From utopia at cs.man.ac.uk Sat May 1 09:49:43 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 01 May 2010 14:49:43 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEntryFromSCOPPath' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEntryFromSCOPPath' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/803 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 May 1 12:12:41 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 01 May 2010 17:12:41 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getFlexAnalysisFromPCZ' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getFlexAnalysisFromPCZ' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1164 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat May 1 15:06:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 01 May 2010 20:06:33 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMemeText' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMemeText' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/774 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat May 1 19:43:22 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 02 May 2010 00:43:22 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:getStructureFromPDB' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:getStructureFromPDB' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/986 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun May 2 14:10:07 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 02 May 2010 19:10:07 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMetaAlignment' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMetaAlignment' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/778 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun May 2 16:48:26 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 02 May 2010 21:48:26 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:cnio.es:runISSComplete' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:cnio.es:runISSComplete' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/977 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun May 2 19:56:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 03 May 2010 00:56:28 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getStructureFromPCZ' changed to Passed 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 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1154 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon May 3 04:19:29 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 03 May 2010 09:19:29 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:showPMUTonStructure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:showPMUTonStructure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/995 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 May 3 09:20:15 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 03 May 2010 14:20:15 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromFASTA' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromFASTA' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/996 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon May 3 09:20:15 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 03 May 2010 14:20:15 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromFASTA' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromFASTA' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/996 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon May 3 12:46:22 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 03 May 2010 17:46:22 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parseAminoAcidSequenceFromPDBText' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parseAminoAcidSequenceFromPDBText' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/990 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon May 3 16:40:08 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 03 May 2010 21:40:08 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:cnio.es:runNCut' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:cnio.es:runNCut' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/970 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon May 3 19:02:04 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 04 May 2010 00:02:04 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:getAminoAcidSequenceFromPDB' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:getAminoAcidSequenceFromPDB' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/988 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon May 3 19:50:31 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 04 May 2010 00:50:31 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPSIBlastpFromFASTA' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPSIBlastpFromFASTA' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1005 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue May 4 03:59:36 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 04 May 2010 08:59:36 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:getPDBFromTransfac' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:getPDBFromTransfac' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1012 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Tue May 4 04:26:27 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 04 May 2010 09:26:27 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: Services dead?] Message-ID: <4BDFDA33.7050007@ebi.ac.uk> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== -------------- next part -------------- An embedded message was scrubbed... From: Christophe Blanchet Subject: Re: Services dead? Date: Mon, 3 May 2010 17:22:02 +0200 Size: 5124 URL: From ericnzuo at ebi.ac.uk Tue May 4 05:07:06 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 04 May 2010 10:07:06 +0100 Subject: [BioCatalogue-developers] latest test result in embrace registry Message-ID: <4BDFE3BA.1090404@ebi.ac.uk> Hi Steve, There is something I have never quite understood about the recent logs for test scripts in the embrace registry. Do they always include the latest result of a test? I see for example that http://www.embraceregistry.net/test/inbgenomeimimesfromgenericsequencetofasta1 failed a month ago. It is unclear to me if that is the last time it was run or that is when it started failing and has failed ever since. In BioCatalogue however, this test *http://www.biocatalogue.org/services/2284#monitoring* is ok since the last two days. Could it be that this test has not been run in the embrace registry over the last two days? 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 May 4 07:12:16 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 4 May 2010 07:12:16 -0400 (EDT) Subject: [BioCatalogue-developers] [1899] branches/service-updates-and-curation/db/migrate/ 20100422104102_create_wsdl_changes.rb: Bugfix for db: migrate script for WsdlChange model - forgot to add soap_service_id Message-ID: <20100504111216.385861858311@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 4 07:22:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 4 May 2010 07:22:07 -0400 (EDT) Subject: [BioCatalogue-developers] [1900] branches/web-service-ownership/app: service ownership work Message-ID: <20100504112207.D64E91858318@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 4 08:24:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 4 May 2010 08:24:14 -0400 (EDT) Subject: [BioCatalogue-developers] [1901] branches/service-updates-and-curation: - updated the clustering script Message-ID: <20100504122414.3FF571858321@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 4 08:38:16 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 4 May 2010 08:38:16 -0400 (EDT) Subject: [BioCatalogue-developers] [1902] branches/web-service-ownership/app/controllers/ responsibility_requests_controller.rb: bugfix - include requester in list of those informed when approval is made Message-ID: <20100504123816.31EEB197813B@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Tue May 4 10:20:25 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 4 May 2010 15:20:25 +0100 Subject: [BioCatalogue-developers] REST base endpoint Message-ID: Hi Eric, The service monitoring shows the following REST service as dead because of the "/" missing at the end of the base URL: http://www.biocatalogue.org/services/2632. Am I right? I tried to add that but it does let me. I have a 'service already submitted' message 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 ytanoh at cs.man.ac.uk Tue May 4 10:31:08 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 4 May 2010 15:31:08 +0100 Subject: [BioCatalogue-developers] [Biocatalogue-support] Your account on BioCatalogue In-Reply-To: <4BE0206B.6080903@ebi.ac.uk> References: <4BE0206B.6080903@ebi.ac.uk> Message-ID: Eric, It will be useful to include a link to the main biocat site in the warning message on the test site. e.g ' PLEASE NOTE: this is a test site and is continually being updated and the data refreshed. Please do not use this for actual annotating and usage. But feel free to test things out and play around here. The main BioCatalogue site can be found at http://www.biocatalogue.org/' Franck On 4 May 2010 14:26, Eric Nzuobontane wrote: > Hi Daniel, > > We have noticed that you created an account on BioCatalogue. Thank you! > Unfortunately that account, http://test.biocatalogue.org/users/415 > was created on out test site. Maybe you want to create an account on the > live site instead http://www.biocatalogue.org/signup > as the test is meant for testing purposes only and subject to unannounced > changes. > > Please contact us if you need any help. > > regards, > > -- > 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-support mailing list > Biocatalogue-support at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-support > -- "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 Tue May 4 10:32:48 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 04 May 2010 15:32:48 +0100 Subject: [BioCatalogue-developers] REST base endpoint In-Reply-To: References: Message-ID: <4BE03010.6000206@ebi.ac.uk> Franck Tanoh wrote: > Hi Eric, > > The service monitoring shows the following REST service as dead > because of the "/" missing at the end of the base URL: > http://www.biocatalogue.org/services/2632. Am I right? > yes > I tried to add that but it does let me. I have a 'service already > submitted' message > Please take a look. > I will fix this in place. The check removed the trailing / I suppose. 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 Tue May 4 10:38:33 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 04 May 2010 15:38:33 +0100 Subject: [BioCatalogue-developers] [Biocatalogue-support] Your account on BioCatalogue In-Reply-To: References: <4BE0206B.6080903@ebi.ac.uk> Message-ID: <4BE03169.1070304@ebi.ac.uk> Yes, indeed. I will do that right now. Eric Franck Tanoh wrote: > Eric, > > It will be useful to include a link to the main biocat site in the > warning message on the test site. > e.g ' PLEASE NOTE: this is a test site and is continually being > updated and the data refreshed. Please do not use this for actual > annotating and usage. But feel free to test things out and play around > here. The main BioCatalogue site can be found at > http://www.biocatalogue.org/' > > Franck > > On 4 May 2010 14:26, Eric Nzuobontane wrote: > >> Hi Daniel, >> >> We have noticed that you created an account on BioCatalogue. Thank you! >> Unfortunately that account, http://test.biocatalogue.org/users/415 >> was created on out test site. Maybe you want to create an account on the >> live site instead http://www.biocatalogue.org/signup >> as the test is meant for testing purposes only and subject to unannounced >> changes. >> >> Please contact us if you need any help. >> >> regards, >> >> -- >> 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-support mailing list >> Biocatalogue-support at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-support >> >> > > > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ytanoh at cs.man.ac.uk Tue May 4 10:40:58 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 4 May 2010 15:40:58 +0100 Subject: [BioCatalogue-developers] REST base endpoint In-Reply-To: <4BE03010.6000206@ebi.ac.uk> References: <4BE03010.6000206@ebi.ac.uk> Message-ID: <7065D731-EC30-4679-B96A-C1F44DCCE46A@cs.man.ac.uk> > I will fix this in place. Thanks > The check removed the trailing / I suppose. Correct Franck On 4 May 2010, at 15:32, Eric Nzuobontane wrote: > Franck Tanoh wrote: >> Hi Eric, >> >> The service monitoring shows the following REST service as dead >> because of the "/" missing at the end of the base URL: >> http://www.biocatalogue.org/services/2632. Am I right? >> > yes >> I tried to add that but it does let me. I have a 'service already >> submitted' message >> Please take a look. >> > I will fix this in place. The check removed the trailing / I suppose. > > 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 May 4 10:43:56 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 4 May 2010 10:43:56 -0400 (EDT) Subject: [BioCatalogue-developers] [1903] branches/service-updates-and-curation: Service updates work: latest work; moving to a manual sync as need to take into account previous WSDLs that were parsed using the old parser . Message-ID: <20100504144356.2A5F91678217@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue May 4 10:51:25 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 04 May 2010 15:51:25 +0100 Subject: [BioCatalogue-developers] [Biocatalogue-support] Your account on BioCatalogue In-Reply-To: References: <4BE0206B.6080903@ebi.ac.uk> Message-ID: <4BE0346D.9070504@ebi.ac.uk> Hi Frank, Could you check the test site for the warning message now? My guess is that people do not actually read this message. That is why to go ahead and register here. Eric Franck Tanoh wrote: > Eric, > > It will be useful to include a link to the main biocat site in the > warning message on the test site. > e.g ' PLEASE NOTE: this is a test site and is continually