatsFromSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/824 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Apr 7 06:46:54 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 7 Apr 2010 06:46:54 -0400 (EDT) Subject: [BioCatalogue-developers] [1811] trunk/app/views/search/show.html.erb: Allow Soap Operations to be shown in the Search UI now. Message-ID: <20100407104654.ACB801858289@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 7 08:05:37 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 7 Apr 2010 08:05:37 -0400 (EDT) Subject: [BioCatalogue-developers] [1812] trunk/app/views/search/show.html.erb: Enhancements to search UI ( for when a single scope search has been carried out): Message-ID: <20100407120537.2AE151858289@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 7 08:36:32 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 7 Apr 2010 08:36:32 -0400 (EDT) Subject: [BioCatalogue-developers] [1813] trunk/app/views/rest_services: updated the RestService listing by additional info in the listing's footer Message-ID: <20100407123632.BAC9B185827F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 7 09:11:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 7 Apr 2010 09:11:42 -0400 (EDT) Subject: [BioCatalogue-developers] [1814] trunk/app/controllers/service_tests_controller.rb: REST API work: bugfix for the /services_tests/{id}/results.xml endpoint, which was losing the .xml format when redirecting. Message-ID: <20100407131142.A3C5E18582EE@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Apr 7 11:48:03 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 07 Apr 2010 16:48:03 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'NetGlycate - Prediction of glycation of ? amino groups of lysines in mammalian proteins' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'NetGlycate - Prediction of glycation of ? amino groups of lysines in mammalian proteins' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1630 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Apr 8 00:28:01 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 08 Apr 2010 05:28:01 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:translateGeneIDGFFPredictions' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:translateGeneIDGFFPredictions' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/768 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 ytanoh at cs.man.ac.uk Thu Apr 8 06:36:40 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 8 Apr 2010 11:36:40 +0100 Subject: [BioCatalogue-developers] Your service submitted to BioCatalogue maybe removed In-Reply-To: References: Message-ID: Hi guys, We need a way to flag services that are going to be removed from the site. Thanks Franck On 8 April 2010 11:33, Franck Tanoh wrote: > Dear BioCatalogue Member, > > Following a curation exercise, We have noticed that the service > (http://www.biocatalogue.org/services/2624) you submitted to the > BioCatalogue is not relevant to the life science community. > It will therefore be removed from the site. > > If you want to further discuss this, please feel free to contact us: > contact at biocatalogue.org > > Best regards, > The BioCatalogue Team > > -- > ?"Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur > -- "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 Thu Apr 8 06:45:12 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 08 Apr 2010 11:45:12 +0100 Subject: [BioCatalogue-developers] Your service submitted to BioCatalogue maybe removed In-Reply-To: References: Message-ID: <4BBDB3B8.8030707@cs.man.ac.uk> Yes! I was just thinking that when I came across that "backlinks" service. Thing is, if you *definitely* think a service is spam then feel free to delete it soon. As I think that is allowed in our terms and conditions. Jits Franck Tanoh wrote: > Hi guys, > > We need a way to flag services that are going to be removed from the site. > > Thanks > Franck > > On 8 April 2010 11:33, Franck Tanoh wrote: > >> Dear BioCatalogue Member, >> >> Following a curation exercise, We have noticed that the service >> (http://www.biocatalogue.org/services/2624) you submitted to the >> BioCatalogue is not relevant to the life science community. >> It will therefore be removed from the site. >> >> If you want to further discuss this, please feel free to contact us: >> contact at biocatalogue.org >> >> Best regards, >> The BioCatalogue Team >> >> -- >> "Science knows no country, because knowledge belongs to humanity, and >> is the torch which illuminates the world." - Louis Pasteur >> >> > > > > From utopia at cs.man.ac.uk Thu Apr 8 06:59:40 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 08 Apr 2010 11:59:40 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'GOR III protein secondary structure prediction (CNRS IBCP)' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'GOR III protein secondary structure prediction (CNRS IBCP)' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/269 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 ytanoh at cs.man.ac.uk Thu Apr 8 06:59:54 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 8 Apr 2010 11:59:54 +0100 Subject: [BioCatalogue-developers] Rest service at the EBI In-Reply-To: <4BBDB0C4.9050800@ebi.ac.uk> References: <4BBDB0C4.9050800@ebi.ac.uk> Message-ID: Hi Hamish, > These services have WADL documents, obviously I would rather the able to > submit/update the services in BioCatalogue using the WADL rather then doing > them manually. As far as I can see there is currently no way to do this. Good point. We thought about WADL but the problem we faced is that there are not really clear standards about WADL. In addition WADL itself is not mature like WSDL for example. So writing parser for WADL would have been a challenge and we may end up with lots of different parsers. But this is still a open discussion. I've (cc) the BioCatalogue developer list, they may have something to add to that. What we have in mind though is the possibility to export manually registered REST service as WADL at some point. How does the WADL document of these EBI REST services look like? Thanks, Franck On 8 April 2010 11:32, Hamish McWilliam wrote: > Hi Franck, > >> Since our last release on Tuesday this week, we now support >> parametrized REST services (i.e. >> http://test.biocatalogue.org/services/2587) in the BioCatalogue. >> We therefore support most of the REST services listed on the EBI web >> service page: http://www.ebi.ac.uk/Tools/webservices/ >> I would like to invite you to register them in the BioCatalogue. >> I would also appreciate your feedback on this new feature. > > These services have WADL documents, obviously I would rather the able to > submit/update the services in BioCatalogue using the WADL rather then doing > them manually. As far as I can see there is currently no way to do this. > > All the best, > > Hamish > -- > ============================================================ > Mr Hamish McWilliam > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge, CB10 1SD, UK > > URL: http://www.ebi.ac.uk/ > ============================================================ > -- "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 Thu Apr 8 07:07:56 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 08 Apr 2010 12:07:56 +0100 Subject: [BioCatalogue-developers] Rest service at the EBI In-Reply-To: References: <4BBDB0C4.9050800@ebi.ac.uk> Message-ID: <4BBDB90C.4070104@cs.man.ac.uk> Hi Hamish, Just to add to what Franck has mentioned... The underlying model is based on the WADL model, and the plan is to now build a WADL parser. Would be useful to get examples of real world WADLs if you have any? Thanks, Jits Franck Tanoh wrote: > Hi Hamish, > > >> These services have WADL documents, obviously I would rather the able to >> submit/update the services in BioCatalogue using the WADL rather then doing >> them manually. As far as I can see there is currently no way to do this. >> > Good point. > We thought about WADL but the problem we faced is that there are not > really clear standards about WADL. In addition WADL itself is not > mature like WSDL for example. So writing parser for WADL would have > been a challenge and we may end up with lots of different parsers. > But this is still a open discussion. I've (cc) the BioCatalogue > developer list, they may have something to add to that. > > What we have in mind though is the possibility to export manually > registered REST service as WADL at some point. > > How does the WADL document of these EBI REST services look like? > > Thanks, > Franck > > On 8 April 2010 11:32, Hamish McWilliam wrote: > >> Hi Franck, >> >> >>> Since our last release on Tuesday this week, we now support >>> parametrized REST services (i.e. >>> http://test.biocatalogue.org/services/2587) in the BioCatalogue. >>> We therefore support most of the REST services listed on the EBI web >>> service page: http://www.ebi.ac.uk/Tools/webservices/ >>> I would like to invite you to register them in the BioCatalogue. >>> I would also appreciate your feedback on this new feature. >>> >> These services have WADL documents, obviously I would rather the able to >> submit/update the services in BioCatalogue using the WADL rather then doing >> them manually. As far as I can see there is currently no way to do this. >> >> All the best, >> >> Hamish >> -- >> ============================================================ >> Mr Hamish McWilliam >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge, CB10 1SD, UK >> >> URL: http://www.ebi.ac.uk/ >> ============================================================ >> >> > > > > From jits at cs.man.ac.uk Thu Apr 8 07:43:59 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 08 Apr 2010 12:43:59 +0100 Subject: [BioCatalogue-developers] Rest service at the EBI In-Reply-To: <4BBDC104.1080308@ebi.ac.uk> References: <4BBDB0C4.9050800@ebi.ac.uk> <4BBDB90C.4070104@cs.man.ac.uk> <4BBDC104.1080308@ebi.ac.uk> Message-ID: <4BBDC17F.6050605@cs.man.ac.uk> Awesome, thanks Hamish. We'll use these as exemplars :-) Jits Hamish McWilliam wrote: > Hi Jits, > >> Just to add to what Franck has mentioned... >> >> The underlying model is based on the WADL model, and the plan is to now >> build a WADL parser. >> >> Would be useful to get examples of real world WADLs if you have any? > > Of course we do... > > http://www.ebi.ac.uk/QuickGO/clients/QuickGO.wadl > http://www.ebi.ac.uk/Tools/webservices/rest/WSDbfetch.wadl > > For the main tool services, we need to do a little more work on the > generation then then they will have WADL available, in a similar way > they provide WSDL, so documentation and schema definitions will be > referenced appropriately. > >>>> These services have WADL documents, obviously I would rather the >>>> able to >>>> submit/update the services in BioCatalogue using the WADL rather >>>> then doing >>>> them manually. As far as I can see there is currently no way to do >>>> this. >>>> >>> Good point. >>> We thought about WADL but the problem we faced is that there are not >>> really clear standards about WADL. In addition WADL itself is not >>> mature like WSDL for example. So writing parser for WADL would have >>> been a challenge and we may end up with lots of different parsers. >>> But this is still a open discussion. I've (cc) the BioCatalogue >>> developer list, they may have something to add to that. >>> >>> What we have in mind though is the possibility to export manually >>> registered REST service as WADL at some point. >>> >>> How does the WADL document of these EBI REST services look like? >>> >>>>> Since our last release on Tuesday this week, we now support >>>>> parametrized REST services (i.e. >>>>> http://test.biocatalogue.org/services/2587) in the BioCatalogue. >>>>> We therefore support most of the REST services listed on the EBI web >>>>> service page: http://www.ebi.ac.uk/Tools/webservices/ >>>>> I would like to invite you to register them in the BioCatalogue. >>>>> I would also appreciate your feedback on this new feature. >>>>> >>>> These services have WADL documents, obviously I would rather the >>>> able to >>>> submit/update the services in BioCatalogue using the WADL rather >>>> then doing >>>> them manually. As far as I can see there is currently no way to do >>>> this. > > Hamish From hpm at ebi.ac.uk Thu Apr 8 07:41:56 2010 From: hpm at ebi.ac.uk (Hamish McWilliam) Date: Thu, 08 Apr 2010 12:41:56 +0100 Subject: [BioCatalogue-developers] Rest service at the EBI In-Reply-To: <4BBDB90C.4070104@cs.man.ac.uk> References: <4BBDB0C4.9050800@ebi.ac.uk> <4BBDB90C.4070104@cs.man.ac.uk> Message-ID: <4BBDC104.1080308@ebi.ac.uk> Hi Jits, > Just to add to what Franck has mentioned... > > The underlying model is based on the WADL model, and the plan is to now > build a WADL parser. > > Would be useful to get examples of real world WADLs if you have any? Of course we do... http://www.ebi.ac.uk/QuickGO/clients/QuickGO.wadl http://www.ebi.ac.uk/Tools/webservices/rest/WSDbfetch.wadl For the main tool services, we need to do a little more work on the generation then then they will have WADL available, in a similar way they provide WSDL, so documentation and schema definitions will be referenced appropriately. >>> These services have WADL documents, obviously I would rather the able to >>> submit/update the services in BioCatalogue using the WADL rather then doing >>> them manually. As far as I can see there is currently no way to do this. >>> >> Good point. >> We thought about WADL but the problem we faced is that there are not >> really clear standards about WADL. In addition WADL itself is not >> mature like WSDL for example. So writing parser for WADL would have >> been a challenge and we may end up with lots of different parsers. >> But this is still a open discussion. I've (cc) the BioCatalogue >> developer list, they may have something to add to that. >> >> What we have in mind though is the possibility to export manually >> registered REST service as WADL at some point. >> >> How does the WADL document of these EBI REST services look like? >> >>>> Since our last release on Tuesday this week, we now support >>>> parametrized REST services (i.e. >>>> http://test.biocatalogue.org/services/2587) in the BioCatalogue. >>>> We therefore support most of the REST services listed on the EBI web >>>> service page: http://www.ebi.ac.uk/Tools/webservices/ >>>> I would like to invite you to register them in the BioCatalogue. >>>> I would also appreciate your feedback on this new feature. >>>> >>> These services have WADL documents, obviously I would rather the able to >>> submit/update the services in BioCatalogue using the WADL rather then doing >>> them manually. As far as I can see there is currently no way to do this. Hamish -- ============================================================ Mr Hamish McWilliam European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD, UK URL: http://www.ebi.ac.uk/ ============================================================ From noreply at rubyforge.org Thu Apr 8 12:01:34 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 8 Apr 2010 12:01:34 -0400 (EDT) Subject: [BioCatalogue-developers] [1815] trunk/app/views: REST support work Message-ID: <20100408160134.9C9231858309@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Apr 8 14:52:50 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 08 Apr 2010 19:52:50 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:removeDuplicatedObjects' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:removeDuplicatedObjects' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/900 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 Apr 9 04:56:18 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 09 Apr 2010 09:56:18 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getPDBIDsFromUniprot' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getPDBIDsFromUniprot' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/909 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 Apr 9 05:38:18 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 09 Apr 2010 10:38:18 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:parsePatternFromMotif' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:parsePatternFromMotif' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/886 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Apr 9 10:05:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 9 Apr 2010 10:05:02 -0400 (EDT) Subject: [BioCatalogue-developers] [1816] branches/discussions/: New branch for discussions work Message-ID: <20100409140502.473A61858314@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Apr 9 10:16:12 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 9 Apr 2010 10:16:12 -0400 (EDT) Subject: [BioCatalogue-developers] [1817] branches/rest-write-api/: New branch for REST Write API work. Message-ID: <20100409141613.0BBB018582F5@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Sat Apr 10 12:24:48 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 10 Apr 2010 17:24:48 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossCuspFromSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossCuspFromSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/812 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 Apr 11 01:04:43 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 11 Apr 2010 06:04:43 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'MkDom2' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'MkDom2' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1899 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Apr 11 07:04:34 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 11 Apr 2010 12:04:34 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:fromGenericToAminoAcidSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:fromGenericToAminoAcidSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/912 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 Apr 11 08:11:21 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 11 Apr 2010 13:11:21 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPHDFromFASTA' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPHDFromFASTA' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/999 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 Apr 11 12:21:42 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 11 Apr 2010 17:21:42 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:WhichNameSpaceForID' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:WhichNameSpaceForID' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/944 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 Apr 11 14:27:42 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 11 Apr 2010 19:27:42 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'BLAST blastp protein similarity search (CNRS IBCP)' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'BLAST blastp protein similarity search (CNRS IBCP)' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/92 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Apr 11 14:42:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 11 Apr 2010 19:42:33 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'blastProDom' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'blastProDom' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/137 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 Apr 11 16:21:18 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 11 Apr 2010 21:21:18 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'GOR III protein secondary structure prediction (CNRS IBCP)' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'GOR III protein secondary structure prediction (CNRS IBCP)' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/269 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Apr 11 18:24:39 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 11 Apr 2010 23:24:39 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:parseSecondaryStructureFromPHDText' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:parseSecondaryStructureFromPHDText' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1101 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Apr 11 20:12:22 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 12 Apr 2010 01:12:22 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossChargeFromSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossChargeFromSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/809 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 Apr 12 02:53:25 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 12 Apr 2010 07:53:25 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'fetchProDom' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'fetchProDom' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/113 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 Apr 12 05:25:32 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 12 Apr 2010 10:25:32 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:plotFeatureAASequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:plotFeatureAASequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1004 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Mon Apr 12 05:46:46 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 12 Apr 2010 05:46:46 -0400 (EDT) Subject: [BioCatalogue-developers] [1818] branches/service-updates-and-curation/: New branch for service updater, curation via spreadsheets, curation reports and curation forms work. Message-ID: <20100412094646.2B1021D78893@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Mon Apr 12 06:01:45 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 12 Apr 2010 11:01:45 +0100 Subject: [BioCatalogue-developers] Service updater work Message-ID: <4BC2EF89.9070909@cs.man.ac.uk> Guys, In order to do the service updater work... do any of you know of a service in the biocat that has an updated WSDL? Thanks, Jits From noreply at rubyforge.org Mon Apr 12 07:09:31 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 12 Apr 2010 07:09:31 -0400 (EDT) Subject: [BioCatalogue-developers] [1819] trunk/app: Added link to the associated service in the SOAP operation partial. Message-ID: <20100412110931.211821D78895@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Apr 12 07:13:29 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 12 Apr 2010 07:13:29 -0400 (EDT) Subject: [BioCatalogue-developers] [1820] trunk/app: Added preferred description in the SOAP operation listing instead of showing all the different descriptions . Message-ID: <20100412111329.489B11D78893@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Mon Apr 12 07:17:56 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 12 Apr 2010 