being > updated and the data refreshed. Please do not use this for actual > annotating and usage. But feel free to test things out and play around > here. The main BioCatalogue site can be found at > http://www.biocatalogue.org/' > > Franck > > On 4 May 2010 14:26, Eric Nzuobontane wrote: > >> Hi Daniel, >> >> We have noticed that you created an account on BioCatalogue. Thank you! >> Unfortunately that account, http://test.biocatalogue.org/users/415 >> was created on out test site. Maybe you want to create an account on the >> live site instead http://www.biocatalogue.org/signup >> as the test is meant for testing purposes only and subject to unannounced >> changes. >> >> Please contact us if you need any help. >> >> regards, >> >> -- >> 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-support mailing list >> Biocatalogue-support at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-support >> >> > > > > -- 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 May 4 11:36:15 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 4 May 2010 11:36:15 -0400 (EDT) Subject: [BioCatalogue-developers] [1904] branches/service-updates-and-curation: changed . find_or_create_by_hostname calls to a more appropriate . Message-ID: <20100504153615.33DF61678217@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Tue May 4 12:11:19 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 4 May 2010 17:11:19 +0100 Subject: [BioCatalogue-developers] REST service error In-Reply-To: References: Message-ID: I'm not sure if that was addressed or not but I'm still having the same error...unable to edit endpoints Franck On 26 April 2010 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 > -- "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 Tue May 4 12:18:40 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 4 May 2010 17:18:40 +0100 Subject: [BioCatalogue-developers] REST service error In-Reply-To: References: Message-ID: Just to point out that i have the same error when i try to delete a service.... On 4 May 2010 17:11, Franck Tanoh wrote: > I'm not sure if that was addressed or not but I'm still having the > same error...unable to edit endpoints > Franck > > On 26 April 2010 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 >> > > > > -- > ?"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 Tue May 4 12:31:23 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 04 May 2010 17:31:23 +0100 Subject: [BioCatalogue-developers] REST service error In-Reply-To: References: Message-ID: <4BE04BDB.5070403@cs.man.ac.uk> The database keeps locking up and the transactions keeps timing out :-( Jits Franck Tanoh wrote: > Just to point out that i have the same error when i try to delete a service.... > > On 4 May 2010 17:11, Franck Tanoh wrote: > >> I'm not sure if that was addressed or not but I'm still having the >> same error...unable to edit endpoints >> Franck >> >> On 26 April 2010 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 >>> >>> >> >> -- >> "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 May 4 12:32:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 4 May 2010 12:32:02 -0400 (EDT) Subject: [BioCatalogue-developers] [1905] branches/service-updates-and-curation/script/biocatalogue/ sanity_check.rb: Added more data sanity checks, in particular for ServiceProviders and ServiceProviderHostnames. Message-ID: <20100504163202.26B861858347@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 4 12:38:29 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 4 May 2010 12:38:29 -0400 (EDT) Subject: [BioCatalogue-developers] [1906] branches/service-updates-and-curation: Removed the ability to set a display_name annotation on a ServiceProvider. Message-ID: <20100504163829.7D232185833A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 4 12:40:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 4 May 2010 12:40:47 -0400 (EDT) Subject: [BioCatalogue-developers] [1907] branches/service-updates-and-curation/lib/bio_catalogue/filtering/ services.rb: Removed display_name hackery from service provider filters generation. Message-ID: <20100504164047.5FE631858339@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue May 4 14:37:20 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 04 May 2010 19:37:20 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'SignalP - Prediction of signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences' changed to Passed 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 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1837 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue May 4 19:09:45 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 05 May 2010 00:09:45 +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 Tue May 4 21:26:13 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 05 May 2010 02:26:13 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'SIDDbase' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'SIDDbase' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1692 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Wed May 5 04:31:58 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 05 May 2010 09:31:58 +0100 Subject: [BioCatalogue-developers] REST service error In-Reply-To: <4BE04BDB.5070403@cs.man.ac.uk> References: <4BE04BDB.5070403@cs.man.ac.uk> Message-ID: <4BE12CFE.7090106@ebi.ac.uk> As I understand it, this is to do with transactions that hit the server transaction timeout error. First thing to is to investigate the transactions and see if something can be done to stop them from hitting the server timeout limit. Eric Jiten Bhagat wrote: > The database keeps locking up and the transactions keeps timing out :-( > > Jits > > > Franck Tanoh wrote: > >> Just to point out that i have the same error when i try to delete a service.... >> >> On 4 May 2010 17:11, Franck Tanoh wrote: >> >> >>> I'm not sure if that was addressed or not but I'm still having the >>> same error...unable to edit endpoints >>> Franck >>> >>> On 26 April 2010 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 >>>> >>>> >>>> >>> -- >>> "Science knows no country, because knowledge belongs to humanity, and >>> is the torch which illuminates the world." - Louis Pasteur >>> >>> >>> >> >> >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Wed May 5 04:41:40 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 05 May 2010 09:41:40 +0100 Subject: [BioCatalogue-developers] REST service error In-Reply-To: <4BE12CFE.7090106@ebi.ac.uk> References: <4BE04BDB.5070403@cs.man.ac.uk> <4BE12CFE.7090106@ebi.ac.uk> Message-ID: <4BE12F44.9020506@cs.man.ac.uk> What is the current server timeout limit? And are we talking about the Apache request/response cycle timeout or a db specific timeout? This is what the error email says... > A ActiveRecord::StatementInvalid occurred in services#destroy: > > Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 46425 Jits Eric Nzuobontane wrote: > As I understand it, this is to do with transactions that hit the > server transaction timeout error. First thing to is to investigate the > transactions and see if something can be done to stop them from > hitting the server timeout limit. > > Eric > > > > Jiten Bhagat wrote: >> The database keeps locking up and the transactions keeps timing out :-( >> >> Jits >> >> >> Franck Tanoh wrote: >> >>> Just to point out that i have the same error when i try to delete a >>> service.... >>> >>> On 4 May 2010 17:11, Franck Tanoh wrote: >>> >>>> I'm not sure if that was addressed or not but I'm still having the >>>> same error...unable to edit endpoints >>>> Franck >>>> >>>> On 26 April 2010 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 >>>>> >>>>> >>>> -- >>>> "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 Wed May 5 04:49:39 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 05 May 2010 09:49:39 +0100 Subject: [BioCatalogue-developers] REST service error In-Reply-To: <4BE12F44.9020506@cs.man.ac.uk> References: <4BE04BDB.5070403@cs.man.ac.uk> <4BE12CFE.7090106@ebi.ac.uk> <4BE12F44.9020506@cs.man.ac.uk> Message-ID: <4BE13123.4040107@ebi.ac.uk> Jiten Bhagat wrote: > What is the current server timeout limit? > I do not know but I believe it should be the default set by mysql > And are we talking about the Apache request/response cycle timeout or a > db specific timeout? > No, I think this is internal to mysql on the duration of transactions on innodb tables. I would expect this to happen when deleting loads of entries perhaps but I am a bit puzzled since it is a single item. > This is what the error email says... > > >> A ActiveRecord::StatementInvalid occurred in services#destroy: >> >> Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 46425 >> > > Services are deleted in a transaction and I believe it is the transaction that is timing out. Eric > Jits > > > > Eric Nzuobontane wrote: > >> As I understand it, this is to do with transactions that hit the >> server transaction timeout error. First thing to is to investigate the >> transactions and see if something can be done to stop them from >> hitting the server timeout limit. >> >> Eric >> >> >> >> Jiten Bhagat wrote: >> >>> The database keeps locking up and the transactions keeps timing out :-( >>> >>> Jits >>> >>> >>> Franck Tanoh wrote: >>> >>> >>>> Just to point out that i have the same error when i try to delete a >>>> service.... >>>> >>>> On 4 May 2010 17:11, Franck Tanoh wrote: >>>> >>>> >>>>> I'm not sure if that was addressed or not but I'm still having the >>>>> same error...unable to edit endpoints >>>>> Franck >>>>> >>>>> On 26 April 2010 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 >>>>>> >>>>>> >>>>>> >>>>> -- >>>>> "Science knows no country, because knowledge belongs to humanity, and >>>>> is the torch which illuminates the world." - Louis Pasteur >>>>> >>>>> >>>>> >>>> >>>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Wed May 5 04:55:56 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 05 May 2010 09:55:56 +0100 Subject: [BioCatalogue-developers] REST service error In-Reply-To: <4BE13123.4040107@ebi.ac.uk> References: <4BE04BDB.5070403@cs.man.ac.uk> <4BE12CFE.7090106@ebi.ac.uk> <4BE12F44.9020506@cs.man.ac.uk> <4BE13123.4040107@ebi.ac.uk> Message-ID: <4BE1329C.6040809@cs.man.ac.uk> Eric Nzuobontane wrote: > > > Jiten Bhagat wrote: [snip] >> db specific timeout? >> > And are we talking about the Apache request/response cycle timeout or a > No, I think this is internal to mysql on the duration of transactions > on innodb tables. I would expect this to happen when deleting loads of > entries perhaps but I am a bit puzzled since it is a single item. >> This is what the error email says... >> >> >>> A ActiveRecord::StatementInvalid occurred in services#destroy: >>> >>> Mysql::Error: Lock wait timeout exceeded; try restarting >>> transaction: DELETE FROM `annotation_versions` WHERE `id` = 46425 >>> >> >> > Services are deleted in a transaction and I believe it is the > transaction that is timing out. Yes, that is what I thought too. What is happening (I think) is that lots of different things are happening within the transaction, many of which lock tables (esp on deletes), which then cause remaining actions in the transaction to timeout. I've heard that MySQL can be a pain with things like this. There are presentations like this - http://www.mysqlconf.com/mysql2008/public/schedule/detail/398 - that might be able to help (no idea where to get the slides though). Jits > > Eric > > > >> Jits >> >> >> >> Eric Nzuobontane wrote: >> >>> As I understand it, this is to do with transactions that hit the >>> server transaction timeout error. First thing to is to investigate the >>> transactions and see if something can be done to stop them from >>> hitting the server timeout limit. >>> >>> Eric >>> >>> >>> >>> Jiten Bhagat wrote: >>> >>>> The database keeps locking up and the transactions keeps timing out >>>> :-( >>>> >>>> Jits >>>> >>>> >>>> Franck Tanoh wrote: >>>> >>>> >>>>> Just to point out that i have the same error when i try to delete a >>>>> service.... >>>>> >>>>> On 4 May 2010 17:11, Franck Tanoh wrote: >>>>> >>>>>> I'm not sure if that was addressed or not but I'm still having the >>>>>> same error...unable to edit endpoints >>>>>> Franck >>>>>> >>>>>> On 26 April 2010 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 >>>>>>> >>>>>>> >>>>>> -- >>>>>> "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 Wed May 5 06:19:44 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 5 May 2010 11:19:44 +0100 Subject: [BioCatalogue-developers] tag to remove In-Reply-To: References: Message-ID: Hi Guys, Did you get my e-mail below ... I've removed the simple one but these 3 are to many to be done manually. Thanks Franck On 27 April 2010 14:20, Franck Tanoh wrote: > 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 > -- "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 May 5 06:27:38 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 5 May 2010 06:27:38 -0400 (EDT) Subject: [BioCatalogue-developers] [1908] branches/service-updates-and-curation/app/models/service_deployment. rb: updated service deployment model to index the associated service provider' s hostnames (by way of a space separated string) Message-ID: <20100505102739.130AB185834C@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Wed May 5 06:39:33 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 05 May 2010 11:39:33 +0100 Subject: [BioCatalogue-developers] tag to remove In-Reply-To: References: Message-ID: <4BE14AE5.4050502@ebi.ac.uk> Maybe you can create a jira task to write a script for this. I believe we will be running this script from time to time so maybe it is better to write is now. Eric Franck Tanoh wrote: > Hi Guys, > > Did you get my e-mail below ... I've removed the simple one but these > 3 are to many to be done manually. > > Thanks > Franck > > On 27 April 2010 14:20, Franck Tanoh wrote: > >> 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 >> >> > > > > -- 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 May 5 08:59:31 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 05 May 2010 13:59:31 +0100 Subject: [BioCatalogue-developers] =?iso-8859-1?q?=5BFwd=3A_Re=3A_=5BFwd?= =?iso-8859-1?q?=3A_Re=3A_=5BBiocatalogue-support=5D_BioCatalogue_feedback?= =?iso-8859-1?q?_from_Mar=EDa_P=E9rez_=28maria=2Eperez=40uji=2Ees=29=5D=5D?= Message-ID: <4BE16BB3.5090206@ebi.ac.uk> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== -------------- next part -------------- An embedded message was scrubbed... From: =?iso-8859-1?b?TWFy7WEg?= =?iso-8859-1?b?UOlyZXog?= =?iso-8859-1?b?Q2F0YWzhbg==?= Subject: Re: [Fwd: Re: [Biocatalogue-support] BioCatalogue feedback from =?iso-8859-1?b?TWFy7WEg?= =?iso-8859-1?b?UOlyZXo=?= (maria.perez at uji.es)] Date: Wed, 05 May 2010 14:39:49 +0200 Size: 7494 URL: From noreply at rubyforge.org Wed May 5 09:58:58 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 5 May 2010 09:58:58 -0400 (EDT) Subject: [BioCatalogue-developers] [1909] branches/service-updates-and-curation/app: - implemented functionality to update ServiceProvider.name Message-ID: <20100505135858.D970A185833B@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Wed May 5 10:09:15 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 05 May 2010 15:09:15 +0100 Subject: [BioCatalogue-developers] =?iso-8859-1?q?=5BFwd=3A_Re=3A_=5BFwd?= =?iso-8859-1?q?=3A_Re=3A_=5BBiocatalogue-support=5D_BioCatalogue_feedback?= =?iso-8859-1?q?_from_Mar=EDa_P=E9rez_=28maria=2Eperez=40uji=2Ees=29=5D=5D?= In-Reply-To: <4BE16BB3.5090206@ebi.ac.uk> References: <4BE16BB3.5090206@ebi.ac.uk> Message-ID: <4BE17C0B.1000809@cs.man.ac.uk> Hi Maria, Eric forwarded your request on... To answer your question, currently we use the Disqus (www.disqus.com) system to provide commenting in the BioCatalogue. However, not many people have used this and it has low adoption within the BioCatalogue (possible because users have to sign up for an account to it), so we will be integrating our own "discussions" system in the near future. Hope that helps. Cheers, Jits Eric Nzuobontane wrote: > > > ------------------------------------------------------------------------ > > Subject: > Re: [Fwd: Re: [Biocatalogue-support] BioCatalogue feedback from Mar?a > P?rez (maria.perez at uji.es)] > From: > Mar?a P?rez Catal?n > Date: > Wed, 05 May 2010 14:39:49 +0200 > To: > Eric Nzuobontane > > To: > Eric Nzuobontane > > > > Hi Eric, > > I have another question ;) Are the comments specified in the API? I > don't find any annotation or attribute related to the comments. > l > Regards, > > Mar?a > > > Eric Nzuobontane escribi?: > >> Hi Maria, >> >> Jiten had to go early so forwarded your mail to me. From what I >> understand you would like to know the number of services that have >> been favourited. These are just 28 at the moment. >> >> I hope that helps. Please do contact me if you require any further >> help... >> >> regards, >> >> Eric >> >> >> >> Jiten Bhagat wrote: >>> Eric, >>> >>> Please could you provide her with the data (as below). >>> >>> I need to head off now to catch a train! >>> >>> Cheers, have a a good weekend. >>> Jits >>> >>> >>> -------- Original Message -------- >>> Subject: Re: [Biocatalogue-support] BioCatalogue feedback from >>> Mar?a >>> P?rez (maria.perez at uji.es) >>> Date: Fri, 30 Apr 2010 09:13:05 +0200 >>> From: Mar?a P?rez Catal?n >>> To: Jiten Bhagat >>> References: >>> <4bd929dd852c1_590b15d3add067cc12c at pweb-4a.ebi.ac.uk.tmail> >>> <4BD953DB.7000207 at cs.man.ac.uk> >>> >>> >>> >>> Hello Jiten, Thanks for your fast answer. About the favourites I >>> would like to know how many >>> services have info in this field. I need only the number. >>> >>> Best regards, >>> >>> Mar?a >>> >>> >>> >>> >>> Missatge citat per Jiten Bhagat : >>> >>> >>>> Hello Maria, >>>> >>>> The ratings data is available as annotations with the annotation >>>> attribute 'http://biocatalogue.org/attribute/ratingDocumentation' [1]. >>>> You can get a list of all these annotations here: >>>> >>>> http://www.biocatalogue.org/annotation_attributes/53/annotations.xml >>>> OR >>>> http://www.biocatalogue.org/annotation_attributes/53/annotations.json >>>> >>>> Below is a summary of the ratings: >>>> >>>> +--------------+-------------------------+ >>>> | rating_value | total_number_of_ratings | >>>> +--------------+-------------------------+ >>>> | 1 | 1 | >>>> | 2 | 1 | >>>> | 3 | 3 | >>>> | 4 | 2 | >>>> | 5 | 6 | >>>> +--------------+-------------------------+ >>>> >>>> We don't yet expose the favourites in the API, but will do so in the >>>> near future. I've bumped up the priority for this in our task list. >>>> Are >>>> you looking for some specific data on this? I can send you a >>>> summary if >>>> you'd like (but I can't include information on who favourited things >>>> until we have an official API for this). >>>> >>>> [1] - http://www.biocatalogue.org/annotation_attributes/53.xml >>>> >>>> Hope that helps. >>>> >>>> Jits >>>> >>>> >>>> contact at biocatalogue.org wrote: >>>> >>>>> BioCatalogue feedback from: Mar??a P??rez (maria.perez at uji.es) >>>>> >>>>> Subject: Information provided by the API >>>>> >>>>> Message: >>>>> >>>>> I would like to know if the information about the ratings of the >>>>> >>>> documentation and the number of "Favourited by" is available in any >>>> document >>>> provided by the API. >>>> >>>>> _______________________________________________ >>>>> Biocatalogue-support mailing list >>>>> Biocatalogue-support at rubyforge.org >>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-support >>>>> >>>> >>>> >>> >>> >>> Mar?a P?rez >>> >>> >> >> >> -- >> 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 >> ================================== >> >> >> > > > > Mar?a P?rez > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From jits at cs.man.ac.uk Wed May 5 10:21:05 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 05 May 2010 15:21:05 +0100 Subject: [BioCatalogue-developers] JIRA task list Message-ID: <4BE17ED1.1040600@cs.man.ac.uk> Guys, I've finally gone through and cleaned up the JIRA task list. I've done my best to assign tasks appropriately and also set who reported them. I have also closed many that have been done. Please could you skim through and have a look. If all is okay I would like to make an announcement on the main list so that the others can know. Remember, when creating new tasks: - please try and use proper sentences, grammar etc wherever possible (it's only polite! ;-)) - please make tasks as specific as possible and describe it as much as possible (eg: instead of "Better REST Services support", split into tasks like "Implement "endpoint" functionality". - for bug reports, please put instructions on how to reproduce the bug (eg: I clicked on this, then clicked on that, etc). Cheers, Jits PS: Eric - well done for being the first to start using the JIRA list properly :-) From ericnzuo at ebi.ac.uk Wed May 5 10:41:51 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 05 May 2010 15:41:51 +0100 Subject: [BioCatalogue-developers] JIRA task list In-Reply-To: <4BE17ED1.1040600@cs.man.ac.uk> References: <4BE17ED1.1040600@cs.man.ac.uk> Message-ID: <4BE183AF.10500@ebi.ac.uk> Thanks. Just to add about bug reports, if there are any files like logs can be attached, that would make understanding the problem easier/quicker, please do add them as well. Eric Jiten Bhagat wrote: > Guys, > > I've finally gone through and cleaned up the JIRA task list. > > I've done my best to assign tasks appropriately and also set who > reported them. I have also closed many that have been done. > > Please could you skim through and have a look. If all is okay I would > like to make an announcement on the main list so that the others can know. > > Remember, when creating new tasks: > - please try and use proper sentences, grammar etc wherever possible > (it's only polite! ;-)) > - please make tasks as specific as possible and describe it as much as > possible (eg: instead of "Better REST Services support", split into > tasks like "Implement "endpoint" functionality". > - for bug reports, please put instructions on how to reproduce the bug > (eg: I clicked on this, then clicked on that, etc). > > Cheers, > Jits > > PS: Eric - well done for being the first to start using the JIRA list > properly :-) > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Wed May 5 10:50:28 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 5 May 2010 10:50:28 -0400 (EDT) Subject: [BioCatalogue-developers] [1910] trunk/config/environments/production.rb: config option to use cronolog to rotate logs in production mode Message-ID: <20100505145028.13C5C1D799BD@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed May 5 11:04:08 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 05 May 2010 16:04:08 +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 ytanoh at cs.man.ac.uk Wed May 5 11:15:08 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 5 May 2010 16:15:08 +0100 Subject: [BioCatalogue-developers] tag to remove In-Reply-To: <4BE14AE5.4050502@ebi.ac.uk> References: <4BE14AE5.4050502@ebi.ac.uk> Message-ID: Hi Eric, >I believe we will be running this script from time to time so maybe it is better to write Probably in the future. But for now there have been so many complaints about the 'simpleParameter' and 'collectionParameter' that it will be most appreciated if we can remove them as soon as possible. Franck On 5 May 2010 11:39, Eric Nzuobontane wrote: > Maybe you can create a jira task to write a script for this. I believe we > will be running this script from time to time so maybe it is better to write > is now. > > Eric > > Franck Tanoh wrote: >> >> Hi Guys, >> >> Did you get my e-mail below ... I've removed the simple one but these >> 3 are to many to be done manually. >> >> Thanks >> Franck >> >> On 27 April 2010 14:20, Franck Tanoh wrote: >> >>> >>> 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 >>> >>> >> >> >> >> > > > -- > 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 May 5 11:15:49 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 5 May 2010 11:15:49 -0400 (EDT) Subject: [BioCatalogue-developers] [1911] branches/service-updates-and-curation: code cleanup to make RestMethod and ServiceProvider a bit more RESTful Message-ID: <20100505151550.0D75416782A0@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Wed May 5 11:31:23 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 05 May 2010 16:31:23 +0100 Subject: [BioCatalogue-developers] tag to remove In-Reply-To: References: <4BE14AE5.4050502@ebi.ac.uk> Message-ID: <4BE18F4B.30709@cs.man.ac.uk> Eric, For now, you should be able to do this in script/console: Annotation.find(:all, :conditions => { :attribute_id => 2, :value => "" }.each { |a| puts "Deleting Annotation (ID: #{a.id})"; a.destroy } and... Annotation.find(:all, :conditions => { :attribute_id => 2, :value => "" }.each { |a| puts "Deleting Annotation (ID: #{a.id})"; a.destroy } and... Annotation.find(:all, :conditions => { :attribute_id => 2, :value => "ObjectHandling" }.each { |a| puts "Deleting Annotation (ID: #{a.id})"; a.destroy } To delete all those tags. Of course, try it first on the test site first! Jits PS: hopefully you wont get any timeouts with Solr. If you do, add a "sleep 1" after the destroy, to make it wait a bit after each destroy. Franck Tanoh wrote: > Hi Eric, > >> I believe we will be running this script from time to time so maybe it is better to write >> > Probably in the future. But for now there have been so many complaints > about the 'simpleParameter' and 'collectionParameter' that it will be > most appreciated if we can remove them as soon as possible. > > Franck > > > On 5 May 2010 11:39, Eric Nzuobontane wrote: > >> Maybe you can create a jira task to write a script for this. I believe we >> will be running this script from time to time so maybe it is better to write >> is now. >> >> Eric >> >> Franck Tanoh wrote: >> >>> Hi Guys, >>> >>> Did you get my e-mail below ... I've removed the simple one but these >>> 3 are to many to be done manually. >>> >>> Thanks >>> Franck >>> >>> On 27 April 2010 14:20, Franck Tanoh wrote: >>> >>> >>>> 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 >>>> >>>> >>>> >>> >>> >>> >> -- >> 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 May 5 11:33:39 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 05 May 2010 16:33:39 +0100 Subject: [BioCatalogue-developers] tag to remove In-Reply-To: <4BE18F4B.30709@cs.man.ac.uk> References: <4BE14AE5.4050502@ebi.ac.uk> <4BE18F4B.30709@cs.man.ac.uk> Message-ID: <4BE18FD3.1030901@cs.man.ac.uk> Oops, typos.... use these instead: Annotation.find(:all, :conditions => { :attribute_id => 2, :value => "" }).each { |a| puts "Deleting Annotation (ID: #{a.id})"; a.destroy } and... Annotation.find(:all, :conditions => { :attribute_id => 2, :value => "" }).each { |a| puts "Deleting Annotation (ID: #{a.id})"; a.destroy } and... Annotation.find(:all, :conditions => { :attribute_id => 2, :value => "ObjectHandling" }).each { |a| puts "Deleting Annotation (ID: #{a.id})"; a.destroy } Jits Jiten Bhagat wrote: > Eric, > > For now, you should be able to do this in script/console: > > Annotation.find(:all, :conditions => { :attribute_id => 2, :value => > "" }.each > { |a| puts "Deleting Annotation (ID: #{a.id})"; a.destroy } > > and... > > Annotation.find(:all, :conditions => { :attribute_id => 2, :value => > "" > }.each { |a| puts "Deleting Annotation (ID: #{a.id})"; a.destroy } > > and... > > Annotation.find(:all, :conditions => { :attribute_id => 2, :value => > "ObjectHandling" }.each { |a| puts "Deleting Annotation (ID: #{a.id})"; > a.destroy } > > To delete all those tags. > > Of course, try it first on the test site first! > > Jits > > PS: hopefully you wont get any timeouts with Solr. If you do, add a > "sleep 1" after the destroy, to make it wait a bit after each destroy. > > > Franck Tanoh wrote: > >> Hi Eric, >> >> >>> I believe we will be running this script from time to time so maybe it is better to write >>> >>> >> Probably in the future. But for now there