12:17:56 +0100 Subject: [BioCatalogue-developers] Service updater work In-Reply-To: <4BC2EF89.9070909@cs.man.ac.uk> References: <4BC2EF89.9070909@cs.man.ac.uk> Message-ID: This one: http://www.biocatalogue.org/services/8 The wsdl location is still the same Franck PS: won't be on line that much as i'm on holidays... On 12 April 2010 11:01, Jiten Bhagat wrote: > Guys, > > In order to do the service updater work... do any of you know of a > service in the biocat that has an updated WSDL? > > Thanks, > Jits > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Mon Apr 12 10:21:19 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 12 Apr 2010 10:21:19 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2752] Better REST services support Message-ID: <20100412142120.02B451D78896@rubyforge.org> Task #2752 has been updated. Project: BioCatalogue Subproject: Main Summary: Better REST services support Complete: 50% Status: Open Description: 1. Parameterized URLs: "Having said that, we are very keen on having some basic functionality in place for this. So would the ability to add parameterised URLs together with some test parameters be useful in meeting your needs? This is something we could potentially release quicker. " ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2752&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Apr 12 11:53:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 12 Apr 2010 11:53:09 -0400 (EDT) Subject: [BioCatalogue-developers] [1821] trunk: Greatly simplified the way the twittering works, in preparation for Status Change tweets and emails. Message-ID: <20100412155310.169D11D78896@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Mon Apr 12 12:42:01 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 12 Apr 2010 17:42:01 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runGeneIDGFF' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runGeneIDGFF' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/769 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Mon Apr 12 13:13:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 12 Apr 2010 13:13:02 -0400 (EDT) Subject: [BioCatalogue-developers] [1822] trunk: Initial work on sending monitoring status changes to twitter and by email to a select few . Message-ID: <20100412171302.614791858289@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Mon Apr 12 13:17:25 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 12 Apr 2010 18:17:25 +0100 Subject: [BioCatalogue-developers] Sending monitoring status changes to twitter and by email Message-ID: <4BC355A5.9040200@cs.man.ac.uk> Eric, In revision 1822 I have done some preliminary work on sending monitoring status changes to twitter and also by email to a select few recipients. Please could you test this out on the test server. You will need to add: MONITORING_STATUS_CHANGE_RECIPIENTS = [ ... ] ... to the biocat_local file to determine who the emails get sent to. Also make sure that twitter is enabled (on the test and live sites). You can then simulate a status change via script/console (ie: create a TestResult with a different status for a service). This is an urgent feature, as requested in the F2F meeting on Friday. Cheers, Jits From noreply at rubyforge.org Mon Apr 12 13:27:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 12 Apr 2010 13:27:47 -0400 (EDT) Subject: [BioCatalogue-developers] [1823] trunk/app/models/test_result.rb: Added timestamps to the status change tweets as twitter blocks duplicate tweets Message-ID: <20100412172748.0DE721D799BA@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Mon Apr 12 14:50:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 12 Apr 2010 19:50:10 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runMBFromMSF' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runMBFromMSF' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1078 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Tue Apr 13 04:02:46 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 13 Apr 2010 09:02:46 +0100 Subject: [BioCatalogue-developers] Sending monitoring status changes to twitter and by email In-Reply-To: <4BC355A5.9040200@cs.man.ac.uk> References: <4BC355A5.9040200@cs.man.ac.uk> Message-ID: <4BC42526.2070401@ebi.ac.uk> Hi Jits, Do you want me to put this on the test site? I can do that now. Eric Jiten Bhagat wrote: > Eric, > > In revision 1822 I have done some preliminary work on sending monitoring > status changes to twitter and also by email to a select few recipients. > Please could you test this out on the test server. > > You will need to add: > > MONITORING_STATUS_CHANGE_RECIPIENTS = [ ... ] > > ... to the biocat_local file to determine who the emails get sent to. > > Also make sure that twitter is enabled (on the test and live sites). > > You can then simulate a status change via script/console (ie: create a > TestResult with a different status for a service). > > This is an urgent feature, as requested in the F2F meeting on Friday. > > Cheers, > Jits > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From utopia at cs.man.ac.uk Tue Apr 13 04:30:16 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 13 Apr 2010 09:30:16 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'fetchProDom' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'fetchProDom' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/113 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From jits at cs.man.ac.uk Tue Apr 13 04:56:45 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 13 Apr 2010 09:56:45 +0100 Subject: [BioCatalogue-developers] Sending monitoring status changes to twitter and by email In-Reply-To: <4BC42526.2070401@ebi.ac.uk> References: <4BC355A5.9040200@cs.man.ac.uk> <4BC42526.2070401@ebi.ac.uk> Message-ID: <4BC431CD.4000007@cs.man.ac.uk> Eric Nzuobontane wrote: > Hi Jits, > > Do you want me to put this on the test site? I can do that now. Yes. And set the recipients to you and me and then simulate a few monitoring status changes in order to see if it all works ok. See further instructions in my original email. Jits > > Eric > > Jiten Bhagat wrote: >> Eric, >> >> In revision 1822 I have done some preliminary work on sending monitoring >> status changes to twitter and also by email to a select few recipients. >> Please could you test this out on the test server. >> >> You will need to add: >> >> MONITORING_STATUS_CHANGE_RECIPIENTS = [ ... ] >> >> ... to the biocat_local file to determine who the emails get sent to. >> >> Also make sure that twitter is enabled (on the test and live sites). >> >> You can then simulate a status change via script/console (ie: create a >> TestResult with a different status for a service). >> >> This is an urgent feature, as requested in the F2F meeting on Friday. >> >> Cheers, >> Jits >> > > From ericnzuo at ebi.ac.uk Tue Apr 13 04:59:22 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 13 Apr 2010 09:59:22 +0100 Subject: [BioCatalogue-developers] Utopia python module Message-ID: <4BC4326A.8020501@ebi.ac.uk> Hi Steve, I need to reinstall the utopia python module on the test harness server. Could you please point me to where I can download it? cheers, Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From utopia at cs.man.ac.uk Tue Apr 13 05:39:45 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 13 Apr 2010 10:39:45 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMultiPairwiseMetaAlignmentGFF' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMultiPairwiseMetaAlignmentGFF' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/783 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Tue Apr 13 06:10:08 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 13 Apr 2010 11:10:08 +0100 Subject: [BioCatalogue-developers] Utopia python module In-Reply-To: References: <4BC4326A.8020501@ebi.ac.uk> Message-ID: <4BC44300.6070500@ebi.ac.uk> Steve Pettifer wrote: > If it's causing problems, you can safely delete it for now. > I am not sure if I can do that. The ddbj blast test script requires the python utopia module. Except there is an different version of the test somewhere that does not require this module that we could run instead? Eric > Steve > > On 13 Apr 2010, at 09:59, Eric Nzuobontane wrote: > > >> Hi Steve, >> >> I need to reinstall the utopia python module on the test harness server. Could you please point me to where I can download it? >> >> cheers, >> >> Eric >> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> >> >> > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Tue Apr 13 06:41:53 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 13 Apr 2010 11:41:53 +0100 Subject: [BioCatalogue-developers] Sending monitoring status changes to twitter and by email In-Reply-To: <4BC431CD.4000007@cs.man.ac.uk> References: <4BC355A5.9040200@cs.man.ac.uk> <4BC42526.2070401@ebi.ac.uk> <4BC431CD.4000007@cs.man.ac.uk> Message-ID: <4BC44A71.90909@ebi.ac.uk> I have updated the test site and executed a test producing a status change. It seems however, that the transition is not registered correctly. It should go from warning to passed but it is indicating otherwise. Could you have a look? Eric Jiten Bhagat wrote: > Eric Nzuobontane wrote: > >> Hi Jits, >> >> Do you want me to put this on the test site? I can do that now. >> > > Yes. And set the recipients to you and me and then simulate a few > monitoring status changes in order to see if it all works ok. See > further instructions in my original email. > > Jits > > >> Eric >> >> Jiten Bhagat wrote: >> >>> Eric, >>> >>> In revision 1822 I have done some preliminary work on sending monitoring >>> status changes to twitter and also by email to a select few recipients. >>> Please could you test this out on the test server. >>> >>> You will need to add: >>> >>> MONITORING_STATUS_CHANGE_RECIPIENTS = [ ... ] >>> >>> ... to the biocat_local file to determine who the emails get sent to. >>> >>> Also make sure that twitter is enabled (on the test and live sites). >>> >>> You can then simulate a status change via script/console (ie: create a >>> TestResult with a different status for a service). >>> >>> This is an urgent feature, as requested in the F2F meeting on Friday. >>> >>> Cheers, >>> Jits >>> >>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Tue Apr 13 07:57:42 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 13 Apr 2010 12:57:42 +0100 Subject: [BioCatalogue-developers] Sending monitoring status changes to twitter and by email In-Reply-To: <4BC44A71.90909@ebi.ac.uk> References: <4BC355A5.9040200@cs.man.ac.uk> <4BC42526.2070401@ebi.ac.uk> <4BC431CD.4000007@cs.man.ac.uk> <4BC44A71.90909@ebi.ac.uk> Message-ID: <4BC45C36.8070609@cs.man.ac.uk> Eric Nzuobontane wrote: > I have updated the test site and executed a test producing a status > change. It seems however, that the transition is not registered > correctly. It should go from warning to passed but it is indicating > otherwise. Could you have a look? I noticed this on the biocat_test twitter account - http://twitter.com/biocat_test/status/12097312833... I assume this was from what you did? So it seems like the email sending is the thing failing. Can you check the delayed_jobs table for any failed email sending jobs? Please could you take some ownership of finishing this piece of work. As I need to move on to many other things like the service updater and curation stuff. Jits > > Eric > > > Jiten Bhagat wrote: >> Eric Nzuobontane wrote: >> >>> Hi Jits, >>> >>> Do you want me to put this on the test site? I can do that now. >>> >> >> Yes. And set the recipients to you and me and then simulate a few >> monitoring status changes in order to see if it all works ok. See >> further instructions in my original email. >> >> Jits >> >> >>> Eric >>> >>> Jiten Bhagat wrote: >>> >>>> Eric, >>>> >>>> In revision 1822 I have done some preliminary work on sending >>>> monitoring >>>> status changes to twitter and also by email to a select few >>>> recipients. >>>> Please could you test this out on the test server. >>>> >>>> You will need to add: >>>> >>>> MONITORING_STATUS_CHANGE_RECIPIENTS = [ ... ] >>>> >>>> ... to the biocat_local file to determine who the emails get sent to. >>>> >>>> Also make sure that twitter is enabled (on the test and live sites). >>>> >>>> You can then simulate a status change via script/console (ie: create a >>>> TestResult with a different status for a service). >>>> >>>> This is an urgent feature, as requested in the F2F meeting on Friday. >>>> >>>> Cheers, >>>> Jits >>>> >>> > > From jits at cs.man.ac.uk Tue Apr 13 08:01:25 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 13 Apr 2010 13:01:25 +0100 Subject: [BioCatalogue-developers] Sending monitoring status changes to twitter and by email In-Reply-To: <4BC45C36.8070609@cs.man.ac.uk> References: <4BC355A5.9040200@cs.man.ac.uk> <4BC42526.2070401@ebi.ac.uk> <4BC431CD.4000007@cs.man.ac.uk> <4BC44A71.90909@ebi.ac.uk> <4BC45C36.8070609@cs.man.ac.uk> Message-ID: <4BC45D15.7050604@cs.man.ac.uk> Ah, the ordering of the status is wrong.... Doh! I will fix this and commit within 5 minutes. Jits Jiten Bhagat wrote: > Eric Nzuobontane wrote: > >> I have updated the test site and executed a test producing a status >> change. It seems however, that the transition is not registered >> correctly. It should go from warning to passed but it is indicating >> otherwise. Could you have a look? >> > > I noticed this on the biocat_test twitter account - > http://twitter.com/biocat_test/status/12097312833... I assume this was > from what you did? So it seems like the email sending is the thing failing. > > Can you check the delayed_jobs table for any failed email sending jobs? > > Please could you take some ownership of finishing this piece of work. As > I need to move on to many other things like the service updater and > curation stuff. > > Jits > > >> Eric >> >> >> Jiten Bhagat wrote: >> >>> Eric Nzuobontane wrote: >>> >>> >>>> Hi Jits, >>>> >>>> Do you want me to put this on the test site? I can do that now. >>>> >>>> >>> Yes. And set the recipients to you and me and then simulate a few >>> monitoring status changes in order to see if it all works ok. See >>> further instructions in my original email. >>> >>> Jits >>> >>> >>> >>>> Eric >>>> >>>> Jiten Bhagat wrote: >>>> >>>> >>>>> Eric, >>>>> >>>>> In revision 1822 I have done some preliminary work on sending >>>>> monitoring >>>>> status changes to twitter and also by email to a select few >>>>> recipients. >>>>> Please could you test this out on the test server. >>>>> >>>>> You will need to add: >>>>> >>>>> MONITORING_STATUS_CHANGE_RECIPIENTS = [ ... ] >>>>> >>>>> ... to the biocat_local file to determine who the emails get sent to. >>>>> >>>>> Also make sure that twitter is enabled (on the test and live sites). >>>>> >>>>> You can then simulate a status change via script/console (ie: create a >>>>> TestResult with a different status for a service). >>>>> >>>>> This is an urgent feature, as requested in the F2F meeting on Friday. >>>>> >>>>> Cheers, >>>>> Jits >>>>> >>>>> >>>> >>>> >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From noreply at rubyforge.org Tue Apr 13 08:03:44 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Apr 2010 08:03:44 -0400 (EDT) Subject: [BioCatalogue-developers] [1824] trunk/app/models/test_result.rb: Fixed ordering of status change statuses in the messages (tweet and email) . Message-ID: <20100413120345.14F1F185830A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 13 08:30:46 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Apr 2010 08:30:46 -0400 (EDT) Subject: [BioCatalogue-developers] [1825] trunk/vendor/wsdl-parsing-service/README.txt: Added note about WSDLUtils not working with PHP 5.3 and greater. Message-ID: <20100413123046.C7CAC185830F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 13 08:46:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Apr 2010 08:46:07 -0400 (EDT) Subject: [BioCatalogue-developers] [1826] branches/service-updates-and-curation/vendor/wsdl-parsing-service/ WSDLToolsREST.pdf: Added WSDLUtils documentation (by Dan Mowbray) to the wsdl-parsing-service folder. Message-ID: <20100413124607.4AC6818582F1@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue Apr 13 09:14:14 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 13 Apr 2010 14:14:14 +0100 Subject: [BioCatalogue-developers] Sending monitoring status changes to twitter and by email In-Reply-To: <4BC45D15.7050604@cs.man.ac.uk> References: <4BC355A5.9040200@cs.man.ac.uk> <4BC42526.2070401@ebi.ac.uk> <4BC431CD.4000007@cs.man.ac.uk> <4BC44A71.90909@ebi.ac.uk> <4BC45C36.8070609@cs.man.ac.uk> <4BC45D15.7050604@cs.man.ac.uk> Message-ID: <4BC46E26.80409@cs.man.ac.uk> Is this working now? When do you think it can go on the live site? Jits Jiten Bhagat wrote: > Ah, the ordering of the status is wrong.... Doh! I will fix this and > commit within 5 minutes. > > Jits > > > > Jiten Bhagat wrote: > >> Eric Nzuobontane wrote: >> >> >>> I have updated the test site and executed a test producing a status >>> change. It seems however, that the transition is not registered >>> correctly. It should go from warning to passed but it is indicating >>> otherwise. Could you have a look? >>> >>> >> I noticed this on the biocat_test twitter account - >> http://twitter.com/biocat_test/status/12097312833... I assume this was >> from what you did? So it seems like the email sending is the thing failing. >> >> Can you check the delayed_jobs table for any failed email sending jobs? >> >> Please could you take some ownership of finishing this piece of work. As >> I need to move on to many other things like the service updater and >> curation stuff. >> >> Jits >> >> >> >>> Eric >>> >>> >>> Jiten Bhagat wrote: >>> >>> >>>> Eric Nzuobontane wrote: >>>> >>>> >>>> >>>>> Hi Jits, >>>>> >>>>> Do you want me to put this on the test site? I can do that now. >>>>> >>>>> >>>>> >>>> Yes. And set the recipients to you and me and then simulate a few >>>> monitoring status changes in order to see if it all works ok. See >>>> further instructions in my original email. >>>> >>>> Jits >>>> >>>> >>>> >>>> >>>>> Eric >>>>> >>>>> Jiten Bhagat wrote: >>>>> >>>>> >>>>> >>>>>> Eric, >>>>>> >>>>>> In revision 1822 I have done some preliminary work on sending >>>>>> monitoring >>>>>> status changes to twitter and also by email to a select few >>>>>> recipients. >>>>>> Please could you test this out on the test server. >>>>>> >>>>>> You will need to add: >>>>>> >>>>>> MONITORING_STATUS_CHANGE_RECIPIENTS = [ ... ] >>>>>> >>>>>> ... to the biocat_local file to determine who the emails get sent to. >>>>>> >>>>>> Also make sure that twitter is enabled (on the test and live sites). >>>>>> >>>>>> You can then simulate a status change via script/console (ie: create a >>>>>> TestResult with a different status for a service). >>>>>> >>>>>> This is an urgent feature, as requested in the F2F meeting on Friday. >>>>>> >>>>>> Cheers, >>>>>> Jits >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>> >>> >> _______________________________________________ >> 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 > From ericnzuo at ebi.ac.uk Tue Apr 13 09:30:47 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 13 Apr 2010 14:30:47 +0100 Subject: [BioCatalogue-developers] Sending monitoring status changes to twitter and by email In-Reply-To: <4BC45C36.8070609@cs.man.ac.uk> References: <4BC355A5.9040200@cs.man.ac.uk> <4BC42526.2070401@ebi.ac.uk> <4BC431CD.4000007@cs.man.ac.uk> <4BC44A71.90909@ebi.ac.uk> <4BC45C36.8070609@cs.man.ac.uk> Message-ID: <4BC47207.30107@ebi.ac.uk> Jiten Bhagat wrote: > Eric Nzuobontane wrote: > >> I have updated the test site and executed a test producing a status >> change. It seems however, that the transition is not registered >> correctly. It should go from warning to passed but it is indicating >> otherwise. Could you have a look? >> > > I noticed this on the biocat_test twitter account - > http://twitter.com/biocat_test/status/12097312833... I assume this was > from what you did? So it seems like the email sending is the thing failing. > I think the email sending is fine. I got the mail and reason you did not get it is bec of the mistake I made in typing your email address > Can you check the delayed_jobs table for any failed email sending jobs? > > Please could you take some ownership of finishing this piece of work. As > I need to move on to many other things like the service updater and > curation stuff. > Yes, I am taking ownership of this and will get back to you for any questions. I tried to manually investigate the failing tests in BioCatalogue and cross check with EMBRACE. But that is clearly not the way to go, as we have about 700 though all are not failing. I will try to come with some better tooling to make this process a bit more manageable. Eric > Jits > > >> Eric >> >> >> Jiten Bhagat wrote: >> >>> Eric Nzuobontane wrote: >>> >>> >>>> Hi Jits, >>>> >>>> Do you want me to put this on the test site? I can do that now. >>>> >>>> >>> Yes. And set the recipients to you and me and then simulate a few >>> monitoring status changes in order to see if it all works ok. See >>> further instructions in my original email. >>> >>> Jits >>> >>> >>> >>>> Eric >>>> >>>> Jiten Bhagat wrote: >>>> >>>> >>>>> Eric, >>>>> >>>>> In revision 1822 I have done some preliminary work on sending >>>>> monitoring >>>>> status changes to twitter and also by email to a select few >>>>> recipients. >>>>> Please could you test this out on the test server. >>>>> >>>>> You will need to add: >>>>> >>>>> MONITORING_STATUS_CHANGE_RECIPIENTS = [ ... ] >>>>> >>>>> ... to the biocat_local file to determine who the emails get sent to. >>>>> >>>>> Also make sure that twitter is enabled (on the test and live sites). >>>>> >>>>> You can then simulate a status change via script/console (ie: create a >>>>> TestResult with a different status for a service). >>>>> >>>>> This is an urgent feature, as requested in the F2F meeting on Friday. >>>>> >>>>> Cheers, >>>>> Jits >>>>> >>>>> >>>> >>>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Tue Apr 13 09:52:13 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Apr 2010 09:52:13 -0400 (EDT) Subject: [BioCatalogue-developers] [1827] trunk: REST support work Message-ID: <20100413135213.9F214185830F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 13 10:23:31 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Apr 2010 10:23:31 -0400 (EDT) Subject: [BioCatalogue-developers] [1828] trunk/app/models/test_result.rb: Added "[BioCatalogue]" to the subject line for status change emails. Message-ID: <20100413142331.D581E185830F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 13 10:26:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Apr 