have been so many complaints >> about the 'simpleParameter' and 'collectionParameter' that it will be >> most appreciated if we can remove them as soon as possible. >> >> Franck >> >> >> On 5 May 2010 11:39, Eric Nzuobontane wrote: >> >> >>> Maybe you can create a jira task to write a script for this. I believe we >>> will be running this script from time to time so maybe it is better to write >>> is now. >>> >>> Eric >>> >>> Franck Tanoh wrote: >>> >>> >>>> Hi Guys, >>>> >>>> Did you get my e-mail below ... I've removed the simple one but these >>>> 3 are to many to be done manually. >>>> >>>> Thanks >>>> Franck >>>> >>>> On 27 April 2010 14:20, Franck Tanoh wrote: >>>> >>>> >>>> >>>>> 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 >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>> -- >>> 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 > From ytanoh at cs.man.ac.uk Wed May 5 11:52:46 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 5 May 2010 16:52:46 +0100 Subject: [BioCatalogue-developers] JIRA task list In-Reply-To: <4BE17ED1.1040600@cs.man.ac.uk> References: <4BE17ED1.1040600@cs.man.ac.uk> Message-ID: Well done Jits! I had a look and it looks fine and tidy. Feel free to announce Franck On 5 May 2010 15:21, Jiten Bhagat wrote: > Guys, > > I've finally gone through and cleaned up the JIRA task list. > > I've done my best to assign tasks appropriately and also set who > reported them. I have also closed many that have been done. > > Please could you skim through and have a look. If all is okay I would > like to make an announcement on the main list so that the others can know. > > Remember, when creating new tasks: > - please try and use proper sentences, grammar etc wherever possible > (it's only polite! ;-)) > - please make tasks as specific as possible and describe it as much as > possible (eg: instead of "Better REST Services support", split into > tasks like "Implement "endpoint" functionality". > - for bug reports, please put instructions on how to reproduce the bug > (eg: I clicked on this, then clicked on that, etc). > > Cheers, > Jits > > PS: Eric - well done for being the first to start using the JIRA list > properly :-) > _______________________________________________ > 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 Wed May 5 12:22:52 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 5 May 2010 12:22:52 -0400 (EDT) Subject: [BioCatalogue-developers] [1912] branches/service-updates-and-curation/app/views/soap_operations/show .html.erb: Updated Soap Operation show page to always show the currently selected tab at the top . Message-ID: <20100505162252.DAF40185831B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed May 5 12:40:58 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 5 May 2010 12:40:58 -0400 (EDT) Subject: [BioCatalogue-developers] [1913] branches/service-updates-and-curation: Show port info in Soap Operation show page. Message-ID: <20100505164058.D9F48185831F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed May 5 13:05:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 5 May 2010 13:05:42 -0400 (EDT) Subject: [BioCatalogue-developers] [1914] branches/service-updates-and-curation: Service updater work: latest work on fleshing out the sync process. Message-ID: <20100505170542.EFE4C1858320@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed May 5 16:35:18 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 05 May 2010 21:35:18 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getStructureFromMD_Trajectory' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getStructureFromMD_Trajectory' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1165 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed May 5 16:46:40 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 05 May 2010 21:46:40 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:www.bioinfo.uma.es:getAminoAcidSequenceCollection' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:www.bioinfo.uma.es:getAminoAcidSequenceCollection' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/961 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed May 5 21:05:37 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 06 May 2010 02:05:37 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromGenericSequenceToFASTA' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromGenericSequenceToFASTA' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/772 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From jits at cs.man.ac.uk Thu May 6 04:55:36 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 06 May 2010 09:55:36 +0100 Subject: [BioCatalogue-developers] JIRA task list In-Reply-To: <4BE17ED1.1040600@cs.man.ac.uk> References: <4BE17ED1.1040600@cs.man.ac.uk> Message-ID: <4BE28408.30709@cs.man.ac.uk> To add to this... I've been speaking to some of the myGrid folks here about the "sub tasks" mechanism and they say it's a great way of defining an initial task as the high level feature (eg: "Implement service update checker") and then sub tasks for the individual things to be actually implemented (eg: "Implement WSDL sync", "Add 'update service' button to service page", etc). Jits Jiten Bhagat wrote: > Guys, > > I've finally gone through and cleaned up the JIRA task list. > > I've done my best to assign tasks appropriately and also set who > reported them. I have also closed many that have been done. > > Please could you skim through and have a look. If all is okay I would > like to make an announcement on the main list so that the others can know. > > Remember, when creating new tasks: > - please try and use proper sentences, grammar etc wherever possible > (it's only polite! ;-)) > - please make tasks as specific as possible and describe it as much as > possible (eg: instead of "Better REST Services support", split into > tasks like "Implement "endpoint" functionality". > - for bug reports, please put instructions on how to reproduce the bug > (eg: I clicked on this, then clicked on that, etc). > > Cheers, > Jits > > PS: Eric - well done for being the first to start using the JIRA list > properly :-) > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From noreply at rubyforge.org Thu May 6 05:45:20 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 05:45:20 -0400 (EDT) Subject: [BioCatalogue-developers] [1915] branches/service-updates-and-curation: Service updater work: modified the SoapServiceChange model so that the 'changelog' field is now an Array of enntries serialised into the db. Message-ID: <20100506094527.CF87D185831A@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Thu May 6 06:07:32 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 6 May 2010 11:07:32 +0100 Subject: [BioCatalogue-developers] mail for SAB Message-ID: Hi guys, I intend to send the following list on features on the SAB list. Can u take a look to make sure i'm not missing anything, pls? ---------- Main Features ? Release of the BioCatalogue API (http://apidocs.biocatalogue.org) ? Full import of all Embrace registry services ? Support test script for service monitoring ? Revamp the BioCatalogue wiki with a new developer section ? Alpha version of the Taverna-BioCatalogue plug-in ? Better support for describing REST Services. ? A more streamlined UI for browsing SOAP (WSDL) operations and REST endpoints of a service. ? SOAP operations are now directly returned in search. ? Content and curation gathering exercises Events ? BioCatalogue presented (poster) and demo at the Integrative Bioinformatics Symposium in Cambridge (http://www.rothamsted.bbsrc.ac.uk/bab/conf/ib2010/absposters.php) ? The BioCatalogue will be presented at the Embrace workshop in June (http://www.cbs.dtu.dk/courses/embrace/2010-06-02/) ? The BioCatalogue will be presented and demo at ISMB 2010 Citations The BioCatalogue is referenced in the following papers: ? Magallanes: a web services discovery and automatic workflow composition tool (http://ukpmc.ac.uk/articlerender.cgi?artid=1840111) ? Towards the integration of mouse databases (http://hzi.openrepository.com/hzi/handle/10033/96658) ? jORCA: easily integrating bioinformatics Web Services (http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/4/553) -------------- Cheers, 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 Thu May 6 06:34:52 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 6 May 2010 11:34:52 +0100 Subject: [BioCatalogue-developers] service monitoring failing Message-ID: Hi Eric, The WSDL of this service works fine: http://www.biocatalogue.org/services/2628 ... I even tested it in Taverna. However the WSDL monitoring test keeps on failing. Any idea what the problem is? Cheers, 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 Thu May 6 06:41:40 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 06:41:40 -0400 (EDT) Subject: [BioCatalogue-developers] [1916] branches/service-updates-and-curation/app: - implemented basic merge of one ServiceProvider into another Message-ID: <20100506104140.7C2B21858336@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu May 6 08:04:05 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 06 May 2010 13:04:05 +0100 Subject: [BioCatalogue-developers] mail for SAB In-Reply-To: References: Message-ID: <4BE2B035.40704@cs.man.ac.uk> Hi Franck, Features look fine to me. One thing we need to do is correlate this with the actions/ideas raised from the last SAB meeting. As I recall a lot of it was centred around improving search, which we haven't really had the time to do. So we should mention what are planning on doing for this. Cheers, Jits Franck Tanoh wrote: > Hi guys, > > I intend to send the following list on features on the SAB list. Can > u take a look to make sure i'm not missing anything, pls? > > ---------- > Main Features > ? Release of the BioCatalogue API (http://apidocs.biocatalogue.org) > ? Full import of all Embrace registry services > ? Support test script for service monitoring > ? Revamp the BioCatalogue wiki with a new developer section > ? Alpha version of the Taverna-BioCatalogue plug-in > ? Better support for describing REST Services. > ? A more streamlined UI for browsing SOAP (WSDL) operations and REST > endpoints of a service. > ? SOAP operations are now directly returned in search. > ? Content and curation gathering exercises > > Events > ? BioCatalogue presented (poster) and demo at the Integrative > Bioinformatics Symposium in Cambridge > (http://www.rothamsted.bbsrc.ac.uk/bab/conf/ib2010/absposters.php) > ? The BioCatalogue will be presented at the Embrace workshop in June > (http://www.cbs.dtu.dk/courses/embrace/2010-06-02/) > ? The BioCatalogue will be presented and demo at ISMB 2010 > > Citations > The BioCatalogue is referenced in the following papers: > ? Magallanes: a web services discovery and automatic workflow > composition tool (http://ukpmc.ac.uk/articlerender.cgi?artid=1840111) > ? Towards the integration of mouse databases > (http://hzi.openrepository.com/hzi/handle/10033/96658) > ? jORCA: easily integrating bioinformatics Web Services > (http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/4/553) > > -------------- > > Cheers, > Franck > > From ericnzuo at ebi.ac.uk Thu May 6 08:19:34 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 06 May 2010 13:19:34 +0100 Subject: [BioCatalogue-developers] service monitoring failing In-Reply-To: References: Message-ID: <4BE2B3D6.40006@ebi.ac.uk> It is bec of the http code returned from access that wsdl. I am not sure if I should include 301 status code as a success. Eric curl -I --max-time 20 -X GET http://quebec.chebi.bio2rdf.org/wsdl HTTP/1.1 301 Moved Permanently Date: Thu, 06 May 2010 12:22:27 GMT Server: Virtuoso/06.01.3126 (Linux) x86_64-unknown-linux-gnu Content-Type: text/html; charset=UTF-8 Accept-Ranges: bytes Location: /wsdl/ Content-Length: 0 Connection: close Franck Tanoh wrote: > Hi Eric, > > The WSDL of this service works fine: > http://www.biocatalogue.org/services/2628 ... I even tested it in > Taverna. > However the WSDL monitoring test keeps on failing. Any idea what the > problem is? > > Cheers, > 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 jits at cs.man.ac.uk Thu May 6 08:24:49 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 06 May 2010 13:24:49 +0100 Subject: [BioCatalogue-developers] service monitoring failing In-Reply-To: <4BE2B3D6.40006@ebi.ac.uk> References: <4BE2B3D6.40006@ebi.ac.uk> Message-ID: <4BE2B511.2040506@cs.man.ac.uk> Eric, 3xx codes are redirects. They are VERY important (part of the web's successful architecture) and MUST be followed to see if the redirected location is alive too. Redirects can also have redirects, so it could be recursive. Cheers, Jits Eric Nzuobontane wrote: > It is bec of the http code returned from access that wsdl. I am not > sure if I should include 301 status code as a success. > > Eric > > > curl -I --max-time 20 -X GET http://quebec.chebi.bio2rdf.org/wsdl > HTTP/1.1 301 Moved Permanently > Date: Thu, 06 May 2010 12:22:27 GMT > Server: Virtuoso/06.01.3126 (Linux) x86_64-unknown-linux-gnu > Content-Type: text/html; charset=UTF-8 > Accept-Ranges: bytes > Location: /wsdl/ > Content-Length: 0 > Connection: close > > > > > Franck Tanoh wrote: > > >> Hi Eric, >> >> The WSDL of this service works fine: >> http://www.biocatalogue.org/services/2628 ... I even tested it in >> Taverna. >> However the WSDL monitoring test keeps on failing. Any idea what the >> problem is? >> >> Cheers, >> Franck >> >> > > From jits at cs.man.ac.uk Thu May 6 08:26:04 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 06 May 2010 13:26:04 +0100 Subject: [BioCatalogue-developers] service monitoring failing In-Reply-To: <4BE2B3D6.40006@ebi.ac.uk> References: <4BE2B3D6.40006@ebi.ac.uk> Message-ID: <4BE2B55C.4080608@cs.man.ac.uk> Also, a 301 "moved permanently" means that we should update the location in our database (as the name suggests, it has moved permanently to a new location). Could be that the monitoring updates the SoapService#wsdl_location in cases like these? Have to make sure we do this in a non-breaking/managed way. Jits Eric Nzuobontane wrote: > It is bec of the http code returned from access that wsdl. I am not > sure if I should include 301 status code as a success. > > Eric > > > curl -I --max-time 20 -X GET http://quebec.chebi.bio2rdf.org/wsdl > HTTP/1.1 301 Moved Permanently > Date: Thu, 06 May 2010 12:22:27 GMT > Server: Virtuoso/06.01.3126 (Linux) x86_64-unknown-linux-gnu > Content-Type: text/html; charset=UTF-8 > Accept-Ranges: bytes > Location: /wsdl/ > Content-Length: 0 > Connection: close > > > > > Franck Tanoh wrote: > > >> Hi Eric, >> >> The WSDL of this service works fine: >> http://www.biocatalogue.org/services/2628 ... I even tested it in >> Taverna. >> However the WSDL monitoring test keeps on failing. Any idea what the >> problem is? >> >> Cheers, >> Franck >> >> > > From noreply at rubyforge.org Thu May 6 09:36:38 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 09:36:38 -0400 (EDT) Subject: [BioCatalogue-developers] [1917] branches/service-updates-and-curation: - add validation to ServiceProvider model Message-ID: <20100506133638.C63C418582FF@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 6 09:36:57 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 09:36:57 -0400 (EDT) Subject: [BioCatalogue-developers] [1918] branches/service-updates-and-curation/app/views: Textual changes in the UI to clarify SOAP Operations and REST Enpoints. Message-ID: <20100506133657.EABAA1858323@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 6 10:21:16 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 10:21:16 -0400 (EDT) Subject: [BioCatalogue-developers] [1919] branches/service-updates-and-curation: [BIOCAT-315] Integrated the fix for Hash#from_xml as provided by Tod Jackson ( Emory University) and updated the legacy WSDL parser to use this. Message-ID: <20100506142116.42E1B1858336@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 6 11:04:16 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 11:04:16 -0400 (EDT) Subject: [BioCatalogue-developers] [1920] branches/service-updates-and-curation: Improvements to the Service listings - moved the annotations counts box down so that there is more room for the name of the service . Message-ID: <20100506150417.110C21858340@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 6 11:28:54 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 11:28:54 -0400 (EDT) Subject: [BioCatalogue-developers] [1921] branches/service-updates-and-curation: Nicer and more standards compliant styling for the annotations counts box. Message-ID: <20100506152854.DEE251D799BC@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 6 11:32:56 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 11:32:56 -0400 (EDT) Subject: [BioCatalogue-developers] [1922] branches/web-service-ownership: removed the redundant responsible. rb module and re-factored function to return all responsibles for service Message-ID: <20100506153256.45747185833B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 6 11:39:40 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 11:39:40 -0400 (EDT) Subject: [BioCatalogue-developers] [1923] branches/service-updates-and-curation/app: - updated indexes for RestParameter and RestRepresentation Message-ID: <20100506153940.47DD1185833B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 6 12:28:21 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 12:28:21 -0400 (EDT) Subject: [BioCatalogue-developers] [1924] branches/service-updates-and-curation/app/models/rest_method.rb: Applied RestMethod comparator operator fix from trunk. Message-ID: <20100506162821.BB0DA1678217@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 6 12:38:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 12:38:14 -0400 (EDT) Subject: [BioCatalogue-developers] [1925] branches/service-updates-and-curation/app/views: Fixed the listings partial for RestMethods - it was expecting a collection of RestResources instead of following the convention of expecting a list of the objects of the type the listing is for (ie: RestMethod in this case). Message-ID: <20100506163814.7105B18582D2@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 6 13:03:31 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 13:03:31 -0400 (EDT) Subject: [BioCatalogue-developers] [1926] branches/service-updates-and-curation/app/views/rest_methods/ _listing.html.erb: Better handling of the "base_endpoint" and "resource" local variables in cases where these can' t be provided easily into the listings partial. Message-ID: <20100506170331.8CE531858347@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu May 6 13:04:01 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 06 May 2010 18:04:01 +0100 Subject: [BioCatalogue-developers] Important: refactorings for REST methods listings partial Message-ID: <4BE2F681.6000408@cs.man.ac.uk> Hi Mannie, I'm trying to implement the Rest Endpoints returning in search results... Please could you take a very close look at commits 1925 and 1926 - I have made some refactorings for the rest_methods listings partial. The commit messages should explain why :-) I need to you take a look and make sure this is okay and that it doesn't break anything else for the REST services support. Also, for the search results I always get "Could not generate URL template" for each endpoint returned, even though the partial is correctly getting the base_endpoint. Please could you investigate why this is happening and fix it. Note for next time: in order to be able to reuse the listings partials (eg: 'rest_methods/listing') in other places, like search results, they MUST follow a convention whereby they expect a list of items of the type the listing is about AND they must only require one local variable to be passed in - the aforementioned items collection. In the refactorings mentioned above I have kept your previous logic but added checks for when things like base_endpoint and resource can't be passed in. Cheers, Jits From noreply at rubyforge.org Thu May 6 13:46:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 13:46:08 -0400 (EDT) Subject: [BioCatalogue-developers] [1927] branches/service-updates-and-curation: Intial work on getting RestMethods returned in search. Message-ID: <20100506174608.2C1211858346@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 6 13:53:39 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 13:53:39 -0400 (EDT) Subject: [BioCatalogue-developers] [1928] branches/service-updates-and-curation/app/models/rest_resource.rb: Applied RestResource comparator operator fix from trunk. Message-ID: <20100506175339.1E081185834A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 6 13:56:35 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 6 May 2010 13:56:35 -0400 (EDT) Subject: [BioCatalogue-developers] [1929] branches/service-updates-and-curation: More work on getting RestMethods returned in search: Message-ID: <20100506175635.F40511858343@rubyforge.org> An HTML attachment was scrubbed... URL: From mannie.tags at googlemail.com Fri May 7 05:33:58 2010 From: mannie.tags at googlemail.com (Mannie Tagarira) Date: Fri, 7 May 2010 10:33:58 +0100 Subject: [BioCatalogue-developers] Important: refactorings for REST methods listings partial In-Reply-To: <4BE2F681.6000408@cs.man.ac.uk> References: <4BE2F681.6000408@cs.man.ac.uk> Message-ID: <7C4A919F-66A6-4895-9590-F08F052FAD13@gmail.com> Hi Jits, On 6 May 2010, at 18:04, Jiten Bhagat wrote: > Hi Mannie, > > I'm trying to implement the Rest Endpoints returning in search > results... > > Please could you take a very close look at commits 1925 and 1926 - I > have made some refactorings for the rest_methods listings partial. The > commit messages should explain why :-) > > I need to you take a look and make sure this is okay and that it > doesn't > break anything else for the REST services support. Okay, I will do so... > Also, for the search results I always get "Could not generate URL > template" for each endpoint returned, even though the partial is > correctly getting the base_endpoint. Please could you investigate why > this is happening and fix it. Hmm, I will look into this and report back when I have found and fixed the bug... > Note for next time: in order to be able to reuse the listings partials > (eg: 'rest_methods/listing') in other places, like search results, > they > MUST follow a convention whereby they expect a list of items of the > type > the listing is about AND they must only require one local variable > to be > passed in - the aforementioned items collection. In the refactorings > mentioned above I have kept your previous logic but added checks for > when things like base_endpoint and resource can't be passed in. Thanks, I will keep this in mind for next time... > Cheers, > Jits Mannie From jits at cs.man.ac.uk Fri May 7 06:32:12 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 07 May 2010 11:32:12 +0100 Subject: [BioCatalogue-developers] [Production ERROR] services#index (ActionView::TemplateError) "undefined method `activated_at' for \"#\":TestScript" In-Reply-To: <4be3e8ee6b7c8_2a6a15a7c5afffc81a5@pweb-3b.ebi.ac.uk.tmail> References: <4be3e8ee6b7c8_2a6a15a7c5afffc81a5@pweb-3b.ebi.ac.uk.tmail> Message-ID: <4BE3EC2C.6020403@cs.man.ac.uk> Eric, Please could you investigate this - I thought I had fixed this for last week's release but it seems like something is still not fixed in the XML output, after the activation refactorings you did. The problem is with this line (line 23 in app/views/test_scripts/api/_test_script.xml.builder): > parent_xml.activatedAt test_script.activated_at.iso8601 Please could you fix this asap and deploy to the live site, as it has broken the API :-( Jits BioCatalogue Errors wrote: > A ActionView::TemplateError occurred in services#index: > > undefined method `activated_at' for "#":TestScript > On line #38 of app/views/test_scripts/api/_test_script.xml.builder > > 35: > 36: # > 37: if test_script.activated? > 38: parent_xml.activatedAt test_script.activated_at.iso8601 > 39: else > 40: parent_xml.activatedAt nil, "xsi:nil" => "true" > 41: end > > app/views/test_scripts/api/_test_script.xml.builder:38:in `_run_builder_app47views47test_scripts47api47_test_script46xml46builder_locals_object_parent_xml_test_script' > app/views/test_scripts/api/_test_script.xml.builder:8:in `_run_builder_app47views47test_scripts47api47_test_script46xml46builder_locals_object_parent_xml_test_script' > app/views/service_tests/api/_core_elements.xml.builder:9:in `_run_builder_app47views47service_tests47api47_core_elements46xml46builder_locals_core_elements_object_parent_xml_service_test' > app/views/service_tests/api/_core_elements.xml.builder:8:in `_run_builder_app47views47service_tests47api47_core_elements46xml46builder_locals_core_elements_object_parent_xml_service_test' > app/views/service_tests/api/_service_test.xml.builder:21:in `_run_builder_app47views47service_tests47api47_service_test46xml46builder_locals_is_root_object_parent_xml_service_test_show_ancestors_show_latest_status_show_related' > app/views/service_tests/api/_service_test.xml.builder:15:in `_run_builder_app47views47service_tests47api47_service_test46xml46builder_locals_is_root_object_parent_xml_service_test_show_ancestors_show_latest_status_show_related' > app/views/service_tests/api/_inline_item.xml.builder:14:in `_run_builder_app47views47service_tests47api47_inline_item46xml46builder_locals_inline_item_object_parent_xml_service_test' > app/views/services/api/_monitoring.xml.builder:16:in `_run_builder_app47views47services47api47_monitoring46xml46builder_locals_monitoring_object_parent_xml_service' > app/views/services/api/_monitoring.xml.builder:15:in `_run_builder_app47views47services47api47_monitoring46xml46builder_locals_monitoring_object_parent_xml_service' > app/views/services/api/_monitoring.xml.builder:13:in `_run_builder_app47views47services47api47_monitoring46xml46builder_locals_monitoring_object_parent_xml_service' > app/views/services/api/_monitoring.xml.builder:8:in `_run_builder_app47views47services47api47_monitoring46xml46builder_locals_monitoring_object_parent_xml_service' > app/views/services/api/_service.xml.builder:43:in `_run_builder_app47views47services47api47_service46xml46builder_locals_object_parent_xml_service_show_deployments_show_monitoring_show_related_show_summary_show_variants' > app/views/services/api/_service.xml.builder:17:in `_run_builder_app47views47services47api47_service46xml46builder_locals_object_parent_xml_service_show_deployments_show_monitoring_show_related_show_summary_show_variants' > app/views/services/api/_result_item.xml.builder:15:in `_run_builder_app47views47services47api47_result_item46xml46builder_locals_object_parent_xml_result_item_service' > app/views/services/index.xml.builder:52:in `_run_builder_app47views47services47index46xml46builder' > app/views/services/index.xml.builder:51:in `each' > app/views/services/index.xml.builder:51:in `_run_builder_app47views47services47index46xml46builder' > app/views/services/index.xml.builder:48:in `_run_builder_app47views47services47index46xml46builder' > app/views/services/index.xml.builder:11:in `_run_builder_app47views47services47index46xml46builder' > app/controllers/services_controller.rb:36:in `index' > passenger (2.2.4) lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' > passenger (2.2.4) lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in `safe_fork' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in `start' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > > ------------------------------- > Request: > ------------------------------- > > * URL : http://www.biocatalogue.org/services.xml?per_page=50&include=all&page=1 > * Method : GET > * IP address: 150.214.45.1 > * Parameters: {"format"=>"xml", "action"=>"index", "controller"=>"services", "per_page"=>"50", "include"=>"all", "page"=>"1"} > * 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 : text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 > * HTTP_ACCEPT_CHARSET : ISO-8859-1,utf-8;q=0.7,*;q=0.7 > * HTTP_ACCEPT_ENCODING : gzip,deflate > * HTTP_ACCEPT_LANGUAGE : es-es,es;q=0.8,en-us;q=0.5,en;q=0.3 > * HTTP_CONNECTION : keep-alive > * HTTP_COOKIE : _session_id=13a0d630d10428bd5a140239927b25b9; __utma=15951013.840227249.1273222774.1273222774.1273227210.2; __utmc=15951013; __utmz=15951013.1273222774.1.1.utmcsr=embraceregistry.net|utmccn=(referral)|utmcmd=referral|utmcct=/; __utmb=15951013.2.10.1273227210 > * HTTP_HOST : www.biocatalogue.org > * HTTP_KEEP_ALIVE : 300 > * HTTP_USER_AGENT : Mozilla/5.0 (Windows; U; Windows NT 5.1; es-ES; rv:1.9.1.8) Gecko/20100202 Firefox/3.5.8 > * HTTP_X_CLUSTER_CLIENT_IP : 150.214.45.1 > * PATH_INFO : /services.xml > * QUERY_STRING : per_page=50&include=all&page=1 > * REMOTE_ADDR : 150.214.45.1 > * REMOTE_PORT : 36987 > * REQUEST_METHOD : GET > * REQUEST_URI : /services.xml?per_page=50&include=all&page=1 > * 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 : per_page50page1includeall > * 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.cookie_hash : __utma15951013.840227249.1273222774.1273222774.1273227210.2__utmb15951013.2.10.1273227210_session_id13a0d630d10428bd5a140239927b25b9__utmc15951013__utmz15951013.1273222774.1.1.utmcsr=embraceregistry.net|utmccn=(referral)|utmcmd=referral|utmcct=/ > * rack.request.cookie_string : _session_id=13a0d630d10428bd5a140239927b25b9; __utma=15951013.840227249.1273222774.1273222774.1273227210.2; __utmc=15951013; __utmz=15951013.1273222774.1.1.utmcsr=embraceregistry.net|utmccn=(referral)|utmcmd=referral|utmcct=/; __utmb=15951013.2.10.1273227210 > * rack.request.query_hash : per_page50page1includeall > * rack.request.query_string : per_page=50&include=all&page=1 > * rack.routing_args : formatxmlactionindexcontrollerservices > * rack.run_once : false > * rack.session : search_show_listing_typesimpleuse_tab_cookiefalse_csrf_tokenu7dXBmvgiXtqSHp09+0cum5C0wj/wqwJJ3p/KGrABbs=services_index_listing_typedetailedflashprevious_url/soap_services/2 > * rack.session.options : expire_aftersecurefalsehttponlytruecookie_onlytruekey_session_idid13a0d630d10428bd5a140239927b25b9domainpath/ > * rack.session.record : # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 10858 > * Server : pweb-3b > > * request.format: application/xml > > ------------------------------- > Backtrace: > ------------------------------- > > On line #38 of app/views/test_scripts/api/_test_script.xml.builder > > 35: > 36: # > 37: if test_script.activated? > 38: parent_xml.activatedAt test_script.activated_at.iso8601 > 39: else > 40: parent_xml.activatedAt nil, "xsi:nil" => "true" > 41: end > > app/views/test_scripts/api/_test_script.xml.builder:38:in `_run_builder_app47views47test_scripts47api47_test_script46xml46builder_locals_object_parent_xml_test_script' > app/views/test_scripts/api/_test_script.xml.builder:8:in `_run_builder_app47views47test_scripts47api47_test_script46xml46builder_locals_object_parent_xml_test_script' > app/views/service_tests/api/_core_elements.xml.builder:9:in `_run_builder_app47views47service_tests47api47_core_elements46xml46builder_locals_core_elements_object_parent_xml_service_test' > app/views/service_tests/api/_core_elements.xml.builder:8:in `_run_builder_app47views47service_tests47api47_core_elements46xml46builder_locals_core_elements_object_parent_xml_service_test' > app/views/service_tests/api/_service_test.xml.builder:21:in `_run_builder_app47views47service_tests47api47_service_test46xml46builder_locals_is_root_object_parent_xml_service_test_show_ancestors_show_latest_status_show_related' > app/views/service_tests/api/_service_test.xml.builder:15:in `_run_builder_app47views47service_tests47api47_service_test46xml46builder_locals_is_root_object_parent_xml_service_test_show_ancestors_show_latest_status_show_related' > app/views/service_tests/api/_inline_item.xml.builder:14:in `_run_builder_app47views47service_tests47api47_inline_item46xml46builder_locals_inline_item_object_parent_xml_service_test' > app/views/services/api/_monitoring.xml.builder:16:in `_run_builder_app47views47services47api47_monitoring46xml46builder_locals_monitoring_object_parent_xml_service' > app/views/services/api/_monitoring.xml.builder:15:in `_run_builder_app47views47services47api47_monitoring46xml46builder_locals_monitoring_object_parent_xml_service' > app/views/services/api/_monitoring.xml.builder:13:in `_run_builder_app47views47services47api47_monitoring46xml46builder_locals_monitoring_object_parent_xml_service' > app/views/services/api/_monitoring.xml.builder:8:in `_run_builder_app47views47services47api47_monitoring46xml46builder_locals_monitoring_object_parent_xml_service' > app/views/services/api/_service.xml.builder:43:in `_run_builder_app47views47services47api47_service46xml46builder_locals_object_parent_xml_service_show_deployments_show_monitoring_show_related_show_summary_show_variants' > app/views/services/api/_service.xml.builder:17:in `_run_builder_app47views47services47api47_service46xml46builder_locals_object_parent_xml_service_show_deployments_show_monitoring_show_related_show_summary_show_variants' > app/views/services/api/_result_item.xml.builder:15:in `_run_builder_app47views47services47api47_result_item46xml46builder_locals_object_parent_xml_result_item_service' > app/views/services/index.xml.builder:52:in `_run_builder_app47views47services47index46xml46builder' > app/views/services/index.xml.builder:51:in `each' > app/views/services/index.xml.builder:51:in `_run_builder_app47views47services47index46xml46builder' > app/views/services/index.xml.builder:48:in `_run_builder_app47views47services47index46xml46builder' > app/views/services/index.xml.builder:11:in `_run_builder_app47views47services47index46xml46builder' > app/controllers/services_controller.rb:36:in `index' > passenger (2.2.4) lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' > passenger (2.2.4) lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in `safe_fork' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in `start' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > > > From noreply at rubyforge.org Fri May 7 07:02:10 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 7 May 2010 07:02:10 -0400 (EDT) Subject: [BioCatalogue-developers] [1930] trunk/app/models/test_script.rb: bugfix : added activated_at method to test script Message-ID: <20100507110210.8802F1D799C1@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 7 10:49:05 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 7 May 2010 10:49:05 -0400 (EDT) Subject: [BioCatalogue-developers] [1931] branches/service-updates-and-curation: - pulled in bug fix for url template from trunk Message-ID: <20100507144905.23B311858322@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 7 11:46:28 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 7 May 2010 11:46:28 -0400 (EDT) Subject: [BioCatalogue-developers] [1932] branches/service-updates-and-curation/app/models: - moved the after_destroy validation from the Service model to the ServiceDeployment model Message-ID: <20100507154628.C62871D799BD@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Sat May 8 18:08:41 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 08 May 2010 23:08:41 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToMD_TrajectoryCRD' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToMD_TrajectoryCRD' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1120 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 May 8 20:30:55 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 09 May 2010 01:30:55 +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 May 9 07:39:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 09 May 2010 12:39:10 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMatScanGFFCollection' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMatScanGFFCollection' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/777 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun May 9 08:43:41 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 09 May 2010 13:43:41 +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 May 9 10:45:41 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 09 May 2010 15:45:41 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromFASTA' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromFASTA' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/996 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 May 10 07:27:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 10 May 2010 12:27:28 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:cnio.es:runFASS' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:cnio.es:runFASS' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/980 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon May 10 07:27:29 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 10 May 2010 12:27:29 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'DASxVO' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'DASxVO' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/206 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 May 10 08:07:44 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 10 May 2010 13:07:44 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPHDFromAminoAcidSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPHDFromAminoAcidSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1001 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 May 10 08:26:09 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 10 May 2010 13:26:09 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: Services dead?] Message-ID: <4BE7FB61.4090701@ebi.ac.uk> Hi Guys, Here is a request for ownership/responsibility for a number of services. This would have been a good test for the ownership work but I am not sure if I should ask them to wait so that we can get this work into production. Basically, I think I am ready to merge but given that there needs to be testing afterwards, I may just go ahead and change the submitter in place. What do you think? 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 ================================== -------------- next part -------------- An embedded message was scrubbed... From: Christelle Eloto Subject: Re: Services dead? Date: Fri, 07 May 2010 12:52:22 +0200 Size: 6962 URL: From ytanoh at cs.man.ac.uk Mon May 10 09:21:10 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 10 May 2010 14:21:10 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: Services dead?] In-Reply-To: <4BE7FB61.4090701@ebi.ac.uk> References: <4BE7FB61.4090701@ebi.ac.uk> Message-ID: Hi Eric, We can't afford to make them wait so as far as i'm concerned change the submitter manually for now. We still have the EBI services to use as test for the ownership work when it's ready. Franck On 10 May 2010 13:26, Eric Nzuobontane wrote: > Hi Guys, > > Here is a request for ownership/responsibility for a number of services. > This would have been a good test for the ownership work but I am not sure if > I should ask them to wait so that we can get this work into production. > Basically, I think I am ready to merge but given that there needs to be > testing afterwards, I may just go ahead and change the submitter in place. > What do you think? > > 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 > ================================== > > > Hi, > > Could you give me the "write" access on the 14 services of CNRS IBCP (listed > below) ? My Embrace registry login is CELOTO and the login of my account > BioCatalogue is CHRISTELLE.ELOTO at IBCP.FR. > > PREDATOR protein secondary structure prediction > GOR III protein secondary structure prediction > DSC protein secondary structure prediction > GOR I protein secondary structure prediction > PcProf predict physico-chemical profiles of proteins > SIMPA protein secondary structure prediction > COILS predict protein coiled-coil regions > CLUSTAL W multiple alignment > MultAlin multiple alignment > CONSENSUS of protein secondary structure prediction > BLAST blastp protein similarity search > GOR IV protein secondary structure prediction > SSearch protein similarity search > FASTA protein similarity search > > Thanks in advance, > Christelle > > -- > Christelle Eloto > > Institut de Biologie et Chimie des Prot?ines - ?CNRS UMR5086 > christelle.eloto at ibcp.fr > > > > On 4/05/10 11:21, Eric Nzuobontane wrote: >> >> Hi Christophe & Christelle, >> >> The EMBRACE registry is being merged with the BioCatalogue registry, >> meaning every service in EMBRACE will be available in BioCatalogue. It would >> make sense for Christelle to create an account BioCatalogue ?as well so that >> we can eventually assign all your services to her. >> http://www.biocatalogue.org/signup >> >> It should be straight forward to sign up but should you encounter any >> problems please let us know. >> >> Eric >> >> >> >> Christophe Blanchet wrote: >>> >>> Dear Eric and Steve, >>> >>> Could you create an account for Christelle ELOTO (in copy) on the EMBRACE >>> registry, and give her the "write" access on the 14 services that we have >>> registered. She will look for the troubles and fix them. >>> >>> Best wishes >>> Christophe >>> >>> Le 27 avr. 2010 ? 