2010 10:26:08 -0400 (EDT) Subject: [BioCatalogue-developers] [1829] trunk/app/views: Improvements to the sign up and sign in pages based on previous feedback from Franck . Message-ID: <20100413142608.6CC4A1858311@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue Apr 13 10:28:42 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 13 Apr 2010 15:28:42 +0100 Subject: [BioCatalogue-developers] text for sign up page... In-Reply-To: References: Message-ID: <4BC47F9A.8000400@cs.man.ac.uk> I know this is quite old but I have made a change along these lines. See the sign up page now - http://sandbox.biocatalogue.org/signup (this has probably gone live now). Jits Franck Tanoh wrote: > guys, > > i think we can add the following text under the header on the sign up > page or somewhere visible to people who want to sign up... > > There are two different ways to sign up to the BioCatalogue: > -create an account using the form on the left > or > -Use your existing OpenID, Google, Yahoo, facebook or Verisign > account. More information on the forms on the right. > > Franck > From ericnzuo at ebi.ac.uk Tue Apr 13 11:04:29 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 13 Apr 2010 16:04:29 +0100 Subject: [BioCatalogue-developers] Utopia python module In-Reply-To: References: <4BC4326A.8020501@ebi.ac.uk> Message-ID: <4BC487FD.5070208@ebi.ac.uk> I believe this module is used by the embrace registry so it should be a matter of just copying it over. It is a python module so should not require machine dependencies. If there is no where that I can download it, then maybe some can just pack it an send to me Steve Pettifer wrote: > If it's causing problems, you can safely delete it for now. > > Steve > > On 13 Apr 2010, at 09:59, Eric Nzuobontane wrote: > > >> Hi Steve, >> >> I need to reinstall the utopia python module on the test harness server. Could you please point me to where I can download it? >> >> cheers, >> >> Eric >> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> >> >> > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Tue Apr 13 11:38:33 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Apr 2010 11:38:33 -0400 (EDT) Subject: [BioCatalogue-developers] [1830] branches/service-updates-and-curation: Curation work: Initial files for a /curation controller. Message-ID: <20100413153833.BBDBA185830A@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue Apr 13 12:08:29 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 13 Apr 2010 17:08:29 +0100 Subject: [BioCatalogue-developers] Utopia python module In-Reply-To: <0D64C4BE-4DA4-4280-8A07-6D7A8C0BF3D2@manchester.ac.uk> References: <4BC4326A.8020501@ebi.ac.uk> <4BC487FD.5070208@ebi.ac.uk> <0D64C4BE-4DA4-4280-8A07-6D7A8C0BF3D2@manchester.ac.uk> Message-ID: <4BC496FD.7050905@ebi.ac.uk> Hi Phil, > Hi Eric, > > Do you mean the module that's imported in files such as http://embraceregistry.net/test/muscle-align - muscle.py > yes > in the line > > "import utopia" ? > > If so, this is actually a shared object library, not Python. On the Embrace Registry server we had installed a copy of Utopia to enable us to do that, which is unlikely to be possible for BioCat. > This might be possible for biocat as the server running the scripts is separate from the application nodes. Could you please point me to where I can get it and instructions on how to install it? cheers, Eric > >> on module so should not require machine dependencies. If there is no where that I can download it, then maybe some can just pack it an send to me >> >> >> Steve Pettifer wrote: >> >>> If it's causing problems, you can safely delete it for now. >>> >>> Steve >>> >>> On 13 Apr 2010, at 09:59, Eric Nzuobontane wrote: >>> >>> >>> >>>> Hi Steve, >>>> >>>> I need to reinstall the utopia python module on the test harness server. Could you please point me to where I can download it? >>>> >>>> cheers, >>>> >>>> Eric >>>> >>>> -- >>>> Eric Nzuobontane >>>> ================================== >>>> European Bioinformatics Institute >>>> Wellcome Trust Genome Campus >>>> Hinxton, Cambridge >>>> CB10 1SD >>>> United Kingdom >>>> >>>> Tel : +44 1223 492654 >>>> email : ericnzuo at ebi.ac.uk >>>> ================================== >>>> >>>> >>>> >>>> >>> >>> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> >> >> > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Tue Apr 13 12:19:34 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 13 Apr 2010 17:19:34 +0100 Subject: [BioCatalogue-developers] Documentation for test scripts Message-ID: <4BC49996.1020300@ebi.ac.uk> Hi Steve, I want to update the documentation for monitoring via test scripts on the biocatalogue wiki. Most of what I would want to write is already available on the EMBRACE registry. Would it be appropriate for me to take some blocks of text from there? http://www.embraceregistry.net/content/information-service-providers Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Tue Apr 13 12:48:18 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Apr 2010 12:48:18 -0400 (EDT) Subject: [BioCatalogue-developers] [1831] branches/service-updates-and-curation/config/environment.rb: Added " seer" gem (http://github.com/Bantik/seer) for easy graphs via the Google Visualization API. Message-ID: <20100413164818.D1132159802F@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Apr 13 13:08:03 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 13 Apr 2010 18:08:03 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getStructureFromPCZ' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getStructureFromPCZ' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1154 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue Apr 13 13:12:24 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Apr 2010 13:12:24 -0400 (EDT) Subject: [BioCatalogue-developers] [1832] branches/service-updates-and-curation/vendor/gems: Vendored the Seer gem. Message-ID: <20100413171224.B96A91D78894@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Apr 13 18:04:00 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 13 Apr 2010 23:04:00 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMetaAlignmentGFF' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMetaAlignmentGFF' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/781 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 philip.mcdermott at manchester.ac.uk Tue Apr 13 11:33:22 2010 From: philip.mcdermott at manchester.ac.uk (Philip McDermott) Date: Tue, 13 Apr 2010 16:33:22 +0100 Subject: [BioCatalogue-developers] Utopia python module In-Reply-To: <4BC487FD.5070208@ebi.ac.uk> References: <4BC4326A.8020501@ebi.ac.uk> <4BC487FD.5070208@ebi.ac.uk> Message-ID: <0D64C4BE-4DA4-4280-8A07-6D7A8C0BF3D2@manchester.ac.uk> Hi Eric, Do you mean the module that's imported in files such as http://embraceregistry.net/test/muscle-align - muscle.py in the line "import utopia" ? If so, this is actually a shared object library, not Python. On the Embrace Registry server we had installed a copy of Utopia to enable us to do that, which is unlikely to be possible for BioCat. Cheers, Philip On 13 Apr 2010, at 16:04, Eric Nzuobontane wrote: > I believe this module is used by the embrace registry so it should be a matter of just copying it over. It is a python module so should not require machine dependencies. If there is no where that I can download it, then maybe some can just pack it an send to me > > > Steve Pettifer wrote: >> If it's causing problems, you can safely delete it for now. >> >> Steve >> >> On 13 Apr 2010, at 09:59, Eric Nzuobontane wrote: >> >> >>> Hi Steve, >>> >>> I need to reinstall the utopia python module on the test harness server. Could you please point me to where I can download it? >>> >>> cheers, >>> >>> Eric >>> >>> -- >>> Eric Nzuobontane >>> ================================== >>> European Bioinformatics Institute >>> Wellcome Trust Genome Campus >>> Hinxton, Cambridge >>> CB10 1SD >>> United Kingdom >>> >>> Tel : +44 1223 492654 >>> email : ericnzuo at ebi.ac.uk >>> ================================== >>> >>> >>> >> >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > From noreply at rubyforge.org Wed Apr 14 09:53:27 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 14 Apr 2010 09:53:27 -0400 (EDT) Subject: [BioCatalogue-developers] [1833] trunk/app: REST support work Message-ID: <20100414135327.303CD185831D@rubyforge.org> An HTML attachment was scrubbed... URL: From philip.mcdermott at manchester.ac.uk Wed Apr 14 10:26:17 2010 From: philip.mcdermott at manchester.ac.uk (Philip McDermott) Date: Wed, 14 Apr 2010 15:26:17 +0100 Subject: [BioCatalogue-developers] Utopia python module In-Reply-To: <4BC496FD.7050905@ebi.ac.uk> References: <4BC4326A.8020501@ebi.ac.uk> <4BC487FD.5070208@ebi.ac.uk> <0D64C4BE-4DA4-4280-8A07-6D7A8C0BF3D2@manchester.ac.uk> <4BC496FD.7050905@ebi.ac.uk> Message-ID: <0CAD1098-B3C3-4C25-8D33-0EFF11A894BC@manchester.ac.uk> Hi, The simplest thing would be to remove this test. There's no particularly easy way to just install Utopia in a way that it could supply this shared object, and it would be overkill for the one or two tests that need it. Cheers, Phil On 13 Apr 2010, at 17:08, Eric Nzuobontane wrote: > Hi Phil, >> Hi Eric, >> >> Do you mean the module that's imported in files such as http://embraceregistry.net/test/muscle-align - muscle.py >> > yes >> in the line >> >> "import utopia" ? >> >> If so, this is actually a shared object library, not Python. On the Embrace Registry server we had installed a copy of Utopia to enable us to do that, which is unlikely to be possible for BioCat. >> > This might be possible for biocat as the server running the scripts is separate from the application nodes. Could you please point me to where I can get it and instructions on how to install it? > > cheers, Eric > >> >>> on module so should not require machine dependencies. If there is no where that I can download it, then maybe some can just pack it an send to me >>> >>> >>> Steve Pettifer wrote: >>> >>>> If it's causing problems, you can safely delete it for now. >>>> >>>> Steve >>>> >>>> On 13 Apr 2010, at 09:59, Eric Nzuobontane wrote: >>>> >>>> >>>>> Hi Steve, >>>>> >>>>> I need to reinstall the utopia python module on the test harness server. Could you please point me to where I can download it? >>>>> >>>>> cheers, >>>>> >>>>> Eric >>>>> >>>>> -- >>>>> Eric Nzuobontane >>>>> ================================== >>>>> European Bioinformatics Institute >>>>> Wellcome Trust Genome Campus >>>>> Hinxton, Cambridge >>>>> CB10 1SD >>>>> United Kingdom >>>>> >>>>> Tel : +44 1223 492654 >>>>> email : ericnzuo at ebi.ac.uk >>>>> ================================== >>>>> >>>>> >>>>> >>>> >>> -- >>> Eric Nzuobontane >>> ================================== >>> European Bioinformatics Institute >>> Wellcome Trust Genome Campus >>> Hinxton, Cambridge >>> CB10 1SD >>> United Kingdom >>> >>> Tel : +44 1223 492654 >>> email : ericnzuo at ebi.ac.uk >>> ================================== >>> >>> >>> >> >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > From noreply at rubyforge.org Wed Apr 14 10:39:29 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 14 Apr 2010 10:39:29 -0400 (EDT) Subject: [BioCatalogue-developers] [1834] trunk: add a setting which when enabled would send a status change notification to the service submitter as well as the listed recipients . Message-ID: <20100414143930.1CFB31D799BC@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Wed Apr 14 10:42:43 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 14 Apr 2010 15:42:43 +0100 Subject: [BioCatalogue-developers] Utopia python module In-Reply-To: <0D64C4BE-4DA4-4280-8A07-6D7A8C0BF3D2@manchester.ac.uk> References: <4BC4326A.8020501@ebi.ac.uk> <4BC487FD.5070208@ebi.ac.uk> <0D64C4BE-4DA4-4280-8A07-6D7A8C0BF3D2@manchester.ac.uk> Message-ID: <4BC5D463.7000108@ebi.ac.uk> Hi Phil, You may have missed my last email. Could please tell me where find the utopia package and how to install it? The machine I intend to install on is running fedora distribution Eric Philip McDermott wrote: > Hi Eric, > > Do you mean the module that's imported in files such as http://embraceregistry.net/test/muscle-align - muscle.py > > in the line > > "import utopia" ? > > If so, this is actually a shared object library, not Python. On the Embrace Registry server we had installed a copy of Utopia to enable us to do that, which is unlikely to be possible for BioCat. > > Cheers, > > Philip > > > On 13 Apr 2010, at 16:04, Eric Nzuobontane wrote: > > >> I believe this module is used by the embrace registry so it should be a matter of just copying it over. It is a python module so should not require machine dependencies. If there is no where that I can download it, then maybe some can just pack it an send to me >> >> >> Steve Pettifer wrote: >> >>> If it's causing problems, you can safely delete it for now. >>> >>> Steve >>> >>> On 13 Apr 2010, at 09:59, Eric Nzuobontane wrote: >>> >>> >>> >>>> Hi Steve, >>>> >>>> I need to reinstall the utopia python module on the test harness server. Could you please point me to where I can download it? >>>> >>>> cheers, >>>> >>>> Eric >>>> >>>> -- >>>> Eric Nzuobontane >>>> ================================== >>>> European Bioinformatics Institute >>>> Wellcome Trust Genome Campus >>>> Hinxton, Cambridge >>>> CB10 1SD >>>> United Kingdom >>>> >>>> Tel : +44 1223 492654 >>>> email : ericnzuo at ebi.ac.uk >>>> ================================== >>>> >>>> >>>> >>>> >>> >>> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> >> >> > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From steve.pettifer at manchester.ac.uk Wed Apr 14 10:49:43 2010 From: steve.pettifer at manchester.ac.uk (Steve Pettifer) Date: Wed, 14 Apr 2010 15:49:43 +0100 Subject: [BioCatalogue-developers] Utopia python module In-Reply-To: <4BC5D463.7000108@ebi.ac.uk> References: <4BC4326A.8020501@ebi.ac.uk> <4BC487FD.5070208@ebi.ac.uk> <0D64C4BE-4DA4-4280-8A07-6D7A8C0BF3D2@manchester.ac.uk> <4BC5D463.7000108@ebi.ac.uk> Message-ID: Eric You really are making this hard for yourself by trying to install the Utopia stuff on the biocat server -- if you really want to build the several hundred dependencies that it will need, you're welcome to try, but it won't achieve anything very useful :) I propose you simply hack the script to *test* the DDBJ, and not worry about the utopia bit. Or alternatively, just remove this test completely for now! Cheers Steve On 14 Apr 2010, at 15:42, Eric Nzuobontane wrote: > Hi Phil, > > You may have missed my last email. Could please tell me where find the utopia package and how to install it? > The machine I intend to install on is running fedora distribution > > Eric > > Philip McDermott wrote: >> Hi Eric, >> >> Do you mean the module that's imported in files such as http://embraceregistry.net/test/muscle-align - muscle.py >> >> in the line >> >> "import utopia" ? >> >> If so, this is actually a shared object library, not Python. On the Embrace Registry server we had installed a copy of Utopia to enable us to do that, which is unlikely to be possible for BioCat. >> >> Cheers, >> >> Philip >> >> >> On 13 Apr 2010, at 16:04, Eric Nzuobontane wrote: >> >> >>> I believe this module is used by the embrace registry so it should be a matter of just copying it over. It is a python module so should not require machine dependencies. If there is no where that I can download it, then maybe some can just pack it an send to me >>> >>> >>> Steve Pettifer wrote: >>> >>>> If it's causing problems, you can safely delete it for now. >>>> >>>> Steve >>>> >>>> On 13 Apr 2010, at 09:59, Eric Nzuobontane wrote: >>>> >>>> >>>>> Hi Steve, >>>>> >>>>> I need to reinstall the utopia python module on the test harness server. Could you please point me to where I can download it? >>>>> >>>>> cheers, >>>>> >>>>> Eric >>>>> >>>>> -- >>>>> Eric Nzuobontane >>>>> ================================== >>>>> European Bioinformatics Institute >>>>> Wellcome Trust Genome Campus >>>>> Hinxton, Cambridge >>>>> CB10 1SD >>>>> United Kingdom >>>>> >>>>> Tel : +44 1223 492654 >>>>> email : ericnzuo at ebi.ac.uk >>>>> ================================== >>>>> >>>>> >>>>> >>>> >>> -- >>> Eric Nzuobontane >>> ================================== >>> European Bioinformatics Institute >>> Wellcome Trust Genome Campus >>> Hinxton, Cambridge >>> CB10 1SD >>> United Kingdom >>> >>> Tel : +44 1223 492654 >>> email : ericnzuo at ebi.ac.uk >>> ================================== >>> >>> >>> >> >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > From noreply at rubyforge.org Wed Apr 14 10:56:27 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 14 Apr 2010 10:56:27 -0400 (EDT) Subject: [BioCatalogue-developers] [1835] trunk/app: code cleanup (use of to_sentence method on some arrays) Message-ID: <20100414145627.63C113C8036@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Wed Apr 14 11:14:43 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 14 Apr 2010 16:14:43 +0100 Subject: [BioCatalogue-developers] Utopia python module In-Reply-To: References: <4BC4326A.8020501@ebi.ac.uk> <4BC487FD.5070208@ebi.ac.uk> <0D64C4BE-4DA4-4280-8A07-6D7A8C0BF3D2@manchester.ac.uk> <4BC5D463.7000108@ebi.ac.uk> Message-ID: <4BC5DBE3.8030909@ebi.ac.uk> Thanks Steve. I did not understand that utopia is not necessary for the script. I will patch it then to make it runnable. Eric Steve Pettifer wrote: > Eric > > You really are making this hard for yourself by trying to install the Utopia stuff on the biocat server -- if you really want to build the several hundred dependencies that it will need, you're welcome to try, but it won't achieve anything very useful :) > > I propose you simply hack the script to *test* the DDBJ, and not worry about the utopia bit. Or alternatively, just remove this test completely for now! > > Cheers > > Steve > > On 14 Apr 2010, at 15:42, Eric Nzuobontane wrote: > > >> Hi Phil, >> >> You may have missed my last email. Could please tell me where find the utopia package and how to install it? >> The machine I intend to install on is running fedora distribution >> >> Eric >> >> Philip McDermott wrote: >> >>> Hi Eric, >>> >>> Do you mean the module that's imported in files such as http://embraceregistry.net/test/muscle-align - muscle.py >>> >>> in the line >>> >>> "import utopia" ? >>> >>> If so, this is actually a shared object library, not Python. On the Embrace Registry server we had installed a copy of Utopia to enable us to do that, which is unlikely to be possible for BioCat. >>> >>> Cheers, >>> >>> Philip >>> >>> >>> On 13 Apr 2010, at 16:04, Eric Nzuobontane wrote: >>> >>> >>> >>>> I believe this module is used by the embrace registry so it should be a matter of just copying it over. It is a python module so should not require machine dependencies. If there is no where that I can download it, then maybe some can just pack it an send to me >>>> >>>> >>>> Steve Pettifer wrote: >>>> >>>> >>>>> If it's causing problems, you can safely delete it for now. >>>>> >>>>> Steve >>>>> >>>>> On 13 Apr 2010, at 09:59, Eric Nzuobontane wrote: >>>>> >>>>> >>>>> >>>>>> Hi Steve, >>>>>> >>>>>> I need to reinstall the utopia python module on the test harness server. Could you please point me to where I can download it? >>>>>> >>>>>> cheers, >>>>>> >>>>>> Eric >>>>>> >>>>>> -- >>>>>> Eric Nzuobontane >>>>>> ================================== >>>>>> European Bioinformatics Institute >>>>>> Wellcome Trust Genome Campus >>>>>> Hinxton, Cambridge >>>>>> CB10 1SD >>>>>> United Kingdom >>>>>> >>>>>> Tel : +44 1223 492654 >>>>>> email : ericnzuo at ebi.ac.uk >>>>>> ================================== >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> -- >>>> 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 >> ================================== >> >> >> > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Wed Apr 14 11:34:30 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 14 Apr 2010 16:34:30 +0100 Subject: [BioCatalogue-developers] Utopia python module In-Reply-To: <0CAD1098-B3C3-4C25-8D33-0EFF11A894BC@manchester.ac.uk> References: <4BC4326A.8020501@ebi.ac.uk> <4BC487FD.5070208@ebi.ac.uk> <0D64C4BE-4DA4-4280-8A07-6D7A8C0BF3D2@manchester.ac.uk> <4BC496FD.7050905@ebi.ac.uk> <0CAD1098-B3C3-4C25-8D33-0EFF11A894BC@manchester.ac.uk> Message-ID: <4BC5E086.7030000@ebi.ac.uk> Thanks, Eric Philip McDermott wrote: > Hi, > > The simplest thing would be to remove this test. There's no particularly easy way to just install Utopia in a way that it could supply this shared object, and it would be overkill for the one or two tests that need it. > > Cheers, > > Phil > > On 13 Apr 2010, at 17:08, Eric Nzuobontane wrote: > > >> Hi Phil, >> >>> Hi Eric, >>> >>> Do you mean the module that's imported in files such as http://embraceregistry.net/test/muscle-align - muscle.py >>> >>> >> yes >> >>> in the line >>> >>> "import utopia" ? >>> >>> If so, this is actually a shared object library, not Python. On the Embrace Registry server we had installed a copy of Utopia to enable us to do that, which is unlikely to be possible for BioCat. >>> >>> >> This might be possible for biocat as the server running the scripts is separate from the application nodes. Could you please point me to where I can get it and instructions on how to install it? >> >> cheers, Eric >> >> >>>> on module so should not require machine dependencies. If there is no where that I can download it, then maybe some can just pack it an send to me >>>> >>>> >>>> Steve Pettifer wrote: >>>> >>>> >>>>> If it's causing problems, you can safely delete it for now. >>>>> >>>>> Steve >>>>> >>>>> On 13 Apr 2010, at 09:59, Eric Nzuobontane wrote: >>>>> >>>>> >>>>> >>>>>> Hi Steve, >>>>>> >>>>>> I need to reinstall the utopia python module on the test harness server. Could you please point me to where I can download it? >>>>>> >>>>>> cheers, >>>>>> >>>>>> Eric >>>>>> >>>>>> -- >>>>>> Eric Nzuobontane >>>>>> ================================== >>>>>> European Bioinformatics Institute >>>>>> Wellcome Trust Genome Campus >>>>>> Hinxton, Cambridge >>>>>> CB10 1SD >>>>>> United Kingdom >>>>>> >>>>>> Tel : +44 1223 492654 >>>>>> email : ericnzuo at ebi.ac.uk >>>>>> ================================== >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> -- >>>> 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 >> ================================== >> >> >> > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From utopia at cs.man.ac.uk Wed Apr 14 13:58:43 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 14 Apr 2010 18:58:43 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossPepcoilFromSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossPepcoilFromSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/822 