11:43, Christophe Blanchet a ?crit : >>> >>> >>>> >>>> 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 >>>> >>>> >>>> >>> >>> -- >>> Dr Christophe BLANCHET ? ? ? ? ? ? ? ? ? ?CNRS, France >>> Institut de Biologie et Chimie des Proteines ? ? ? ?IBCP >>> Christophe.Blanchet at ibcp.fr ? ? ? ? http://gbio-pbil.ibcp.fr/cblanchet > > _______________________________________________ > 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 May 10 09:35:09 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 10 May 2010 14:35:09 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'DASxVO' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'DASxVO' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/206 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon May 10 11:43:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 10 May 2010 16:43:06 +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 Mon May 10 16:07:41 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 10 May 2010 21:07:41 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runSGP2GFF' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runSGP2GFF' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/770 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon May 10 16:19:37 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 10 May 2010 21:19:37 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMatScanGFF' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMatScanGFF' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/776 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon May 10 19:52:38 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 11 May 2010 00:52:38 +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 Mon May 10 19:59:32 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 11 May 2010 00:59:32 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:translateGeneIDGFFPredictions' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:translateGeneIDGFFPredictions' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/768 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue May 11 01:03:24 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 11 May 2010 06:03:24 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parseFeatureAASequenceFromPMUTText' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parseFeatureAASequenceFromPMUTText' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/997 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue May 11 02:15:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 11 May 2010 07:15:10 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:parseMotifMatricesFromMEME' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:parseMotifMatricesFromMEME' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/775 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue May 11 04:15:58 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 11 May 2010 04:15:58 -0400 (EDT) Subject: [BioCatalogue-developers] [1933] trunk/test: updated REST support functional and unit tests Message-ID: <20100511081558.3ED4D16782A0@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue May 11 08:47:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 11 May 2010 13:47:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-319) Add /soap_services/wsdl_locations to XML Schema for REST API Message-ID: <32175098.1.1273582037157.JavaMail.jira@rosalind.cs.man.ac.uk> Add /soap_services/wsdl_locations to XML Schema for REST API ------------------------------------------------------------ Key: BIOCAT-319 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-319 Project: BioCatalogue Issue Type: Task Components: REST API Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Minor -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue May 11 08:51:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 11 May 2010 13:51:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-320) Add /soap_services/wsdl_locations to REST API documentation Message-ID: <5755038.2.1273582277250.JavaMail.jira@rosalind.cs.man.ac.uk> Add /soap_services/wsdl_locations to REST API documentation ----------------------------------------------------------- Key: BIOCAT-320 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-320 Project: BioCatalogue Issue Type: Task Components: REST API Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Minor -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue May 11 09:04:31 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 11 May 2010 09:04:31 -0400 (EDT) Subject: [BioCatalogue-developers] [1934] trunk: REST API work: implemented /soap_services/wsdl_locations, as requested by Javier Rios. Message-ID: <20100511130432.60B8A185831E@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue May 11 11:20:04 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 11 May 2010 16:20:04 +0100 Subject: [BioCatalogue-developers] [Fwd: [MYGRID] Upgraded jira and wiki] Message-ID: <4BE975A4.2@cs.man.ac.uk> FYI -------- Original Message -------- Subject: [MYGRID] Upgraded jira and wiki Date: Tue, 11 May 2010 14:54:29 +0100 From: Stian Soiland-Reyes Reply-To: mygrid at listserv.manchester.ac.uk To: MYGRID at listserv.manchester.ac.uk hi! I've upgraded our installations of Jira and Confluence. Atlassian has kindly renewed our free licences for open source projects. See http://www.mygrid.org.uk/dev/wiki/ and http://www.mygrid.org.uk/dev/issues/ - and report to me if something is not working as expected. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From jits at cs.man.ac.uk Tue May 11 11:30:40 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 11 May 2010 16:30:40 +0100 Subject: [BioCatalogue-developers] About the BioCatalogue API In-Reply-To: <4BE96DD0.5020705@cs.man.ac.uk> References: <4BE80538.8050502@uma.es> <4BE95BFC.7080800@cs.man.ac.uk> <4BE96C5F.2050407@uma.es> <4BE96DD0.5020705@cs.man.ac.uk> Message-ID: <4BE97820.2050008@cs.man.ac.uk> Hi Javier, Good news! The live site has been updated. You may use this new, faster API call for your purposes now :-) Let us know if there's anything else we can help with. Cheers, Jits Jiten Bhagat wrote: > Hi Javier, > > Great! I'll see what we can do about getting the new API endpoint on to > the live site (hopefully within next couple of days). We'll release it > as a "hidden" endpoint just for your use (I will need to eventually add > it to the schema and documentation, if others find it useful). > > I'll let you know when it goes live. > > Cheers, > Jits > > > Javier Rios wrote: > >> Hi, >> >> Thanks a lot for the fast response. >> >> The first call works very well for me, really the second one is faster >> and provides me all the info that currently I need. >> >> Could you implement the second call to the main BioCatalogue repository? >> Currently it's enough with the first call, but I want to be faster. >> >> Kind Regards, >> Javier >> >> El 11/05/2010 15:30, Jiten Bhagat escribi?: >> >>> Hi Javier, >>> >>> Thanks for the suggestion. >>> >>> This... >>> >>> >>> >>>> http://www.biocatalogue.org/services.xml?t=[SOAP]&per_page=50&page=&include=variants >>>> >>>> >>>> >>> ... should get back the information you need. But I can see that you >>> need a far more efficient way of getting just the list of WSDL >>> locations. >>> >>> Can you try this please: >>> >>> http://sandbox.biocatalogue.org/soap_services/wsdl_locations.xml >>> >>> (database last updated from the live site on April 28th) >>> >>> Is this the kind of thing you need? >>> >>> Cheers, >>> Jits >>> >>> >>> >>> Javier Rios wrote: >>> >>> >>>> Hi, >>>> >>>> I'm starting to use the BioCatalogue REST API and I have a request for >>>> you. >>>> >>>> Could be a way to retrieve all the WSDL locations on one query? >>>> >>>> For now I need to go page per page getting the services' id and then >>>> get all the service info. If there is 30 pages with 50 services each >>>> one, I'll do about 1530 API calls. But if you add the WSDL location to >>>> the info retrieve on search I only will need 30 calls. >>>> >>>> The calls I do are: >>>> 1. >>>> http://www.biocatalogue.org/services.xml?t=[SOAP]&per_page=50&page= >>>> >>>> >>>> 2. http://www.biocatalogue.org/services/.xml >>>> >>>> Maybe a solution will be something like: >>>> http://www.biocatalogue.org/services.xml?t=[SOAP]&per_page=50&page=&include=variants >>>> >>>> >>>> >>>> Thanks a lot, >>>> Javier >>>> >>>> >>> >>> > > > From ericnzuo at ebi.ac.uk Tue May 11 11:33:30 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 11 May 2010 16:33:30 +0100 Subject: [BioCatalogue-developers] FYI Message-ID: <4BE978CA.8030305@ebi.ac.uk> the following files have been updated on the live site to fulfill user request and fix a bug: config/routes.rb app/models/test_script.rb app/controllers/soap_services.controller app/views/soap_services/wsdl_locations.xml.builder -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From issues at mygrid.org.uk Tue May 11 11:50:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 11 May 2010 16:50:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-321) Fix cronolog log rotation problem Message-ID: <15149277.3.1273593017551.JavaMail.jira@rosalind.cs.man.ac.uk> Fix cronolog log rotation problem --------------------------------- Key: BIOCAT-321 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-321 Project: BioCatalogue Issue Type: Bug Components: Misc Codebase Environment: biocatalogue production environment(RoR) Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Cronolog is used on the live server to rotate logs. This makes log files management and archiving easier by preventing longs from getting excessively large. The production environment file was updated with configuration parameter enable the use of cronolog but this does not seem to be working properly. Files affected: config/environments/production.rb -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue May 11 12:07:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 11 May 2010 17:07:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-305) Allow users to take ownership/claim responsibility of services Message-ID: <8052961.4.1273594037053.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-305?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-305 started by Eric Nzuobontane. > Allow users to take ownership/claim responsibility of services > -------------------------------------------------------------- > > Key: BIOCAT-305 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-305 > Project: BioCatalogue > Issue Type: New Feature > Components: Service Container > Environment: RoR > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Allow people that did not submit services to the given the permissions to manage the service entries in BioCatalogue -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue May 11 12:13:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 11 May 2010 17:13:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-307) Implement SoapService WSDL sync process Message-ID: <26729561.5.1273594397004.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-307?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-307 started by Jiten Bhagat. > Implement SoapService WSDL sync process > --------------------------------------- > > Key: BIOCAT-307 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-307 > Project: BioCatalogue > Issue Type: Sub-task > Components: SOAP Services Support > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Original Estimate: 3 days > Remaining Estimate: 3 days > > As part of the service update checker work, the SoapService model needs to have a special update method that syncs the current model state with the latest WSDL. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue May 11 12:42:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 11 May 2010 12:42:47 -0400 (EDT) Subject: [BioCatalogue-developers] [1935] branches/service-updates-and-curation/app/models/soap_service.rb: Service update checker work: initial, complete sync method for the SoapService model. Message-ID: <20100511164247.4269A1D799BA@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue May 11 13:15:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 11 May 2010 18:15:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-322) Show "archived operations/inputs/outputs" in UI Message-ID: <20270271.6.1273598117035.JavaMail.jira@rosalind.cs.man.ac.uk> Show "archived operations/inputs/outputs" in UI ----------------------------------------------- Key: BIOCAT-322 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-322 Project: BioCatalogue Issue Type: Sub-task Reporter: Jiten Bhagat Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue May 11 13:27:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 11 May 2010 18:27:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-323) Show archived things in greyed out box and text (and possibly collapsed) Message-ID: <13694223.7.1273598836996.JavaMail.jira@rosalind.cs.man.ac.uk> Show archived things in greyed out box and text (and possibly collapsed) ------------------------------------------------------------------------ Key: BIOCAT-323 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-323 Project: BioCatalogue Issue Type: Task Components: Web Interface Reporter: Jiten Bhagat Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue May 11 13:29:25 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 11 May 2010 13:29:25 -0400 (EDT) Subject: [BioCatalogue-developers] [1936] branches/service-updates-and-curation: [BIOCAT-233] Initial implementation of the acts_as_archived mechanism. Message-ID: <20100511172925.BB9F61D799BA@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue May 11 15:11:43 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 11 May 2010 20:11:43 +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 Tue May 11 18:53:36 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 11 May 2010 23:53:36 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runDisruptionPhysicalProperties' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runDisruptionPhysicalProperties' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1020 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue May 11 22:07:41 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 12 May 2010 03:07:41 +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 Wed May 12 00:21:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 12 May 2010 05:21:33 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPSIBlastpFromFASTA' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPSIBlastpFromFASTA' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1005 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Wed May 12 04:49:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 09:49:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-233) Need to take into account old/deprecated/deleted services Message-ID: <28272156.20.1273654157008.