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Apr 14 14:13:32 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 14 Apr 2010 19:13:32 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getTrajectoryRmsFromMD_Trajectory' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getTrajectoryRmsFromMD_Trajectory' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1128 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Apr 14 18:33:17 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 14 Apr 2010 23:33:17 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossConsFromAlignment' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossConsFromAlignment' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/811 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Apr 14 19:12:17 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 14 Apr 2010 19:12:17 -0400 (EDT) Subject: [BioCatalogue-developers] [1836] trunk/app: show only activated test scripts in UI Message-ID: <20100414231217.99AAF1858313@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Apr 14 21:53:49 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 15 Apr 2010 02:53:49 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossDigestFromSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossDigestFromSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/872 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 Apr 15 01:50:13 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 15 Apr 2010 06:50:13 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'Genome Atlas' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'Genome Atlas' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1694 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Apr 15 04:53:49 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 15 Apr 2010 09:53:49 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:plotArrayXYData' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:plotArrayXYData' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/925 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 Apr 15 05:50:45 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 15 Apr 2010 10:50:45 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS dreg' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS dreg' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/586 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Thu Apr 15 06:09:04 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 15 Apr 2010 06:09:04 -0400 (EDT) Subject: [BioCatalogue-developers] [1837] trunk/app/models: fix to show only activated service tests by default Message-ID: <20100415100904.E611C1D78897@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Apr 15 06:10:17 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 15 Apr 2010 06:10:17 -0400 (EDT) Subject: [BioCatalogue-developers] [1838] trunk/db: migration to add activated at field for url monitors Message-ID: <20100415101017.4269C18582D2@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Apr 15 06:38:15 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 15 Apr 2010 11:38:15 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS dreg' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS dreg' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/586 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Apr 15 07:44:26 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 15 Apr 2010 12:44:26 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runPratt' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runPratt' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/930 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Thu Apr 15 08:01:53 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 15 Apr 2010 08:01:53 -0400 (EDT) Subject: [BioCatalogue-developers] [1839] trunk/app/controllers: REST support work Message-ID: <20100415120153.6F0B41858320@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Apr 15 08:44:52 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 15 Apr 2010 13:44:52 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getLindemannFromPCZ' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getLindemannFromPCZ' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1171 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Thu Apr 15 09:47:23 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 15 Apr 2010 09:47:23 -0400 (EDT) Subject: [BioCatalogue-developers] [1840] trunk: monotoring status work: show only activated test bugfix Message-ID: <20100415134723.AEC5E1858314@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Apr 15 12:02:25 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 15 Apr 2010 12:02:25 -0400 (EDT) Subject: [BioCatalogue-developers] [1841] trunk/script/biocatalogue/monitoring_report.rb: Simple script that could be extended to generate simple monitoring reports . Message-ID: <20100415160225.EFA9D1D78892@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Apr 15 12:05:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 15 Apr 2010 12:05:22 -0400 (EDT) Subject: [BioCatalogue-developers] [1842] trunk/script/biocatalogue/monitoring_report.rb: minor changes in doc section Message-ID: <20100415160522.9E2AB1858314@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Apr 15 18:45:12 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 15 Apr 2010 23:45:12 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:frommmCifToNDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:frommmCifToNDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/934 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 Apr 15 22:04:59 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 16 Apr 2010 03:04:59 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromFASTAToDNASequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromFASTAToDNASequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/784 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 Apr 15 22:58:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 16 Apr 2010 03:58:28 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runTTSFinder' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runTTSFinder' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1104 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Apr 16 00:01:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 16 Apr 2010 05:01:06 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:displayAlignmentFromTreeDetAnnotation' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:displayAlignmentFromTreeDetAnnotation' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1091 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Apr 16 09:35:22 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 16 Apr 2010 14:35:22 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'NetChop - Prediction of proteasomal cleavages (MHC ligands)' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'NetChop - Prediction of proteasomal cleavages (MHC ligands)' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1626 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Fri Apr 16 09:42:21 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 16 Apr 2010 14:42:21 +0100 Subject: [BioCatalogue-developers] inaccessible wsdl Message-ID: <4BC8693D.2030408@ebi.ac.uk> Hi Franck, Could you check with the nactem people about this entry? http://www.biocatalogue.org/services/169#overview -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Fri Apr 16 11:52:32 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 16 Apr 2010 11:52:32 -0400 (EDT) Subject: [BioCatalogue-developers] [1843] trunk/app: REST support work Message-ID: <20100416155232.2CCD91D7888F@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Fri Apr 16 12:18:36 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 16 Apr 2010 17:18:36 +0100 Subject: [BioCatalogue-developers] Contacting jrmacias Message-ID: <4BC88DDC.3070905@ebi.ac.uk> Hi Steve, I believe we agreed during face to face that you would contact this user about their services having localhost as host machine for the endpoint. Could you please also remind them that the wsdl files do not seem to be accessible( from EMBRACE or BioCatalogue) http://www.biocatalogue.org/users/384#services Have a nice weekend. -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From utopia at cs.man.ac.uk Fri Apr 16 23:05:26 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 17 Apr 2010 04:05:26 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getStatisticalLog' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getStatisticalLog' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1073 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Apr 17 10:23:47 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 17 Apr 2010 15:23:47 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getHSSPIDsFromUniprot' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getHSSPIDsFromUniprot' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/907 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 Apr 17 14:25:45 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 17 Apr 2010 19:25:45 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEntryFromEMBL' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEntryFromEMBL' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/791 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Apr 17 18:33:55 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 17 Apr 2010 23:33:55 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromFASTAToAminoAcidSequence' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromFASTAToAminoAcidSequence' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/785 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Apr 18 04:54:23 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 18 Apr 2010 09:54:23 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromFASTAToDNASequenceCollection' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromFASTAToDNASequenceCollection' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/786 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Apr 18 04:57:12 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 18 Apr 2010 09:57:12 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromFASTAToAminoAcidSequenceCollection' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromFASTAToAminoAcidSequenceCollection' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/787 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Apr 18 06:29:15 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 18 Apr 2010 11:29:15 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:cnio.es:runFASSFromMSF' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:cnio.es:runFASSFromMSF' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/978 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Apr 18 06:59:59 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 18 Apr 2010 11:59:59 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:getStatisticalLog' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:getStatisticalLog' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1062 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 Apr 18 08:01:40 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 18 Apr 2010 13:01:40 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEntryFromRefSeq' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEntryFromRefSeq' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/793 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Apr 18 10:46:24 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 18 Apr 2010 15:46:24 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' changed to Passed 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 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1155 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Apr 18 11:09:04 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 18 Apr 2010 16:09:04 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPHDFromAminoAcidSequence' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPHDFromAminoAcidSequence' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1001 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Apr 18 11:21:48 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 18 Apr 2010 16:21:48 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:fromFASTA_NA_multiToNucleotideSeqCollection' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:fromFASTA_NA_multiToNucleotideSeqCollection' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1076 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Apr 18 11:50:22 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 18 Apr 2010 16:50:22 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:www.cnb.uam.es:getStatisticalLog' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:www.cnb.uam.es:getStatisticalLog' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1027 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 Apr 19 00:31:02 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 19 Apr 2010 05:31:02 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runPrank' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runPrank' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1095 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Apr 19 04:49:31 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 19 Apr 2010 09:49:31 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossWaterFromSequences' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossWaterFromSequences' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/831 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Mon Apr 19 05:18:54 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 19 Apr 2010 10:18:54 +0100 Subject: [BioCatalogue-developers] BioCatalogue Service status change emails Message-ID: <4BCC1FFE.4090100@ebi.ac.uk> Hi Steve, Do you mind me adding you to the list of people receiving the service status change emails from BioCatalogue? The emails are currently sent to Franck, Jits and myself only. cheers, Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ytanoh at cs.man.ac.uk Mon Apr 19 06:09:15 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 19 Apr 2010 11:09:15 +0100 Subject: [BioCatalogue-developers] text for sign up page... In-Reply-To: <4BC47F9A.8000400@cs.man.ac.uk> References: <4BC47F9A.8000400@cs.man.ac.uk> Message-ID: Hi Jits, Thanks for the changes. Franck On 13 April 2010 15:28, Jiten Bhagat wrote: > I know this is quite old but I have made a change along these lines. > > See the sign up page now - http://sandbox.biocatalogue.org/signup (this > has probably gone live now). > > Jits > > > Franck Tanoh wrote: >> guys, >> >> i think we can add the following text under the header on the sign up >> page or somewhere visible to people who want to sign up... >> >> There are two different ways to sign up to the BioCatalogue: >> -create an account using the form on the left >> ?or >> -Use your existing OpenID, Google, Yahoo, facebook or Verisign >> account. More information on the forms on the right. >> >> Franck >> > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Mon Apr 19 06:20:55 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 19 Apr 2010 06:20:55 -0400 (EDT) Subject: [BioCatalogue-developers] [1844] trunk/app/models/test_result.rb: bugfix for submitter notification Message-ID: <20100419102055.598221858314@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Apr 19 07:24:50 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 19 Apr 2010 07:24:50 -0400 (EDT) Subject: [BioCatalogue-developers] [1845] trunk/app/models/test_result.rb: bugfix, monitoring status mails Message-ID: <20100419112450.2296C1858282@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Mon Apr 19 09:03:51 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 19 Apr 2010 14:03:51 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getSymbolDefinitionsXML' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getSymbolDefinitionsXML' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1085 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Mon Apr 19 09:03:48 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 19 Apr 2010 14:03:48 +0100 Subject: [BioCatalogue-developers] becoming a biocatalogue admin Message-ID: <4BCC54B4.7090806@ebi.ac.uk> Hi Alan, I have just received a request from Jits to make you and admin on BioCatalogue. I am supposing that he has discussed this with you. Just wanted to confirm with you before I go ahead with the request. cheers, Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Mon Apr 19 11:17:41 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 19 Apr 2010 16:17:41 +0100 Subject: [BioCatalogue-developers] duplicate entries in BioCatalogue Message-ID: <4BCC7415.2040602@ebi.ac.uk> Hi Guys, We do have some duplicate entries in BioCatalogue. What should we do with those. These seem to be from the early days when duplication checking was changing. Should we be removing those? Example: http://www.biocatalogue.org/services/611 http://www.biocatalogue.org/services/612 Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Mon Apr 19 11:32:03 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 19 Apr 2010 16:32:03 +0100 Subject: [BioCatalogue-developers] duplicate entries in BioCatalogue In-Reply-To: <4BCC7415.2040602@ebi.ac.uk> References: <4BCC7415.2040602@ebi.ac.uk> Message-ID: <4BCC7773.8040503@ebi.ac.uk> In addition, I think the endpoints of these services are not correct. I believe they should be http://www.ebi.ac.uk/Tools/picr/ which will actually make the monitoring work as well. I intend to change those, except someone thinks otherwise Eric Eric Nzuobontane wrote: > Hi Guys, > > We do have some duplicate entries in BioCatalogue. What should we do > with those. These seem to be from the early days when duplication > checking was changing. Should we be removing those? > Example: > http://www.biocatalogue.org/services/611 > http://www.biocatalogue.org/services/612 > > Eric > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Mon Apr 19 11:36:22 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 19 Apr 2010 16:36:22 +0100 Subject: [BioCatalogue-developers] duplicate entries in BioCatalogue In-Reply-To: <4BCC7773.8040503@ebi.ac.uk> References: <4BCC7415.2040602@ebi.ac.uk> <4BCC7773.8040503@ebi.ac.uk> Message-ID: <4BCC7876.704@cs.man.ac.uk> Eric Nzuobontane wrote: > In addition, I think the endpoints of these services are not correct. > I believe they should be http://www.ebi.ac.uk/Tools/picr/ > which will actually make the monitoring work as well. I intend to > change those, except someone thinks otherwise That would make sense to me. As that's the base URL of the REST service. Jits > > Eric > > > Eric Nzuobontane wrote: >> Hi Guys, >> >> We do have some duplicate entries in BioCatalogue. What should we do >> with those. These seem to be from the early days when duplication >> checking was changing. Should we be removing those? >> Example: >> http://www.biocatalogue.org/services/611 >> http://www.biocatalogue.org/services/612 >> >> Eric >> > > From ericnzuo at ebi.ac.uk Mon Apr 19 11:47:55 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 19 Apr 2010 16:47:55 +0100 Subject: [BioCatalogue-developers] duplicate entries in BioCatalogue In-Reply-To: <4BCC7876.704@cs.man.ac.uk> References: <4BCC7415.2040602@ebi.ac.uk> <4BCC7773.8040503@ebi.ac.uk> <4BCC7876.704@cs.man.ac.uk> Message-ID: <4BCC7B2B.8070505@ebi.ac.uk> OK, I have made that change. Now, Franck, could you let us know which if these entries we should keep? Eric Jiten Bhagat wrote: > Eric Nzuobontane wrote: > >> In addition, I think the endpoints of these services are not correct. >> I believe they should be http://www.ebi.ac.uk/Tools/picr/ >> which will actually make the monitoring work as well. I intend to >> change those, except someone thinks otherwise >> > > That would make sense to me. As that's the base URL of the REST service. > > Jits > > > >> Eric >> >> >> Eric Nzuobontane wrote: >> >>> Hi Guys, >>> >>> We do have some duplicate entries in BioCatalogue. What should we do >>> with those. These seem to be from the early days when duplication >>> checking was changing. Should we be removing those? >>> Example: >>> http://www.biocatalogue.org/services/611 >>> http://www.biocatalogue.org/services/612 >>> >>> Eric >>> >>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Mon Apr 19 11:55:15 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 19 Apr 2010 11:55:15 -0400 (EDT) Subject: [BioCatalogue-developers] [1846] trunk/app: REST support work Message-ID: <20100419155515.C751E185831C@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Mon Apr 19 12:23:01 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 19 Apr 2010 17:23:01 +0100 Subject: [BioCatalogue-developers] duplicate entries in BioCatalogue In-Reply-To: <4BCC7B2B.8070505@ebi.ac.uk> References: <4BCC7415.2040602@ebi.ac.uk> <4BCC7773.8040503@ebi.ac.uk> <4BCC7876.704@cs.man.ac.uk> <4BCC7B2B.8070505@ebi.ac.uk> Message-ID: I've removed service number 612 Franck On 19 April 2010 16:47, Eric Nzuobontane wrote: > OK, I have made that change. Now, Franck, could you let us know which if > these entries we should keep? > > Eric > > > Jiten Bhagat wrote: >> >> Eric Nzuobontane wrote: >> >>> >>> In addition, I think the endpoints of these services are not correct. >>> I believe they should be http://www.ebi.ac.uk/Tools/picr/ >>> which will actually make the monitoring work as well. I intend to >>> change those, except someone thinks otherwise >>> >> >> That would make sense to me. As that's the base URL of the REST service. >> >> Jits >> >> >> >>> >>> Eric >>> >>> >>> Eric Nzuobontane wrote: >>> >>>> >>>> Hi Guys, >>>> >>>> We do have some duplicate entries in BioCatalogue. What should we do >>>> with those. These seem to be from the early days when duplication >>>> checking was changing. Should we be removing those? >>>> Example: >>>> http://www.biocatalogue.org/services/611 >>>> http://www.biocatalogue.org/services/612 >>>> >>>> Eric >>>> >>>> >>> >>> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel ? : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From utopia at cs.man.ac.uk Mon Apr 19 14:07:57 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 19 Apr 2010 19:07:57 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:parseMWfromMWAnnotatedAASequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:parseMWfromMWAnnotatedAASequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/927 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 Apr 19 17:48:20 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 19 Apr 2010 22:48:20 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getUniprotIDsFromGOTerm' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getUniprotIDsFromGOTerm' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/894 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 Apr 19 17:55:04 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 19 Apr 2010 22:55:04 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:computeCorrelationsFromMD_TrajectoryCRD' changed to Passed 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 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1151 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Apr 19 19:19:22 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 20 Apr 2010 00:19:22 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromFASTAToAminoAcidSequenceCollection' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromFASTAToAminoAcidSequenceCollection' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/787 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Apr 20 02:40:58 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 20 Apr 2010 07:40:58 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'NetCTL - Prediction of CTL epitopes in protein sequences' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'NetCTL - Prediction of CTL epitopes in protein sequences' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1625 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From jits at cs.man.ac.uk Tue Apr 20 05:08:29 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 20 Apr 2010 10:08:29 +0100 Subject: [BioCatalogue-developers] [Biocatalogue-support] [BioCatalogue] Service 'BioMart - REST and SOAP' has a test change status from FAILED to PASSED In-Reply-To: <4BCD6E5D.4000901@ebi.ac.uk> References: <4bcd2dfe61ff6_715c1559b027bfcc58cd@pweb-4a.ebi.ac.uk.tmail> <4BCD6E5D.4000901@ebi.ac.uk> Message-ID: <4BCD6F0D.3090405@cs.man.ac.uk> Eric, there is a bug in the UI for the test scripts - for the descriptions of the test scripts it says "from provider's description doc (about 1 month ago)". Should it not be the submitter of the test script? Jits Eric Nzuobontane wrote: > I have seen that as well and I am puzzled by it. There may be a bug > in the code as I do not see why that should be amber. I am investigating. > > Eric > > > Franck Tanoh wrote: >> Hi Eric, >> >> The message below says that the service status has changed but the >> service still amber in the BioCatalogue. The REST validation still >> failing, it looks like. >> >> Cheers, >> Franck >> >> On 20 April 2010 05:30, wrote: >> >>> A monitoring test status change has occurred! Service 'BioMart - >>> REST and SOAP' has a test (UrlMonitor, ID: 2099) change status from >>> FAILED to PASSED. Last test result message: This check was >>> successful. Go to Service: http://www.biocatalogue.org/services/2033 >>> >>> >> >> >> >> > > From ericnzuo at ebi.ac.uk Tue Apr 20 05:54:02 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 20 Apr 2010 10:54:02 +0100 Subject: [BioCatalogue-developers] [Biocatalogue-support] [BioCatalogue] Service 'BioMart - REST and SOAP' has a test change status from FAILED to PASSED In-Reply-To: <4BCD6F0D.3090405@cs.man.ac.uk> References: <4bcd2dfe61ff6_715c1559b027bfcc58cd@pweb-4a.ebi.ac.uk.tmail> <4BCD6E5D.4000901@ebi.ac.uk> <4BCD6F0D.3090405@cs.man.ac.uk> Message-ID: <4BCD79BA.6010500@ebi.ac.uk> Hi Jits, Since we have had this discussion more than once before, maybe we should change it. We agreed that for test script submission, the information provided at the time of submission should go into the main table for the script and any other description as annotation. We even checked that Mannie was doing a similar thing for rest services. Eric Jiten Bhagat wrote: > Eric, there is a bug in the UI for the test scripts - for the > descriptions of the test scripts it says "from provider's description > doc (about 1 month ago)". Should it not be the submitter of the test script? > > Jits > > > Eric Nzuobontane wrote: > >> I have seen that as well and I am puzzled by it. There may be a bug >> in the code as I do not see why that should be amber. I am investigating. >> >> Eric >> >> >> Franck Tanoh wrote: >> >>> Hi Eric, >>> >>> The message below says that the service status has changed but the >>> service still amber in the BioCatalogue. The REST validation still >>> failing, it looks like. >>> >>> Cheers, >>> Franck >>> >>> On 20 April 2010 05:30, wrote: >>> >>> >>>> A monitoring test status change has occurred! Service 'BioMart - >>>> REST and SOAP' has a test (UrlMonitor, ID: 2099) change status from >>>> FAILED to PASSED. Last test result message: This check was >>>> successful. Go to Service: http://www.biocatalogue.org/services/2033 >>>> >>>> >>>> >>> >>> >>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Tue Apr 20 06:17:07 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 20 Apr 2010 11:17:07 +0100 Subject: [BioCatalogue-developers] DTU services test clients Message-ID: <4BCD7F23.8020508@ebi.ac.uk> Hi Steve, I am seeing a failure in some script which seems to be related to the change in XML::Compile version from 0.78 to 2.x . Would you be able to find the resources to get these scripts to work against XML::Compile 2.x? Maybe Peter would be interested in making his scripts work against other version of XML::Compile as well and could be willing to update them himself. Here are Peter's services we imported from embrace http://www.biocatalogue.org/users/463#services Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Tue Apr 20 06:20:32 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 20 Apr 2010 11:20:32 +0100 Subject: [BioCatalogue-developers] [Biocatalogue-support] [BioCatalogue] Service 'BioMart - REST and SOAP' has a test change status from FAILED to PASSED In-Reply-To: <4BCD79BA.6010500@ebi.ac.uk> References: <4bcd2dfe61ff6_715c1559b027bfcc58cd@pweb-4a.ebi.ac.uk.tmail> <4BCD6E5D.4000901@ebi.ac.uk> <4BCD6F0D.3090405@cs.man.ac.uk> <4BCD79BA.6010500@ebi.ac.uk> Message-ID: <4BCD7FF0.4040503@cs.man.ac.uk> Hi Eric, I do remember in the very early days of the REST model design that you and I did, we decided on what you said below. But things have changed since then, especially since we want to now consider WADL imports. For the REST stuff, all descriptions, example data, etc * added by users are stored as annotations and never stored in the tables. So for WADL imports we can then add the descriptions from the WADL directly into the tables but right now we use the annotations mechanism as much as possible. * Note: only certain things like "constrained_options" (ie: the possible values acceptable) are NOT stored as annotations because with that it's an all or nothing situation where only one metadata field is allowed. I suggest you either: - update the code to migrate existing descriptions as annotations, and then new descriptions as annotations, OR, temporarily: - hack the view to not show the "from provider's description..." text. Jits Eric Nzuobontane wrote: > Hi Jits, > > Since we have had this discussion more than once before, maybe we > should change it. We agreed that for test script submission, the > information provided at the time of submission should go into the main > table for the script and any other description as annotation. We even > checked that Mannie was doing a similar thing for rest services. > > Eric > > > > Jiten Bhagat wrote: >> Eric, there is a bug in the UI for the test scripts - for the >> descriptions of the test scripts it says "from provider's description >> doc (about 1 month ago)". Should it not be the submitter of the test >> script? >> >> Jits >> >> >> Eric Nzuobontane wrote: >> >>> I have seen that as well and I am puzzled by it. There may be a bug >>> in the code as I do not see why that should be amber. I am >>> investigating. >>> >>> Eric >>> >>> >>> Franck Tanoh wrote: >>> >>>> Hi Eric, >>>> >>>> The message below says that the service status has changed but the >>>> service still amber in the BioCatalogue. The REST validation still >>>> failing, it looks like. >>>> >>>> Cheers, >>>> Franck >>>> >>>> On 20 April 2010 05:30, wrote: >>>> >>>> >>>>> A monitoring test status change has occurred! Service 'BioMart - >>>>> REST and SOAP' has a test (UrlMonitor, ID: 2099) change status from >>>>> FAILED to PASSED. Last test result message: This check was >>>>> successful. Go to Service: http://www.biocatalogue.org/services/2033 >>>>> >>>>> >>>> >>>> >>> > > From ericnzuo at ebi.ac.uk Tue Apr 20 06:32:46 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 20 Apr 2010 11:32:46 +0100 Subject: [BioCatalogue-developers] [Biocatalogue-support] [BioCatalogue] Service 'BioMart - REST and SOAP' has a test change status from FAILED to PASSED In-Reply-To: <4BCD7FF0.4040503@cs.man.ac.uk> References: <4bcd2dfe61ff6_715c1559b027bfcc58cd@pweb-4a.ebi.ac.uk.tmail> <4BCD6E5D.4000901@ebi.ac.uk> <4BCD6F0D.3090405@cs.man.ac.uk> <4BCD79BA.6010500@ebi.ac.uk> <4BCD7FF0.4040503@cs.man.ac.uk> Message-ID: <4BCD82CE.6090806@ebi.ac.uk> > Hi Eric, > > I do remember in the very early days of the REST model design that you > and I did, we decided on what you said below. But things have changed > since then, especially since we want to now consider WADL imports. > > For the REST stuff, all descriptions, example data, etc * added by users > are stored as annotations and never stored in the tables. So for WADL > imports we can then add the descriptions from the WADL directly into the > tables but right now we use the annotations mechanism as much as possible. > > * Note: only certain things like "constrained_options" (ie: the possible > values acceptable) are NOT stored as annotations because with that it's > an all or nothing situation where only one metadata field is allowed. > > I suggest you either: > - update the code to migrate existing descriptions as annotations, and > then new descriptions as annotations, OR, temporarily: > - hack the view to not show the "from provider's description..." text. > In that case migrating the data will be a more sensible option than hacking the text. > Jits > > > Eric Nzuobontane wrote: > >> Hi Jits, >> >> Since we have had this discussion more than once before, maybe we >> should change it. We agreed that for test script submission, the >> information provided at the time of submission should go into the main >> table for the script and any other description as annotation. We even >> checked that Mannie was doing a similar thing for rest services. >> >> Eric >> >> >> >> Jiten Bhagat wrote: >> >>> Eric, there is a bug in the UI for the test scripts - for the >>> descriptions of the test scripts it says "from provider's description >>> doc (about 1 month ago)". Should it not be the submitter of the test >>> script? >>> >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>> >>> >>>> I have seen that as well and I am puzzled by it. There may be a bug >>>> in the code as I do not see why that should be amber. I am >>>> investigating. >>>> >>>> Eric >>>> >>>> >>>> Franck Tanoh wrote: >>>> >>>> >>>>> Hi Eric, >>>>> >>>>> The message below says that the service status has changed but the >>>>> service still amber in the BioCatalogue. The REST validation still >>>>> failing, it looks like. >>>>> >>>>> Cheers, >>>>> Franck >>>>> >>>>> On 20 April 2010 05:30, wrote: >>>>> >>>>> >>>>> >>>>>> A monitoring test status change has occurred! Service 'BioMart - >>>>>> REST and SOAP' has a test (UrlMonitor, ID: 2099) change status from >>>>>> FAILED to PASSED. Last test result message: This check was >>>>>> successful. Go to Service: http://www.biocatalogue.org/services/2033 >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From utopia at cs.man.ac.uk Tue Apr 20 06:55:46 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 20 Apr 2010 11:55:46 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossGetorfFromSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossGetorfFromSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/816 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 jits at cs.man.ac.uk Tue Apr 20 09:03:20 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 20 Apr 2010 14:03:20 +0100 Subject: [BioCatalogue-developers] Outputs from the two different WSDL parsers Message-ID: <4BCDA618.600@cs.man.ac.uk> Hi Eric, Can I just check something with you - do the outputs from... BioCatalogue::WsdlParser.parse(...) ... and ... BioCatalogue::WSDLUtils::WSDLParser.parse(..) ... follow the *exact* same spec? Ie: can I treat them interchangeably? I am assuming that the SoapService#populate method treats both as the same structure/spec? This is crucial to the diffing of the WSDLs (I am not using the EMBRACE one now because all it does is return a textual diff and compares to an internal cached version which we have no way of tracking). Cheers, Jits From noreply at rubyforge.org Tue Apr 20 09:15:35 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 20 Apr 2010 09:15:35 -0400 (EDT) Subject: [BioCatalogue-developers] [1847] branches/service-updates-and-curation: Service Updater work: refactored the relationship between SoapServices and WsdlFiles to be a one-to-many relationships , ie: so that a SoapService can have multiple WSDL files. Message-ID: <20100420131535.DD2F21858289@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Apr 20 09:55:13 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 20 Apr 2010 14:55:13 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runSGP2GFF' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runSGP2GFF' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/770 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue Apr 20 10:24:21 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 20 Apr 2010 10:24:21 -0400 (EDT) Subject: [BioCatalogue-developers] [1848] trunk/script/biocatalogue/sanity_check.rb: check for service providers with no services Message-ID: <20100420142421.52A751858319@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue Apr 20 10:26:34 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 20 Apr 2010 15:26:34 +0100 Subject: [BioCatalogue-developers] Outputs from the two different WSDL parsers In-Reply-To: <4BCDA618.600@cs.man.ac.uk> References: <4BCDA618.600@cs.man.ac.uk> Message-ID: <4BCDB99A.5090501@ebi.ac.uk> The structure of the output is the same for both parse functions... Jiten Bhagat wrote: > Hi Eric, > > Can I just check something with you - do the outputs from... > > BioCatalogue::WsdlParser.parse(...) > > ... and ... > > BioCatalogue::WSDLUtils::WSDLParser.parse(..) > > ... follow the *exact* same spec? Ie: can I treat them interchangeably? > I am assuming that the SoapService#populate method treats both as the > same structure/spec? > > This is crucial to the diffing of the WSDLs (I am not using the EMBRACE > one now because all it does is return a textual diff and compares to an > internal cached version which we have no way of tracking). > > Cheers, > Jits > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From utopia at cs.man.ac.uk Tue Apr 20 10:35:31 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 20 Apr 2010 15:35:31 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'mprap' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'mprap' has changed status from 'Untested' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/2803 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue Apr 20 11:05:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 20 Apr 2010 11:05:22 -0400 (EDT) Subject: [BioCatalogue-developers] [1849] trunk: Better error handling, in particular for cases where unactivated users are returned by the search engine . Message-ID: <20100420150523.0958E185830F@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Apr 20 11:43:25 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 20 Apr 2010 16:43:25 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:fromNDBTextTommCif' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:fromNDBTextTommCif' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/936 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue Apr 20 11:55:45 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 20 Apr 2010 11:55:45 -0400 (EDT) Subject: [BioCatalogue-developers] [1850] trunk/app: REST support work Message-ID: <20100420155545.ECE6C159802F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 20 12:00:21 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 20 Apr 2010 12:00:21 -0400 (EDT) Subject: [BioCatalogue-developers] [1851] trunk/app/views/rest_parameters/_default_value.html.erb: minor style change Message-ID: <20100420160021.D2E7C185830F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 20 12:11:25 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 20 Apr 2010 12:11:25 -0400 (EDT) Subject: [BioCatalogue-developers] [1852] trunk/vendor/plugins/acts_as_solr/lib: Bugfix for acts_as_solr - the rebuild_solr_index was not taking into account the if condition for determining whether an object should be indexed or not . Message-ID: <20100420161125.C403C185830F@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Apr 20 22:37:18 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 21 Apr 2010 03:37:18 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runGenewise' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runGenewise' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/836 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Apr 21 04:36:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Apr 2010 04:36:42 -0400 (EDT) Subject: [BioCatalogue-developers] [1853] trunk: allow enabling and disabling of service test from UI Message-ID: <20100421083642.1397B185830F@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Apr 21 06:16:12 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 21 Apr 2010 11:16:12 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'GOR IV protein secondary structure prediction (CNRS IBCP)' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'GOR IV protein secondary structure prediction (CNRS IBCP)' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/270 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Apr 21 06:20:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Apr 2010 06:20:47 -0400 (EDT) Subject: [BioCatalogue-developers] [1854] trunk/app/models/annotation.rb: Fixed annotation category validation Message-ID: <20100421102047.424BA185831A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 21 06:33:19 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Apr 2010 06:33:19 -0400 (EDT) Subject: [BioCatalogue-developers] [1855] trunk/config/initializers/biocat_local.rb.pre: Any config option in biocat_local. rb that is a mutable type should be frozen to prevent it being changed inadvertently . Message-ID: <20100421103319.9CCC81858316@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 21 06:40:51 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Apr 2010 06:40:51 -0400 (EDT) Subject: [BioCatalogue-developers] [1856] branches/service-updates-and-curation/app/models/soap_service.rb: Removed legacy monitoring methods. Message-ID: <20100421104051.B3A261858318@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 21 07:11:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Apr 2010 07:11:08 -0400 (EDT) Subject: [BioCatalogue-developers] [1857] trunk: REST support work Message-ID: <20100421111108.2F173167829F@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Apr 21 09:08:40 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 21 Apr 2010 14:08:40 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'SignalP - Prediction of signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'SignalP - Prediction of signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1837 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Apr 21 10:40:21 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Apr 2010 10:40:21 -0400 (EDT) Subject: [BioCatalogue-developers] [1858] trunk/app: REST support work Message-ID: <20100421144021.6134A1D78898@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 21 10:55:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Apr 2010 10:55:09 -0400 (EDT) Subject: [BioCatalogue-developers] [1859] trunk/app/views/rest_methods/edit_resource_path_popup.html.erb: help text update Message-ID: <20100421145509.D5BDA185831C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 21 11:11:53 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Apr 2010 11:11:53 -0400 (EDT) Subject: [BioCatalogue-developers] [1860] trunk: monitoring work : enable/disable test script in UI Message-ID: <20100421151153.6E4F91858318@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 21 11:20:54 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Apr 2010 11:20:54 -0400 (EDT) Subject: [BioCatalogue-developers] [1861] trunk: Bugfix and refactoring for Tag deletion. Message-ID: <20100421152054.CA84418582CE@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 21 11:25:35 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Apr 2010 11:25:35 -0400 (EDT) Subject: [BioCatalogue-developers] [1862] trunk: Better logging of errors when entries in the activity log can 't be built (eg: in cases when the referenced object has been deleted). Message-ID: <20100421152536.112DE18582F5@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 21 11:39:15 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Apr 2010 11:39:15 -0400 (EDT) Subject: [BioCatalogue-developers] [1863] trunk/app/views/rest_methods/show.html.erb: truncated a long string Message-ID: <20100421153915.728CA185831D@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Wed Apr 21 12:18:02 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 21 Apr 2010 17:18:02 +0100 Subject: [BioCatalogue-developers] inaccessible wsdl In-Reply-To: <4BC8693D.2030408@ebi.ac.uk> References: <4BC8693D.2030408@ebi.ac.uk> Message-ID: Hi Eric, This service has be discontinued ... they have now moved to REST: http://www.nactem.ac.uk/software/acromine/rest.html We need to do something with those dead services. With all the medata added to them I don't think deleting is the best option. Carole mentioned a kind of 'graveyard' for dead services... Franck On 16 April 2010 14:42, Eric Nzuobontane wrote: > Hi Franck, > > Could you check with the nactem people about this entry? > http://www.biocatalogue.org/services/169#overview > > -- > 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 > ================================== > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Wed Apr 21 12:26:03 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Apr 2010 12:26:03 -0400 (EDT) Subject: [BioCatalogue-developers] [1864] trunk/app: fix for scripts enable/disable work Message-ID: <20100421162603.822BB1858322@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Wed Apr 21 12:28:32 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 21 Apr 2010 17:28:32 +0100 Subject: [BioCatalogue-developers] inaccessible wsdl In-Reply-To: References: <4BC8693D.2030408@ebi.ac.uk> Message-ID: <4BCF27B0.2060007@cs.man.ac.uk> We can add a very simple: "if service is marked as dead then show as grey" and then worry about filtering out dead services? Jits Franck Tanoh wrote: > Hi Eric, > This service has be discontinued ... they have now moved to REST: > http://www.nactem.ac.uk/software/acromine/rest.html > We need to do something with those dead services. With all the medata > added to them I don't think deleting is the best option. > Carole mentioned a kind of 'graveyard' for dead services... > > Franck > > On 16 April 2010 14:42, Eric Nzuobontane wrote: > >> Hi Franck, >> >> Could you check with the nactem people about this entry? >> http://www.biocatalogue.org/services/169#overview >> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> >> >> > > > > From noreply at rubyforge.org Wed Apr 21 12:38:05 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Apr 2010 12:38:05 -0400 (EDT) Subject: [BioCatalogue-developers] [1865] trunk/app: bugfix : enable/disable test script. Message-ID: <20100421163805.CE2791858325@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Wed Apr 21 12:42:48 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 21 Apr 2010 17:42:48 +0100 Subject: [BioCatalogue-developers] inaccessible wsdl In-Reply-To: <4BCF27B0.2060007@cs.man.ac.uk> References: <4BC8693D.2030408@ebi.ac.uk> <4BCF27B0.2060007@cs.man.ac.uk> Message-ID: That will be useful. Franck On 21 April 2010 17:28, Jiten Bhagat wrote: > We can add a very simple: "if service is marked as dead then show as > grey" and then worry about filtering out dead services? > > Jits > > > Franck Tanoh wrote: >> Hi Eric, >> This service has be discontinued ... they have now moved to REST: >> http://www.nactem.ac.uk/software/acromine/rest.html >> We need to do something with those dead services. ?With all the medata >> added to them I don't think deleting is the best option. >> Carole mentioned a kind of 'graveyard' for dead services... >> >> Franck >> >> On 16 April 2010 14:42, Eric Nzuobontane wrote: >> >>> Hi Franck, >>> >>> Could you check with the nactem people about this entry? >>> http://www.biocatalogue.org/services/169#overview >>> >>> -- >>> 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 >>> ================================== >>> >>> >>> >> >> >> >> > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From utopia at cs.man.ac.uk Wed Apr 21 15:25:07 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 21 Apr 2010 20:25:07 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:showPMUTonStructure' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:showPMUTonStructure' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/995 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Apr 21 19:43:14 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 22 Apr 2010 00:43:14 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getNucleotideSequence' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getNucleotideSequence' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/940 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Apr 21 22:58:55 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 22 Apr 2010 03:58:55 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getSymbolDefinitionsXML' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getSymbolDefinitionsXML' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1085 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Apr 21 23:46:02 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 22 Apr 2010 04:46:02 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:cnio.es:runFASSFromClustalw' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:cnio.es:runFASSFromClustalw' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/979 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Thu Apr 22 08:12:19 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 22 Apr 2010 08:12:19 -0400 (EDT) Subject: [BioCatalogue-developers] [1866] trunk: updated REST support unit tests Message-ID: <20100422121223.23EF9185830F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Apr 22 09:38:01 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 22 Apr 2010 09:38:01 -0400 (EDT) Subject: [BioCatalogue-developers] [1867] trunk/script/biocatalogue/sanity_check.rb: Added some TODOs Message-ID: <20100422133801.5E087159802D@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Apr 22 09:48:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 22 Apr 2010 09:48:02 -0400 (EDT) Subject: [BioCatalogue-developers] [1868] trunk/app/models/service_test.rb: bugfix Message-ID: <20100422134802.4052818582F6@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Apr 22 10:08:00 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 22 Apr 2010 15:08:00 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'MkDom2' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'MkDom2' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1899 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Thu Apr 22 11:05:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 22 Apr 2010 11:05:02 -0400 (EDT) Subject: [BioCatalogue-developers] [1869] branches/service-updates-and-curation: Service Update work: Message-ID: <20100422150502.DF7161858319@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Apr 22 11:31:30 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 22 Apr 2010 11:31:30 -0400 (EDT) Subject: [BioCatalogue-developers] [1870] trunk/vendor/embrace_scripts/src/script_listing_writer.py: update of the script runner. Message-ID: <20100422153130.914EB159802D@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Apr 22 12:14:37 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 22 Apr 2010 12:14:37 -0400 (EDT) Subject: [BioCatalogue-developers] [1871] branches/service-updates-and-curation: Refactored "end_point" to " endpoint" to keep things consistent! Message-ID: <20100422161437.2B37E18582EE@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Apr 22 18:09:49 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 22 Apr 2010 23:09:49 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runPrank' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runPrank' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1095 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Apr 22 19:30:50 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 23 Apr 2010 00:30:50 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:www.cnb.uam.es:getStatisticalLog' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:www.cnb.uam.es:getStatisticalLog' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1027 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Apr 23 12:35:41 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 23 Apr 2010 17:35:41 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromMetaAlignmentsToTextScoreMatrix' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromMetaAlignmentsToTextScoreMatrix' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/788 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Apr 25 21:32:20 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 26 Apr 2010 02:32:20 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEntryFromRefSeq' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEntryFromRefSeq' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/793 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Mon Apr 26 05:53:45 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Apr 2010 05:53:45 -0400 (EDT) Subject: [BioCatalogue-developers] [1872] trunk/app/views/rest_parameters: minor ui tweak Message-ID: <20100426095346.120691858316@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Mon Apr 26 09:24:00 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 26 Apr 2010 14:24:00 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromFASTAToAminoAcidSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromFASTAToAminoAcidSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/785 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Mon Apr 26 09:44:01 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Apr 2010 09:44:01 -0400 (EDT) Subject: [BioCatalogue-developers] [1873] trunk/app/controllers/search_controller.rb: Bugfix for the error handling when a bad search term is used. Message-ID: <20100426134402.0C7DC185830D@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Apr 26 09:48:33 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Apr 2010 09:48:33 -0400 (EDT) Subject: [BioCatalogue-developers] [1874] trunk/app/views/soap_operations/show.html.erb: Updated the " Back to Service" button on the SoapOperation page to a) take the user to the Overview tab of the Service ( and not the Operations tab), and b) remove the name of the Service from the button itself as it is redundant and may get very long . Message-ID: <20100426134833.DD44E185830D@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Apr 26 11:05:16 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Apr 2010 11:05:16 -0400 (EDT) Subject: [BioCatalogue-developers] [1875] branches/service-provider-mapping/: the branch where the service provider remapping work will be done Message-ID: <20100426150516.B7104167829F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Apr 26 11:07:21 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Apr 2010 11:07:21 -0400 (EDT) Subject: [BioCatalogue-developers] [1876] branches/service-provider-mapping/: removed incorrectly created branch Message-ID: <20100426150721.3E3681858319@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Apr 26 11:08:39 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Apr 2010 11:08:39 -0400 (EDT) Subject: [BioCatalogue-developers] [1877] branches/service-provider-mapping/: recreated branch: the branch where the service provider remapping work will be done Message-ID: <20100426150839.3776B1858319@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Mon Apr 26 11:20:33 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 26 Apr 2010 16:20:33 +0100 Subject: [BioCatalogue-developers] BioMoby Service in BioCatalogue Message-ID: For your info: The BioMoby services in the biocat are: All services tag with BioMoby + service submitted by INB_Embrace(http://www.biocatalogue.org/users/397#services). The INB_Embrace services have the term 'getMobywsdl' in their WSDL. Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From ytanoh at cs.man.ac.uk Mon Apr 26 11:41:46 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 26 Apr 2010 16:41:46 +0100 Subject: [BioCatalogue-developers] Embrace import submitter Message-ID: Hi Eric, I mentioned it at the meeting today before you joined... there are couple of services in the BioCatalogue from the embrace import that kept 'Embrace registry' as the submitter: http://www.biocatalogue.org/registries/3#services . When I checked the Embrace registry I found them with their real submitter, for example PDB_fix submitted by stockholm_dbb (http://www.embraceregistry.net/service/pdb-fix) Any idea what happened? There are only 8 services so if the automated mechanism doesn't work I can do it manually. Just tell me how. Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Mon Apr 26 12:07:33 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Apr 2010 12:07:33 -0400 (EDT) Subject: [BioCatalogue-developers] [1878] trunk: Scripts for auto tagging and auto descriptions cloning for BioMoby services . Message-ID: <20100426160734.09275185831D@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Apr 26 12:14:58 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Apr 2010 12:14:58 -0400 (EDT) Subject: [BioCatalogue-developers] [1879] trunk/script/biocatalogue/biomoby_descriptions.rb: Updated the BioMoby descriptions cloner script to output the IDs of the services that don 't have a description (on the SoapService object). Message-ID: <20100426161458.DF1D91858320@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Apr 26 12:20:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Apr 2010 12:20:02 -0400 (EDT) Subject: [BioCatalogue-developers] [1880] trunk/app/views/test_scripts/api/_test_script.xml.builder: REST API work: bugfix to take into account recent changes to the ServiceTest model, to do with activated? Message-ID: <20100426162002.9CDE4185831D@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Apr 26 12:21:28 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Apr 2010 12:21:28 -0400 (EDT) Subject: [BioCatalogue-developers] [1881] trunk/script/biocatalogue/biomoby_descriptions.rb: bugfix Message-ID: <20100426162128.BEEA41678217@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Apr 26 12:30:11 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Apr 2010 12:30:11 -0400 (EDT) Subject: [BioCatalogue-developers] [1882] trunk/script/biocatalogue/sanity_check.rb: Added more sanity checks for SoapOperations, SoapInputs and SoapOutputs. Message-ID: <20100426163018.398711858322@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Mon Apr 26 12:30:24 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 26 Apr 2010 17:30:24 +0100 Subject: [BioCatalogue-developers] REST service error Message-ID: Hi Mannie, Anytime I try to update a REST endpoint for example replace the '?" by '&' I have an internal server error... please take a look Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Mon Apr 26 18:38:48 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Apr 2010 18:38:48 -0400 (EDT) Subject: [BioCatalogue-developers] [1883] branches/web-service-ownership: service ownership/ responsibility request work Message-ID: <20100426223849.17853185831B@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue Apr 27 04:41:38 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 27 Apr 2010 09:41:38 +0100 Subject: [BioCatalogue-developers] Fwd: Services dead? In-Reply-To: References: <8FB6E3E4-74AB-41EF-88FC-F19640A50E07@ibcp.fr> Message-ID: <4BD6A342.205@ebi.ac.uk> Hi Christophe, I believe the problem in the registry is that some wsdls seem to have been moved since the services were registered. For example, for the service http://www.embraceregistry.net/service/clustal-w-multiple-alignment-cnrs-ibcp the wsdl location is http://gbio-pbil.ibcp.fr/ws/ClustalwWS.wsdl/ which is wrong. I believe the correct location according your website http://gbio-pbil.ibcp.fr/media/wsdl/ClustalwWS.wsdl So the services are probably working fine, but the information in the registry does not seem to be up to date. Eric Steve Pettifer wrote: > > > Begin forwarded message: > >> *From: *Christophe Blanchet > > >> *Date: *27 April 2010 00:53:38 GMT+01:00 >> *To: *Steve Pettifer > > >> *Subject: **Re: Services dead?* >> >> Hi Steve, >> >> I just have checked our 14 services. All seem to look fine except two >> of them: SSearch and GOR-1. I will investigate and keep you informed. >> >> best wishes >> christophe >> >> Le 20 avr. 2010 ? 13:57, Steve Pettifer a ?crit : >> >>> Hi Christophe >>> >>> I've just been looking through the registry to tidy up a few loose >>> ends, and it looks like a lot of the services you've submitted are >>> failing -- which probably means we have out-of-date info in the >>> registry. Do you have anything you could update on those by any chance? >>> >>> Best wishes >>> >>> Steve >>> >> >> -- >> Dr Christophe BLANCHET CNRS, France >> Institut de Biologie et Chimie des Proteines IBCP >> Christophe.Blanchet at ibcp.fr >> http://gbio-pbil.ibcp.fr/cblanchet >> >> >> > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From mannie.tags at googlemail.com Tue Apr 27 05:01:14 2010 From: mannie.tags at googlemail.com (Mannie Tagarira) Date: Tue, 27 Apr 2010 10:01:14 +0100 Subject: [BioCatalogue-developers] REST service error In-Reply-To: References: Message-ID: Hi Franck, I will look into this... Jits: would you be able to forward me the error report produced please. Mannie On 26 Apr 2010, at 17:30, Franck Tanoh wrote: > Hi Mannie, > > Anytime I try to update a REST endpoint for example replace the '?" by > '&' I have an internal server error... please take a look > > Franck > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From ericnzuo at ebi.ac.uk Tue Apr 27 05:07:02 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 27 Apr 2010 10:07:02 +0100 Subject: [BioCatalogue-developers] possible problem with the data? Message-ID: <4BD6A936.9030800@ebi.ac.uk> I see a number of emails with related to the data on the live site wrt to soap operations. I will investigate these later today. This morning, 11am I am meeting Jon Isilon who is working on EDAM to get some initial notions on EDAM. Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Tue Apr 27 05:12:34 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 27 Apr 2010 10:12:34 +0100 Subject: [BioCatalogue-developers] possible problem with the data? In-Reply-To: <4BD6A936.9030800@ebi.ac.uk> References: <4BD6A936.9030800@ebi.ac.uk> Message-ID: <4BD6AA82.6000307@cs.man.ac.uk> Eric, Eric Nzuobontane wrote: > I see a number of emails with related to the data on the live site wrt > to soap operations. Yes, I have added some checks for this to the sanity checker script in trunk... > I will investigate these later today. This morning, 11am I am meeting > Jon Isilon who is working on EDAM to get some initial notions on EDAM. ... speaking of which, will the release happen this morning? Together with the running of the auto_tagger and biomoby_descriptions scripts? As discussed yesterday evening. Jits > > Eric > From jits at cs.man.ac.uk Tue Apr 27 05:13:36 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 27 Apr 2010 10:13:36 +0100 Subject: [BioCatalogue-developers] REST service error In-Reply-To: References: Message-ID: <4BD6AAC0.4060000@cs.man.ac.uk> Mannie Tagarira wrote: > Hi Franck, > > I will look into this... > > Jits: would you be able to forward me the error report produced please. There were no error emails afaics... and it looked like a non application error (ie: looked like an error from apache), so will require working with Eric to solve it. Jits > > Mannie > > > > On 26 Apr 2010, at 17:30, Franck Tanoh wrote: > >> Hi Mannie, >> >> Anytime I try to update a REST endpoint for example replace the '?" by >> '&' I have an internal server error... please take a look >> >> Franck >> >> -- >> "Science knows no country, because knowledge belongs to humanity, and >> is the torch which illuminates the world." - Louis Pasteur >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From MAILER-DAEMON at ebi.ac.uk Tue Apr 27 05:48:53 2010 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Tue, 27 Apr 2010 10:48:53 +0100 (BST) Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201004270948.o3R9mrjl028429@wolin.ebi.ac.uk> The original message was received at Tue, 27 Apr 2010 10:48:53 +0100 (BST) from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.1.1 User unknown) ericnzuo at imap.ebi.ac.uk (reason: 550 5.1.1 User unknown) (expanded from: ) ----- Transcript of session follows ----- 550 5.1.1 ericnzuo at imap.ebi.ac.uk... User unknown 550 5.1.1 ... User unknown -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] rest_methods#show (ActionView::TemplateError) "comparison of RestResource with RestResource failed" Date: Tue, 27 Apr 2010 10:48:19 +0100 Size: 10904 URL: From MAILER-DAEMON at ebi.ac.uk Tue Apr 27 05:49:00 2010 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Tue, 27 Apr 2010 10:49:00 +0100 (BST) Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201004270949.o3R9n0dE028463@wolin.ebi.ac.uk> The original message was received at Tue, 27 Apr 2010 10:49:00 +0100 (BST) from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.1.1 User unknown) ericnzuo at imap.ebi.ac.uk (reason: 550 5.1.1 User unknown) (expanded from: ) ----- Transcript of session follows ----- 550 5.1.1 ericnzuo at imap.ebi.ac.uk... User unknown 550 5.1.1 ... User unknown -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] rest_methods#show (ActionView::TemplateError) "comparison of RestResource with RestResource failed" Date: Tue, 27 Apr 2010 10:48:28 +0100 Size: 10879 URL: From MAILER-DAEMON at ebi.ac.uk Tue Apr 27 05:49:06 2010 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Tue, 27 Apr 2010 10:49:06 +0100 (BST) Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201004270949.o3R9n6sM028510@wolin.ebi.ac.uk> The original message was received at Tue, 27 Apr 2010 10:49:06 +0100 (BST) from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.1.1 User unknown) ericnzuo at imap.ebi.ac.uk (reason: 550 5.1.1 User unknown) (expanded from: ) ----- Transcript of session follows ----- 550 5.1.1 ericnzuo at imap.ebi.ac.uk... User unknown 550 5.1.1 ... User unknown -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] rest_methods#show (ActionView::TemplateError) "comparison of RestResource with RestResource failed" Date: Tue, 27 Apr 2010 10:48:33 +0100 Size: 10864 URL: From MAILER-DAEMON at ebi.ac.uk Tue Apr 27 05:50:14 2010 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Tue, 27 Apr 2010 10:50:14 +0100 (BST) Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201004270950.o3R9oEeY028727@wolin.ebi.ac.uk> The original message was received at Tue, 27 Apr 2010 10:50:14 +0100 (BST) from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.1.1 User unknown) ericnzuo at imap.ebi.ac.uk (reason: 550 5.1.1 User unknown) (expanded from: ) ----- Transcript of session follows ----- 550 5.1.1 ericnzuo at imap.ebi.ac.uk... User unknown 550 5.1.1 ... User unknown -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#show (ActionView::TemplateError) "comparison of RestResource with RestResource failed" Date: Tue, 27 Apr 2010 10:49:40 +0100 Size: 11340 URL: From MAILER-DAEMON at ebi.ac.uk Tue Apr 27 05:50:36 2010 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Tue, 27 Apr 2010 10:50:36 +0100 (BST) Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201004270950.o3R9oaCE028829@wolin.ebi.ac.uk> The original message was received at Tue, 27 Apr 2010 10:50:36 +0100 (BST) from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.1.1 User unknown) ericnzuo at imap.ebi.ac.uk (reason: 550 5.1.1 User unknown) (expanded from: ) ----- Transcript of session follows ----- 550 5.1.1 ericnzuo at imap.ebi.ac.uk... User unknown 550 5.1.1 ... User unknown -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#show (ActionView::TemplateError) "comparison of RestResource with RestResource failed" Date: Tue, 27 Apr 2010 10:50:04 +0100 Size: 11256 URL: From MAILER-DAEMON at ebi.ac.uk Tue Apr 27 05:51:32 2010 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Tue, 27 Apr 2010 10:51:32 +0100 (BST) Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201004270951.o3R9pWZM028977@wolin.ebi.ac.uk> The original message was received at Tue, 27 Apr 2010 10:51:32 +0100 (BST) from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.1.1 User unknown) ericnzuo at imap.ebi.ac.uk (reason: 550 5.1.1 User unknown) (expanded from: ) ----- Transcript of session follows ----- 550 5.1.1 ericnzuo at imap.ebi.ac.uk... User unknown 550 5.1.1 ... User unknown -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#show (ActionView::TemplateError) "comparison of RestResource with RestResource failed" Date: Tue, 27 Apr 2010 10:50:58 +0100 Size: 11260 URL: From MAILER-DAEMON at ebi.ac.uk Tue Apr 27 05:49:15 2010 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Tue, 27 Apr 2010 10:49:15 +0100 (BST) Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201004270949.o3R9nF9R028551@wolin.ebi.ac.uk> The original message was received at Tue, 27 Apr 2010 10:49:15 +0100 (BST) from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.1.1 User unknown) ericnzuo at imap.ebi.ac.uk (reason: 550 5.1.1 User unknown) (expanded from: ) ----- Transcript of session follows ----- 550 5.1.1 ericnzuo at imap.ebi.ac.uk... User unknown 550 5.1.1 ... User unknown -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] rest_methods#show (ActionView::TemplateError) "comparison of RestResource with RestResource failed" Date: Tue, 27 Apr 2010 10:48:43 +0100 Size: 10839 URL: From MAILER-DAEMON at ebi.ac.uk Tue Apr 27 05:49:10 2010 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Tue, 27 Apr 2010 10:49:10 +0100 (BST) Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201004270949.o3R9nA45028535@wolin.ebi.ac.uk> The original message was received at Tue, 27 Apr 2010 10:49:10 +0100 (BST) from spike.ebi.ac.uk [193.62.196.9] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.1.1 User unknown) ericnzuo at imap.ebi.ac.uk (reason: 550 5.1.1 User unknown) (expanded from: ) ----- Transcript of session follows ----- 550 5.1.1 ericnzuo at imap.ebi.ac.uk... User unknown 550 5.1.1 ... User unknown -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] rest_methods#show (ActionView::TemplateError) "comparison of RestResource with RestResource failed" Date: Tue, 27 Apr 2010 10:48:36 +0100 Size: 10864 URL: From jits at cs.man.ac.uk Tue Apr 27 07:07:59 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 27 Apr 2010 12:07:59 +0100 Subject: [BioCatalogue-developers] [1883] branches/web-service-ownership: service ownership/ responsibility request work In-Reply-To: <20100426223849.17853185831B@rubyforge.org> References: <20100426223849.17853185831B@rubyforge.org> Message-ID: <4BD6C58F.5080906@cs.man.ac.uk> Hi Eric, One quick comment about this work: For any ActiveRecord models - please could you add a 'bang' (ie: exclamation mark - !) at the end of any methods that actually change the state of the record. E.g.: methods like 'approve', Cheers, Jits noreply at rubyforge.org wrote: > > Revision > 1883 > Author > ebontane > Date > 2010-04-26 18:38:48 -0400 (Mon, 26 Apr 2010) > > > Log Message > > service ownership/responsibility request work > > > Modified Paths > > * branches/web-service-ownership/app/controllers/responsibility_requests_controller.rb > <#brancheswebserviceownershipappcontrollersresponsibility_requests_controllerrb> > * branches/web-service-ownership/app/models/responsibility_request.rb > <#brancheswebserviceownershipappmodelsresponsibility_requestrb> > * branches/web-service-ownership/app/models/service_responsible.rb > <#brancheswebserviceownershipappmodelsservice_responsiblerb> > * branches/web-service-ownership/app/models/user_mailer.rb > <#brancheswebserviceownershipappmodelsuser_mailerrb> > * branches/web-service-ownership/app/views/responsibility_requests/index.html.erb > <#brancheswebserviceownershipappviewsresponsibility_requestsindexhtmlerb> > * branches/web-service-ownership/app/views/responsibility_requests/new.html.erb > <#brancheswebserviceownershipappviewsresponsibility_requestsnewhtmlerb> > * branches/web-service-ownership/app/views/services/show.html.erb > <#brancheswebserviceownershipappviewsservicesshowhtmlerb> > * branches/web-service-ownership/app/views/user_mailer/responsibility_request_notification.html.erb > <#brancheswebserviceownershipappviewsuser_mailerresponsibility_request_notificationhtmlerb> > * branches/web-service-ownership/config/routes.rb > <#brancheswebserviceownershipconfigroutesrb> > * branches/web-service-ownership/db/migrate/20100315133520_create_responsibility_requests.rb > <#brancheswebserviceownershipdbmigrate20100315133520_create_responsibility_requestsrb> > * branches/web-service-ownership/db/schema.rb > <#brancheswebserviceownershipdbschemarb> > * branches/web-service-ownership/lib/bio_catalogue/auth.rb > <#brancheswebserviceownershiplibbio_catalogueauthrb> > * branches/web-service-ownership/lib/bio_catalogue/responsibility.rb > <#brancheswebserviceownershiplibbio_catalogueresponsibilityrb> > > > Added Paths > > * branches/web-service-ownership/app/views/responsibility_requests/_deny_responsibility.html.erb > <#brancheswebserviceownershipappviewsresponsibility_requests_deny_responsibilityhtmlerb> > * branches/web-service-ownership/app/views/responsibility_requests/turn_down.html.erb > <#brancheswebserviceownershipappviewsresponsibility_requeststurn_downhtmlerb> > * branches/web-service-ownership/app/views/user_mailer/responsibility_request_approval.html.erb > <#brancheswebserviceownershipappviewsuser_mailerresponsibility_request_approvalhtmlerb> > * branches/web-service-ownership/app/views/user_mailer/responsibility_request_cancellation.html.erb > <#brancheswebserviceownershipappviewsuser_mailerresponsibility_request_cancellationhtmlerb> > * branches/web-service-ownership/app/views/user_mailer/responsibility_request_refusal.html.erb > <#brancheswebserviceownershipappviewsuser_mailerresponsibility_request_refusalhtmlerb> > * branches/web-service-ownership/db/migrate/20100412154338_modify_responsibility_request.rb > <#brancheswebserviceownershipdbmigrate20100412154338_modify_responsibility_requestrb> > * branches/web-service-ownership/lib/bio_catalogue/jobs/service_claimant_request_notification.rb > <#brancheswebserviceownershiplibbio_cataloguejobsservice_claimant_request_notificationrb> > * branches/web-service-ownership/lib/bio_catalogue/jobs/service_owner_request_notification.rb > <#brancheswebserviceownershiplibbio_cataloguejobsservice_owner_request_notificationrb> > * branches/web-service-ownership/lib/bio_catalogue/jobs/service_responsibility_request_approval.rb > <#brancheswebserviceownershiplibbio_cataloguejobsservice_responsibility_request_approvalrb> > * branches/web-service-ownership/lib/bio_catalogue/jobs/service_responsibility_request_cancellation.rb > <#brancheswebserviceownershiplibbio_cataloguejobsservice_responsibility_request_cancellationrb> > * branches/web-service-ownership/lib/bio_catalogue/jobs/service_responsibility_request_refusal.rb > <#brancheswebserviceownershiplibbio_cataloguejobsservice_responsibility_request_refusalrb> > [snip] From noreply at rubyforge.org Tue Apr 27 07:33:52 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 27 Apr 2010 07:33:52 -0400 (EDT) Subject: [BioCatalogue-developers] [1884] trunk/app/helpers/rest_services_helper.rb: bugfix for REST support URL template Message-ID: <20100427113352.4B24F1D799C9@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue Apr 27 07:56:28 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 27 Apr 2010 12:56:28 +0100 Subject: [BioCatalogue-developers] updated test site Message-ID: <4BD6D0EC.5040804@ebi.ac.uk> Hi Guys, Could you please check that the updated test site is does show the expected improvements? Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Tue Apr 27 08:02:18 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 27 Apr 2010 08:02:18 -0400 (EDT) Subject: [BioCatalogue-developers] [1885] trunk/app/models: bugfix for the custom sort methods for RestResource and RestMethod Message-ID: <20100427120219.089A41858315@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 27 08:09:56 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 27 Apr 2010 08:09:56 -0400 (EDT) Subject: [BioCatalogue-developers] [1886] trunk/app/helpers/rest_services_helper.rb: url template update Message-ID: <20100427120956.C14AD1D799CC@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 27 09:05:00 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 27 Apr 2010 09:05:00 -0400 (EDT) Subject: [BioCatalogue-developers] [1887] trunk/app/views/rest_services/_show_service_tabs.html.erb: bug fix for "Add Endpoints" button not showing Message-ID: <20100427130500.A6A491D799C1@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 27 09:15:41 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 27 Apr 2010 09:15:41 -0400 (EDT) Subject: [BioCatalogue-developers] [1888] trunk/app/helpers/activity_feeds_helper.rb: Ignore activity log entries created by Agents, for now. Message-ID: <20100427131541.D01211858300@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 27 09:24:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 27 Apr 2010 09:24:42 -0400 (EDT) Subject: [BioCatalogue-developers] [1889] trunk/app/controllers/rest_resources_controller.rb: bug fix for " Add Endpoints" button not showing Message-ID: <20100427132442.7D29718582FF@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Tue Apr 27 09:20:17 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 27 Apr 2010 14:20:17 +0100 Subject: [BioCatalogue-developers] tag to remove Message-ID: Hi Guys, Can you remove the following tags please: 1-simpleParameter: http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter 2-collectionParameter: http://www.mygrid.org.uk/mygrid-moby-service#collectionParameter 3-ObjectHandling Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Tue Apr 27 10:26:41 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 27 Apr 2010 10:26:41 -0400 (EDT) Subject: [BioCatalogue-developers] [1890] trunk/app: Implemented the show page for agents, and reenabled showing of activity log entries by agents. Message-ID: <20100427142641.D3D901D799C1@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 27 10:29:33 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 27 Apr 2010 10:29:33 -0400 (EDT) Subject: [BioCatalogue-developers] [1891] trunk/app/views/agents/show.html.erb: Agent show page now has description annotation field. Message-ID: <20100427142933.345B01678312@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 27 10:48:12 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 27 Apr 2010 10:48:12 -0400 (EDT) Subject: [BioCatalogue-developers] [1892] trunk/app/helpers/rest_services_helper.rb: REST support template update Message-ID: <20100427144812.D262918582F6@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Apr 27 14:41:51 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 27 Apr 2010 19:41:51 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'blastProDom' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'blastProDom' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/137 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Apr 27 20:53:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 28 Apr 2010 01:53:33 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'NetPhos - Prediction of generic phosphorylation sites in eukaryotic proteins' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'NetPhos - Prediction of generic phosphorylation sites in eukaryotic proteins' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1627 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Apr 27 22:05:29 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 28 Apr 2010 03:05:29 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEntryFromSCOPPath' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEntryFromSCOPPath' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/803 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Wed Apr 28 04:15:54 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 28 Apr 2010 09:15:54 +0100 Subject: [BioCatalogue-developers] [Production ERROR] application#show (ActionView::TemplateError) "undefined method `service' for nil:NilClass" In-Reply-To: <4bd708925a29f_6d7e1579e6cf27d414d@pweb-3b.ebi.ac.uk.tmail> References: <4bd708925a29f_6d7e1579e6cf27d414d@pweb-3b.ebi.ac.uk.tmail> Message-ID: <4BD7EEBA.1030305@ebi.ac.uk> This error message is generated by googlebot and it is not yet clear how google bot got the url. This will be looked at later. For now we just ignore the error messages. Eric BioCatalogue Errors wrote: > A ActionView::TemplateError occurred in application#show: > > undefined method `service' for nil:NilClass > On line #16 of app/views/soap_operations/_breadcrumbs.html.erb > > 13: <% if controller.action_name.downcase == "show" -%> > 14:
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    • > 19: > > app/views/soap_operations/_breadcrumbs.html.erb:16 > app/helpers/application_helper.rb:492:in `render_breadcrumbs_after_home' > app/views/widgets/_breadcrumbs_bar.html.erb:18 > app/views/layouts/application_wide.html.erb:52 > passenger (2.2.4) lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' > passenger (2.2.4) lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in `safe_fork' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in `start' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > > ------------------------------- > Request: > ------------------------------- > > * URL : http://www.biocatalogue.org/soap_operations/9875 > * Method : GET > * IP address: 66.249.65.247 > * Parameters: {"action"=>"show", "id"=>"9875", "controller"=>"soap_operations"} > * Rails root: /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue > > ------------------------------- > Session: > ------------------------------- > > * session id: nil > * data: nil > > ------------------------------- > Environment: > ------------------------------- > > * DOCUMENT_ROOT : /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue/public > * HTTP_ACCEPT : */* > * HTTP_ACCEPT_ENCODING : gzip,deflate > * HTTP_CONNECTION : Keep-alive > * HTTP_FROM : googlebot(at)googlebot.com > * HTTP_HOST : www.biocatalogue.org > * HTTP_USER_AGENT : Mozilla/5.0 (compatible; Googlebot/2.1; +http://www.google.com/bot.html) > * HTTP_X_CLUSTER_CLIENT_IP : 66.249.65.247 > * PATH_INFO : /soap_operations/9875 > * QUERY_STRING : > * REMOTE_ADDR : 66.249.65.247 > * REMOTE_PORT : 45743 > * REQUEST_METHOD : GET > * REQUEST_URI : /soap_operations/9875 > * SCRIPT_NAME : > * SERVER_ADDR : 172.18.1.108 > * SERVER_ADMIN : root at localhost > * SERVER_NAME : www.biocatalogue.org > * SERVER_PORT : 80 > * SERVER_PROTOCOL : HTTP/1.1 > * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) > * _ : _ > * action_controller.request.query_parameters : > * action_controller.request.request_parameters: > * action_controller.rescue.request : # > * action_controller.rescue.response : # > * rack.errors : # > * rack.input : # > * rack.multiprocess : true > * rack.multithread : false > * rack.request : # > * rack.request.query_hash : > * rack.request.query_string : > * rack.routing_args : actionshowid9875controllersoap_operations > * rack.run_once : false > * rack.session : use_tab_cookiefalse_csrf_tokenoSedepCdWQctpquRA46UMewVSVwI/LuBM1p0MsQZcBM=previous_url/soap_operations/9875 > * rack.session.options : securefalseexpire_afterhttponlytruekey_session_ididcef3a2768adaa020e1951928acbfb34edomaincookie_onlytruepath/ > * rack.session.record : # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 28030 > * Server : pweb-3b > > * request.format: */* > > ------------------------------- > Backtrace: > ------------------------------- > > On line #16 of app/views/soap_operations/_breadcrumbs.html.erb > > 13: <% if controller.action_name.downcase == "show" -%> > 14:
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    • > 17: > 18:
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    • > 19: > > app/views/soap_operations/_breadcrumbs.html.erb:16 > app/helpers/application_helper.rb:492:in `render_breadcrumbs_after_home' > app/views/widgets/_breadcrumbs_bar.html.erb:18 > app/views/layouts/application_wide.html.erb:52 > passenger (2.2.4) lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' > passenger (2.2.4) lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in `safe_fork' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in `start' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > > -------------- next part -------------- A non-text attachment was scrubbed... Name: ericnzuo.vcf Type: text/x-vcard Size: 248 bytes Desc: not available URL: From ericnzuo at ebi.ac.uk Wed Apr 28 04:41:29 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 28 Apr 2010 09:41:29 +0100 Subject: [BioCatalogue-developers] xception-errnoepipe-in-passenger-requesthandler-broken-pipe Message-ID: <4BD7F4B9.20109@ebi.ac.uk> I am seeing the error discussed here in the apache logs http://stackoverflow.com/questions/1082166/exception-errnoepipe-in-passenger-requesthandler-broken-pipe -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Wed Apr 28 04:52:12 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 28 Apr 2010 09:52:12 +0100 Subject: [BioCatalogue-developers] xception-errnoepipe-in-passenger-requesthandler-broken-pipe In-Reply-To: <4BD7F4B9.20109@ebi.ac.uk> References: <4BD7F4B9.20109@ebi.ac.uk> Message-ID: <4BD7F73C.9030806@cs.man.ac.uk> Do we need to upgrade Passenger? Jits Eric Nzuobontane wrote: > I am seeing the error discussed here in the apache logs > > http://stackoverflow.com/questions/1082166/exception-errnoepipe-in-passenger-requesthandler-broken-pipe > > From ericnzuo at ebi.ac.uk Wed Apr 28 05:47:08 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 28 Apr 2010 10:47:08 +0100 Subject: [BioCatalogue-developers] xception-errnoepipe-in-passenger-requesthandler-broken-pipe In-Reply-To: <4BD7F73C.9030806@cs.man.ac.uk> References: <4BD7F4B9.20109@ebi.ac.uk> <4BD7F73C.9030806@cs.man.ac.uk> Message-ID: <4BD8041C.4070907@ebi.ac.uk> I am not sure as it was not clear to me from the discussion whether an upgrade solves the problem. I have created a ticket on the EBI internal ticketing system so that the web admins can make an evaluation as to whether an upgrade is necessary. I see that we are running on passenger-2.2.2 Eric Jiten Bhagat wrote: > Do we need to upgrade Passenger? > > Jits > > > Eric Nzuobontane wrote: > >> I am seeing the error discussed here in the apache logs >> >> http://stackoverflow.com/questions/1082166/exception-errnoepipe-in-passenger-requesthandler-broken-pipe >> >> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ytanoh at cs.man.ac.uk Wed Apr 28 07:16:52 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 28 Apr 2010 12:16:52 +0100 Subject: [BioCatalogue-developers] Fwd: TFmodeller web service References: <4BD817DE.70604@eead.csic.es> Message-ID: Begin forwarded message: > From: Bruno Contreras Moreira > Date: 28 April 2010 12:11:26 BST > To: Franck Tanoh > Subject: Re: TFmodeller web service > > Dear Franck, > thanks for the feedback, it should be OK now, > Bruno >> Hello, >> >> The TFmodeller web service (http://maya.ccg.unam.mx/~tfmodell/ >> ws.html) >> is not accessible for few days now >> (http://www.biocatalogue.org/services/70#monitoring). >> Is it a temporary issue or has the service been disconnected? >> >> Regards, >> Franck Tanoh >> BioCatalogue team >> University of Manchester, UK >> Tel: +(44)1612750145 >> > > > -- > Bruno Contreras Moreira > Estaci?n Experimental de Aula Dei /CSIC > Av.Monta?ana 1.005, 50059 Zaragoza (Espa?a). > Tel:(+34) 976716089 Fax:(+34) 976716145 > bcontreras at eead.csic.es http://www.eead.csic.es/compbio > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Wed Apr 28 08:31:52 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 28 Apr 2010 13:31:52 +0100 Subject: [BioCatalogue-developers] Fwd: TFmodeller web service In-Reply-To: References: <4BD817DE.70604@eead.csic.es> Message-ID: <4BD82AB8.1040404@cs.man.ac.uk> Nice one, Franck. Jits Franck Tanoh wrote: > > > Begin forwarded message: > >> *From: *Bruno Contreras Moreira > > >> *Date: *28 April 2010 12:11:26 BST >> *To: *Franck Tanoh > >> *Subject: **Re: TFmodeller web service* >> >> Dear Franck, >> thanks for the feedback, it should be OK now, >> Bruno >>> Hello, >>> >>> The TFmodeller web service >>> (http://maya.ccg.unam.mx/~tfmodell/ws.html >>> ) >>> is not accessible for few days now >>> (http://www.biocatalogue.org/services/70#monitoring). >>> Is it a temporary issue or has the service been disconnected? >>> >>> Regards, >>> Franck Tanoh >>> BioCatalogue team >>> University of Manchester, UK >>> Tel: +(44)1612750145 >>> >> >> >> -- >> Bruno Contreras Moreira >> Estaci?n Experimental de Aula Dei /CSIC >> Av.Monta?ana 1.005, 50059 Zaragoza (Espa?a). >> Tel:(+34) 976716089 Fax:(+34) 976716145 >> bcontreras at eead.csic.es http://www.eead.csic.es/compbio >> > > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From ericnzuo at ebi.ac.uk Wed Apr 28 08:51:54 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 28 Apr 2010 13:51:54 +0100 Subject: [BioCatalogue-developers] Fwd: TFmodeller web service In-Reply-To: <4BD82AB8.1040404@cs.man.ac.uk> References: <4BD817DE.70604@eead.csic.es> <4BD82AB8.1040404@cs.man.ac.uk> Message-ID: <4BD82F6A.1040003@ebi.ac.uk> Cool! Franck could you in the future copy those mails to the developers or contact list so that we are all aware of what is going on? Eric Jiten Bhagat wrote: > Nice one, Franck. > > Jits > > > Franck Tanoh wrote: > >> Begin forwarded message: >> >> >>> *From: *Bruno Contreras Moreira >> > >>> *Date: *28 April 2010 12:11:26 BST >>> *To: *Franck Tanoh > >>> *Subject: **Re: TFmodeller web service* >>> >>> Dear Franck, >>> thanks for the feedback, it should be OK now, >>> Bruno >>> >>>> Hello, >>>> >>>> The TFmodeller web service >>>> (http://maya.ccg.unam.mx/~tfmodell/ws.html >>>> ) >>>> is not accessible for few days now >>>> (http://www.biocatalogue.org/services/70#monitoring). >>>> Is it a temporary issue or has the service been disconnected? >>>> >>>> Regards, >>>> Franck Tanoh >>>> BioCatalogue team >>>> University of Manchester, UK >>>> Tel: +(44)1612750145 >>>> >>>> >>> -- >>> Bruno Contreras Moreira >>> Estaci?n Experimental de Aula Dei /CSIC >>> Av.Monta?ana 1.005, 50059 Zaragoza (Espa?a). >>> Tel:(+34) 976716089 Fax:(+34) 976716145 >>> bcontreras at eead.csic.es http://www.eead.csic.es/compbio >>> >>> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 ================================== From ytanoh at cs.man.ac.uk Wed Apr 28 09:37:23 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 28 Apr 2010 14:37:23 +0100 Subject: [BioCatalogue-developers] Fwd: TFmodeller web service In-Reply-To: <4BD82F6A.1040003@ebi.ac.uk> References: <4BD817DE.70604@eead.csic.es> <4BD82AB8.1040404@cs.man.ac.uk> <4BD82F6A.1040003@ebi.ac.uk> Message-ID: Sure On 28 April 2010 13:51, Eric Nzuobontane wrote: > Cool! Franck could you in the future copy those mails to the developers or > contact list so that we are all aware of what is going on? > > Eric > > > > Jiten Bhagat wrote: >> >> Nice one, Franck. >> >> Jits >> >> >> Franck Tanoh wrote: >> >>> >>> Begin forwarded message: >>> >>> >>>> >>>> *From: *Bruno Contreras Moreira >>> > >>>> *Date: *28 April 2010 12:11:26 BST >>>> *To: *Franck Tanoh > >>>> *Subject: **Re: TFmodeller web service* >>>> >>>> Dear Franck, >>>> thanks for the feedback, it should be OK now, >>>> Bruno >>>> >>>>> >>>>> Hello, >>>>> >>>>> The TFmodeller web service >>>>> (http://maya.ccg.unam.mx/~tfmodell/ws.html >>>>> ) >>>>> is not accessible for few days now >>>>> (http://www.biocatalogue.org/services/70#monitoring). >>>>> Is it a temporary issue or has the service been disconnected? >>>>> >>>>> Regards, >>>>> Franck Tanoh >>>>> BioCatalogue team >>>>> University of Manchester, UK >>>>> Tel: +(44)1612750145 >>>>> >>>> >>>> -- >>>> Bruno Contreras Moreira >>>> Estaci?n Experimental de Aula Dei /CSIC >>>> Av.Monta?ana 1.005, 50059 Zaragoza (Espa?a). >>>> Tel:(+34) 976716089 Fax:(+34) 976716145 >>>> bcontreras at eead.csic.es http://www.eead.csic.es/compbio >>>> >>>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> 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 > ================================== > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From utopia at cs.man.ac.uk Wed Apr 28 23:45:38 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 29 Apr 2010 04:45:38 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromAminoAcidSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromAminoAcidSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1000 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Thu Apr 29 04:26:17 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 29 Apr 2010 04:26:17 -0400 (EDT) Subject: [BioCatalogue-developers] [1893] branches/web-service-ownership: service ownership work Message-ID: <20100429082617.D01791858323@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Apr 29 04:31:49 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 29 Apr 2010 04:31:49 -0400 (EDT) Subject: [BioCatalogue-developers] [1894] trunk/lib/bio_catalogue/monitoring.rb: activate url checks by default Message-ID: <20100429083151.C01111858349@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Apr 29 06:21:14 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 29 Apr 2010 11:21:14 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'WHAT IF Web Services' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'WHAT IF Web Services' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/2777 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Thu Apr 29 07:22:54 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 29 Apr 2010 07:22:54 -0400 (EDT) Subject: [BioCatalogue-developers] [1895] trunk/script/biocatalogue/embrace_test_scripts_import.rb: bugfix to account for the activation of scripts Message-ID: <20100429112254.C70A51858349@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Apr 29 08:26:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 29 Apr 2010 08:26:07 -0400 (EDT) Subject: [BioCatalogue-developers] [1896] trunk/app/views/layouts/_footer.html.erb: Added For Developers link to footer Message-ID: <20100429122607.AD4B3185827F@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Thu Apr 29 11:39:01 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 29 Apr 2010 16:39:01 +0100 Subject: [BioCatalogue-developers] test script enable Message-ID: Hi Eric, I 've noticed that when I submit a test script for a service, it's by default disable...is that correct for any members as well? If that's the case, I think the opposite is better... that is, enable after submission. Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From ericnzuo at ebi.ac.uk Thu Apr 29 12:00:04 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 29 Apr 2010 17:00:04 +0100 Subject: [BioCatalogue-developers] test script enable In-Reply-To: References: Message-ID: <4BD9AD04.1000006@ebi.ac.uk> Franck that is the default and the reason is that of security. We want to actively enable test scripts rather than just allowing them to be run by default Eric Franck Tanoh wrote: > Hi Eric, > > I 've noticed that when I submit a test script for a service, it's by > default disable...is that correct for any members as well? > If that's the case, I think the opposite is better... that is, enable > after submission. > > Franck > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Thu Apr 29 12:03:18 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 29 Apr 2010 17:03:18 +0100 Subject: [BioCatalogue-developers] test script enable In-Reply-To: References: Message-ID: <4BD9ADC6.7080804@ebi.ac.uk> just to add that the url checks are now enabled by default. It makes more sense to do it that way for those. I have already committed a fix for that. Eric Franck Tanoh wrote: > Hi Eric, > > I 've noticed that when I submit a test script for a service, it's by > default disable...is that correct for any members as well? > If that's the case, I think the opposite is better... that is, enable > after submission. > > Franck > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ytanoh at cs.man.ac.uk Thu Apr 29 12:26:01 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 29 Apr 2010 17:26:01 +0100 Subject: [BioCatalogue-developers] test script enable In-Reply-To: <4BD9AD04.1000006@ebi.ac.uk> References: <4BD9AD04.1000006@ebi.ac.uk> Message-ID: So we have to manually enable every single test script... 3 questions in my mind: 1-do we display any message to inform the submitter that his test will be activated after some kind of curation 3-how do we know when a member submits a test? 3-might not be scalable to manually check every single test...in the long run we may need to find better ways. Franck On 29 Apr 2010, at 17:00, Eric Nzuobontane wrote: > Franck that is the default and the reason is that of security. We > want to actively enable test scripts rather than just allowing them > to be run by default > > Eric > > > Franck Tanoh wrote: >> Hi Eric, >> >> I 've noticed that when I submit a test script for a service, it's by >> default disable...is that correct for any members as well? >> If that's the case, I think the opposite is better... that is, enable >> after submission. >> >> Franck >> >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > From ytanoh at cs.man.ac.uk Thu Apr 29 12:26:51 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 29 Apr 2010 17:26:51 +0100 Subject: [BioCatalogue-developers] test script enable In-Reply-To: <4BD9ADC6.7080804@ebi.ac.uk> References: <4BD9ADC6.7080804@ebi.ac.uk> Message-ID: <44E55856-5BDB-4684-9270-43309228F2A1@cs.man.ac.uk> Not sure i understand that message. Franck On 29 Apr 2010, at 17:03, Eric Nzuobontane wrote: > just to add that the url checks are now enabled by default. It makes > more sense to do it that way for those. I have already committed a > fix for that. > > Eric > > > Franck Tanoh wrote: >> Hi Eric, >> >> I 've noticed that when I submit a test script for a service, it's by >> default disable...is that correct for any members as well? >> If that's the case, I think the opposite is better... that is, enable >> after submission. >> >> Franck >> >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > From utopia at cs.man.ac.uk Thu Apr 29 19:51:37 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 30 Apr 2010 00:51:37 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'BLASTatlas' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'BLASTatlas' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1690 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Apr 30 04:45:15 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 30 Apr 2010 09:45:15 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:getProdomDomainsFromUniProt' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:getProdomDomainsFromUniProt' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1060 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Fri Apr 30 05:23:34 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 30 Apr 2010 10:23:34 +0100 Subject: [BioCatalogue-developers] test script enable In-Reply-To: References: <4BD9AD04.1000006@ebi.ac.uk> Message-ID: <4BDAA196.8050002@ebi.ac.uk> Hi Franck, Honestly I do not know what the right solution is for this one. If people think that these things should be enabled automatically, then well, I will do it. About scalability, I think you are right. It is not scalable. If you have lots test scripts being uploaded, then that method would not work. But if only a few are added from time to time, then maybe there would not be a problem. About knowing when test are added, we can use emailing(yet again) or we can just list them as part of the curators dash board. Eric Franck Tanoh wrote: > So we have to manually enable every single test script... > 3 questions in my mind: > 1-do we display any message to inform the submitter that his test will > be activated after some kind of curation > 3-how do we know when a member submits a test? > 3-might not be scalable to manually check every single test...in the > long run we may need to find better ways. > > Franck > > On 29 Apr 2010, at 17:00, Eric Nzuobontane wrote: > >> Franck that is the default and the reason is that of security. We >> want to actively enable test scripts rather than just allowing them >> to be run by default >> >> Eric >> >> >> Franck Tanoh wrote: >>> Hi Eric, >>> >>> I 've noticed that when I submit a test script for a service, it's by >>> default disable...is that correct for any members as well? >>> If that's the case, I think the opposite is better... that is, enable >>> after submission. >>> >>> Franck >>> >>> >> >> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Fri Apr 30 05:51:38 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 30 Apr 2010 05:51:38 -0400 (EDT) Subject: [BioCatalogue-developers] [1897] trunk/app/models/test_script.rb: activate test scripts by default Message-ID: <20100430095138.AEB3B185832F@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Fri Apr 30 09:32:08 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 30 Apr 2010 14:32:08 +0100 Subject: [BioCatalogue-developers] test script enable In-Reply-To: <4BDAA196.8050002@ebi.ac.uk> References: <4BD9AD04.1000006@ebi.ac.uk> <4BDAA196.8050002@ebi.ac.uk> Message-ID: > About knowing when test are added, we can use emailing(yet again) or we can > just list them as part of the curators dash board. e-mail is the best option we have at the moment, the curators dashboard does not exist yet...don't think we can wait for it, specially if we need to enable every single test. By the way is the test monitoring working fine? I submitted the following test yesterday and it has not been tested yet. http://www.biocatalogue.org/services/116#testscripts Franck On 30 April 2010 10:23, Eric Nzuobontane wrote: > Hi Franck, > Honestly I do not know what the right solution is for this one. If people > think that these things should be enabled automatically, then well, I will > do it. About scalability, I think you are right. It is not scalable. If you > have lots test scripts being uploaded, then that method would not work. But > if only a few are added from time to time, then maybe there would not be a > problem. > > About knowing when test are added, we can use emailing(yet again) or we can > just list them as part of the curators dash board. > > Eric > > > Franck Tanoh wrote: >> >> So we have to manually enable every single test script... >> 3 ?questions in my mind: >> 1-do we display any message to inform the submitter that his test will be >> activated after some kind of curation >> 3-how do we know when a member submits a test? >> 3-might not be scalable to manually check every single test...in the long >> run we may need to find better ways. >> >> Franck >> >> On 29 Apr 2010, at 17:00, Eric Nzuobontane wrote: >> >>> Franck that is the default and the reason is that of security. We want to >>> actively enable test scripts rather than just allowing them to be run by >>> default >>> >>> Eric >>> >>> >>> Franck Tanoh wrote: >>>> >>>> Hi Eric, >>>> >>>> I 've noticed that when I submit a test script for a service, it's by >>>> default disable...is that correct for any members as well? >>>> If that's the case, I think the opposite is better... that is, enable >>>> after submission. >>>> >>>> Franck >>>> >>>> >>> >>> >>> -- >>> 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 > ================================== > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From ericnzuo at ebi.ac.uk Fri Apr 30 10:01:27 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 30 Apr 2010 15:01:27 +0100 Subject: [BioCatalogue-developers] test script enable In-Reply-To: References: <4BD9AD04.1000006@ebi.ac.uk> <4BDAA196.8050002@ebi.ac.uk> Message-ID: <4BDAE2B7.10909@ebi.ac.uk> > e-mail is the best option we have at the moment, the curators > dashboard does not exist yet...don't think we can wait for it, > specially if we need to enable every single test. > I have changed this to make them enabled by default > By the way is the test monitoring working fine? I submitted the > following test yesterday and it has not been tested yet. > http://www.biocatalogue.org/services/116#testscripts > There was a bug which the meant the list of activated test was not updated. I have fixed that now. However, the test itself fails because of a missing perl module Can't locate Bio/SeqIO.pm in @INC (@INC contains: /usr/local/lib/perl5/site_perl/5.10.0/i386-linux-thread-multi /usr/local/lib/perl5/site_perl/5.10.0 /usr/lib/perl5/vendor_perl/5.10.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.10.0/i386-linux-thread-multi /usr/lib/perl5/5.10.0 /usr/lib/perl5/site_perl .) at ./DBSubLoc.pl line 142. Eric > Franck > > On 30 April 2010 10:23, Eric Nzuobontane wrote: > >> Hi Franck, >> Honestly I do not know what the right solution is for this one. If people >> think that these things should be enabled automatically, then well, I will >> do it. About scalability, I think you are right. It is not scalable. If you >> have lots test scripts being uploaded, then that method would not work. But >> if only a few are added from time to time, then maybe there would not be a >> problem. >> >> About knowing when test are added, we can use emailing(yet again) or we can >> just list them as part of the curators dash board. >> >> Eric >> >> >> Franck Tanoh wrote: >> >>> So we have to manually enable every single test script... >>> 3 questions in my mind: >>> 1-do we display any message to inform the submitter that his test will be >>> activated after some kind of curation >>> 3-how do we know when a member submits a test? >>> 3-might not be scalable to manually check every single test...in the long >>> run we may need to find better ways. >>> >>> Franck >>> >>> On 29 Apr 2010, at 17:00, Eric Nzuobontane wrote: >>> >>> >>>> Franck that is the default and the reason is that of security. We want to >>>> actively enable test scripts rather than just allowing them to be run by >>>> default >>>> >>>> Eric >>>> >>>> >>>> Franck Tanoh wrote: >>>> >>>>> Hi Eric, >>>>> >>>>> I 've noticed that when I submit a test script for a service, it's by >>>>> default disable...is that correct for any members as well? >>>>> If that's the case, I think the opposite is better... that is, enable >>>>> after submission. >>>>> >>>>> Franck >>>>> >>>>> >>>>> >>>> -- >>>> 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 >> ================================== >> >> >> > > > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ytanoh at cs.man.ac.uk Fri Apr 30 10:17:10 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 30 Apr 2010 15:17:10 +0100 Subject: [BioCatalogue-developers] test script enable In-Reply-To: <4BDAE2B7.10909@ebi.ac.uk> References: <4BD9AD04.1000006@ebi.ac.uk> <4BDAA196.8050002@ebi.ac.uk> <4BDAE2B7.10909@ebi.ac.uk> Message-ID: > I have changed this to make them enabled by default Cool. Thanks > Can't locate Bio/SeqIO.pm in @INC (@INC contains: > /usr/local/lib/perl5/site_perl/5.10.0/i386-linux-thread-multi > /usr/local/lib/perl5/site_perl/5.10.0 > /usr/lib/perl5/vendor_perl/5.10.0/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl > /usr/lib/perl5/5.10.0/i386-linux-thread-multi /usr/lib/perl5/5.10.0 > /usr/lib/perl5/site_perl .) at ./DBSubLoc.pl line 142. It uses some Bioperl modules. Can we install bioperl in the Perl version we're using? It's widely used in Bioinformatic: www.bioperl.org Franck On 30 April 2010 15:01, Eric Nzuobontane wrote: > >> e-mail is the best option we have at the moment, the curators >> dashboard does not exist yet...don't think we can wait for it, >> specially if we need to enable every single test. >> > > I have changed this to make them enabled by default > >> By the way is the test monitoring working fine? I submitted the >> following test yesterday and it has not been tested yet. >> http://www.biocatalogue.org/services/116#testscripts >> > > There was a bug which the meant the list of activated test was not updated. > I have fixed that now. However, the test itself fails because of a missing > perl module > > Can't locate Bio/SeqIO.pm in @INC (@INC contains: > /usr/local/lib/perl5/site_perl/5.10.0/i386-linux-thread-multi > /usr/local/lib/perl5/site_perl/5.10.0 > /usr/lib/perl5/vendor_perl/5.10.0/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl > /usr/lib/perl5/5.10.0/i386-linux-thread-multi /usr/lib/perl5/5.10.0 > /usr/lib/perl5/site_perl .) at ./DBSubLoc.pl line 142. > > Eric > >> Franck >> >> On 30 April 2010 10:23, Eric Nzuobontane wrote: >> >>> >>> Hi Franck, >>> Honestly I do not know what the right solution is for this one. If people >>> think that these things should be enabled automatically, then well, I >>> will >>> do it. About scalability, I think you are right. It is not scalable. If >>> you >>> have lots test scripts being uploaded, then that method would not work. >>> But >>> if only a few are added from time to time, then maybe there would not be >>> a >>> problem. >>> >>> About knowing when test are added, we can use emailing(yet again) or we >>> can >>> just list them as part of the curators dash board. >>> >>> Eric >>> >>> >>> Franck Tanoh wrote: >>> >>>> >>>> So we have to manually enable every single test script... >>>> 3 ?questions in my mind: >>>> 1-do we display any message to inform the submitter that his test will >>>> be >>>> activated after some kind of curation >>>> 3-how do we know when a member submits a test? >>>> 3-might not be scalable to manually check every single test...in the >>>> long >>>> run we may need to find better ways. >>>> >>>> Franck >>>> >>>> On 29 Apr 2010, at 17:00, Eric Nzuobontane wrote: >>>> >>>> >>>>> >>>>> Franck that is the default and the reason is that of security. We want >>>>> to >>>>> actively enable test scripts rather than just allowing them to be run >>>>> by >>>>> default >>>>> >>>>> Eric >>>>> >>>>> >>>>> Franck Tanoh wrote: >>>>> >>>>>> >>>>>> Hi Eric, >>>>>> >>>>>> I 've noticed that when I submit a test script for a service, it's by >>>>>> default disable...is that correct for any members as well? >>>>>> If that's the case, I think the opposite is better... that is, enable >>>>>> after submission. >>>>>> >>>>>> Franck >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> 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 >>> ================================== >>> >>> >>> >> >> >> >> > > > -- > 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 > ================================== > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Fri Apr 30 12:05:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 30 Apr 2010 12:05:02 -0400 (EDT) Subject: [BioCatalogue-developers] [1898] branches/service-updates-and-curation: script to cluster Service Providers Message-ID: <20100430160502.947D01858317@rubyforge.org> An HTML attachment was scrubbed... URL: From christophe.blanchet at ibcp.fr Tue Apr 27 05:43:56 2010 From: christophe.blanchet at ibcp.fr (Christophe Blanchet) Date: Tue, 27 Apr 2010 11:43:56 +0200 Subject: [BioCatalogue-developers] Services dead? In-Reply-To: <4BD6A342.205@ebi.ac.uk> References: <8FB6E3E4-74AB-41EF-88FC-F19640A50E07@ibcp.fr> <4BD6A342.205@ebi.ac.uk> Message-ID: Hi Eric, OK. Now I understand. Thanks for this info. will look at the wsdl registrations in the embrace registry. best regards Christophe Le 27 avr. 2010 ? 10:41, Eric Nzuobontane a ?crit : > Hi Christophe, > > I believe the problem in the registry is that some wsdls seem to have been moved since the services were registered. > For example, for the service > http://www.embraceregistry.net/service/clustal-w-multiple-alignment-cnrs-ibcp > the wsdl location is > http://gbio-pbil.ibcp.fr/ws/ClustalwWS.wsdl/ > > which is wrong. > > I believe the correct location according your website > > http://gbio-pbil.ibcp.fr/media/wsdl/ClustalwWS.wsdl > > > So the services are probably working fine, but the information in the registry does not seem to be up to date. > > > Eric > > > > Steve Pettifer wrote: >> >> >> Begin forwarded message: >> >>> *From: *Christophe Blanchet > >>> *Date: *27 April 2010 00:53:38 GMT+01:00 >>> *To: *Steve Pettifer > >>> *Subject: **Re: Services dead?* >>> >>> Hi Steve, >>> >>> I just have checked our 14 services. All seem to look fine except two of them: SSearch and GOR-1. I will investigate and keep you informed. >>> >>> best wishes >>> christophe >>> >>> Le 20 avr. 2010 ? 13:57, Steve Pettifer a ?crit : >>> >>>> Hi Christophe >>>> >>>> I've just been looking through the registry to tidy up a few loose ends, and it looks like a lot of the services you've submitted are failing -- which probably means we have out-of-date info in the registry. Do you have anything you could update on those by any chance? >>>> >>>> Best wishes >>>> >>>> Steve >>>> >>> >>> -- >>> Dr Christophe BLANCHET CNRS, France >>> Institut de Biologie et Chimie des Proteines IBCP >>> Christophe.Blanchet at ibcp.fr http://gbio-pbil.ibcp.fr/cblanchet >>> >>> >>> >> > > > -- > 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 > ================================== > -- Dr Christophe BLANCHET CNRS, France Institut de Biologie et Chimie des Proteines IBCP Christophe.Blanchet at ibcp.fr http://gbio-pbil.ibcp.fr/cblanchet