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-233?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-233 started by Jiten Bhagat. > Need to take into account old/deprecated/deleted services > --------------------------------------------------------- > > Key: BIOCAT-233 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-233 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 days > Remaining Estimate: 3 days > > From Steve: > "Perhaps a wikipedia-like approach, where something gets marked for > deletion and gets a big warning badge in the meantime, giving people a > chance to comment / complain before it goes in the bin. " -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 04:49:18 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 09:49:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-307) Implement SoapService WSDL sync process Message-ID: <1291217.21.1273654158264.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-307?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-307 stopped by Jiten Bhagat. > Implement SoapService WSDL sync process > --------------------------------------- > > Key: BIOCAT-307 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-307 > Project: BioCatalogue > Issue Type: Sub-task > Components: SOAP Services Support > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Original Estimate: 3 days > Remaining Estimate: 3 days > > As part of the service update checker work, the SoapService model needs to have a special update method that syncs the current model state with the latest WSDL. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 04:51:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 09:51:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-307) Implement SoapService WSDL sync process Message-ID: <28665082.22.1273654277001.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-307?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10320 ] Jiten Bhagat logged work on BIOCAT-307: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-12 09:49 Start Date: 2010-05-12 09:49 Worklog Time Spent: 2 days Work Description: Initial sync algorithm completed. Needs to be tested and then integrated into the UI. Issue Time Tracking ------------------- Remaining Estimate: 1 day (was: 3 days) Time Spent: 2 days > Implement SoapService WSDL sync process > --------------------------------------- > > Key: BIOCAT-307 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-307 > Project: BioCatalogue > Issue Type: Sub-task > Components: SOAP Services Support > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Original Estimate: 3 days > Time Spent: 2 days > Remaining Estimate: 1 day > > As part of the service update checker work, the SoapService model needs to have a special update method that syncs the current model state with the latest WSDL. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 04:53:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 09:53:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-233) Need to take into account old/deprecated/deleted services Message-ID: <21112923.24.1273654397846.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-233?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-233 stopped by Jiten Bhagat. > Need to take into account old/deprecated/deleted services > --------------------------------------------------------- > > Key: BIOCAT-233 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-233 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 days > Remaining Estimate: 3 days > > From Steve: > "Perhaps a wikipedia-like approach, where something gets marked for > deletion and gets a big warning badge in the meantime, giving people a > chance to comment / complain before it goes in the bin. " -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 04:53:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 09:53:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-233) Need to take into account old/deprecated/deleted services Message-ID: <19907988.23.1273654397018.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-233?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14912#action_14912 ] Jiten Bhagat commented on BIOCAT-233: ------------------------------------- Implemented an "acts_as_archived" module. > Need to take into account old/deprecated/deleted services > --------------------------------------------------------- > > Key: BIOCAT-233 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-233 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 days > Remaining Estimate: 3 days > > From Steve: > "Perhaps a wikipedia-like approach, where something gets marked for > deletion and gets a big warning badge in the meantime, giving people a > chance to comment / complain before it goes in the bin. " -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 04:53:18 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 09:53:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-233) Need to take into account old/deprecated/deleted services Message-ID: <6664725.25.1273654398825.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-233?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10321 ] Jiten Bhagat logged work on BIOCAT-233: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-12 09:53 Start Date: 2010-05-11 17:00 Worklog Time Spent: 6 hours Issue Time Tracking ------------------- Remaining Estimate: 2 days, 2 hours (was: 3 days) Time Spent: 6 hours > Need to take into account old/deprecated/deleted services > --------------------------------------------------------- > > Key: BIOCAT-233 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-233 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 days > Time Spent: 6 hours > Remaining Estimate: 2 days, 2 hours > > From Steve: > "Perhaps a wikipedia-like approach, where something gets marked for > deletion and gets a big warning badge in the meantime, giving people a > chance to comment / complain before it goes in the bin. " -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 05:56:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 10:56:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-323) Show archived things in greyed out box and text (and possibly collapsed) In-Reply-To: <13694223.7.1273598836996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26041732.57.1273658177005.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-323?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-323: -------------------------------- Issue Type: Sub-task (was: Task) Parent: BIOCAT-233 > Show archived things in greyed out box and text (and possibly collapsed) > ------------------------------------------------------------------------ > > Key: BIOCAT-323 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-323 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 hours > Remaining Estimate: 3 hours > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 05:58:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 10:58:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-324) Archived services should not be monitored anymore Message-ID: <5845695.58.1273658296994.JavaMail.jira@rosalind.cs.man.ac.uk> Archived services should not be monitored anymore ------------------------------------------------- Key: BIOCAT-324 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-324 Project: BioCatalogue Issue Type: Sub-task Components: Service Monitoring Reporter: Jiten Bhagat Assignee: Eric Nzuobontane Services that are archived should be removed from the monitoring subsystem. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 06:00:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 11:00:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-325) Implement filter for "Archived Services" Message-ID: <2148229.59.1273658417012.JavaMail.jira@rosalind.cs.man.ac.uk> Implement filter for "Archived Services" ---------------------------------------- Key: BIOCAT-325 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-325 Project: BioCatalogue Issue Type: Sub-task Reporter: Jiten Bhagat Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 06:00:18 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 11:00:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-326) Implement option in services listing to ignore archived services Message-ID: <14174500.60.1273658418251.JavaMail.jira@rosalind.cs.man.ac.uk> Implement option in services listing to ignore archived services ---------------------------------------------------------------- Key: BIOCAT-326 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-326 Project: BioCatalogue Issue Type: Sub-task Reporter: Jiten Bhagat Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 06:00:19 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 11:00:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-327) Implement option in search results to ignore archived items Message-ID: <20298642.61.1273658419378.JavaMail.jira@rosalind.cs.man.ac.uk> Implement option in search results to ignore archived items ----------------------------------------------------------- Key: BIOCAT-327 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-327 Project: BioCatalogue Issue Type: Sub-task Reporter: Jiten Bhagat Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:37:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:37:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-328) For items that are archived add a "this is archived" message at the top of the 'show' page for the item Message-ID: <17913058.63.1273667836992.JavaMail.jira@rosalind.cs.man.ac.uk> For items that are archived add a "this is archived" message at the top of the 'show' page for the item ------------------------------------------------------------------------------------------------------- Key: BIOCAT-328 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-328 Project: BioCatalogue Issue Type: Sub-task Reporter: Jiten Bhagat Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:37:19 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:37:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-329) Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI Message-ID: <18542635.64.1273667839433.JavaMail.jira@rosalind.cs.man.ac.uk> Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI ---------------------------------------------------------------------------------- Key: BIOCAT-329 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329 Project: BioCatalogue Issue Type: Sub-task Reporter: Jiten Bhagat Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:34:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:34:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-328) For items that are archived add a "this is archived" message at the top of the 'show' page for the item Message-ID: <19635844.62.1273667656998.JavaMail.jira@rosalind.cs.man.ac.uk> For items that are archived add a "this is archived" message at the top of the 'show' page for the item ------------------------------------------------------------------------------------------------------- Key: BIOCAT-328 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-328 Project: BioCatalogue Issue Type: Sub-task Reporter: Jiten Bhagat Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:39:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:39:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-330) Implement button to allow curators/admins to mark a service as archived Message-ID: <17543975.65.1273667956999.JavaMail.jira@rosalind.cs.man.ac.uk> Implement button to allow curators/admins to mark a service as archived ----------------------------------------------------------------------- Key: BIOCAT-330 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-330 Project: BioCatalogue Issue Type: Sub-task Reporter: Jiten Bhagat Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:41:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:41:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Deleted: (BIOCAT-314) Show changelogs on service show page Message-ID: <20585212.66.1273668076999.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-314?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat deleted BIOCAT-314: -------------------------------- > Show changelogs on service show page > ------------------------------------ > > Key: BIOCAT-314 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-314 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 5 hours > Remaining Estimate: 5 hours > > When viewing a service, should be able to see the full list of changelogs for that service. > Ensure that: > - Must explain that any changes recorded in the SOAP service changelog may be from updates in the actual WSDL OR from things that we are now able to parse from the WSDL. > - It is clarified that info from SoapServiceChange is specifically about the SOAP/WSDL based service. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:43:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:43:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Deleted: (BIOCAT-322) Show "archived operations/inputs/outputs" in UI Message-ID: <18418944.67.1273668197000.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-322?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat deleted BIOCAT-322: -------------------------------- > Show "archived operations/inputs/outputs" in UI > ----------------------------------------------- > > Key: BIOCAT-322 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-322 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Remaining Estimate: 2 hours > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:47:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:47:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-331) Show changelogs on service show page Message-ID: <29588368.68.1273668436995.JavaMail.jira@rosalind.cs.man.ac.uk> Show changelogs on service show page ------------------------------------ Key: BIOCAT-331 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-331 Project: BioCatalogue Issue Type: Sub-task Components: Web Interface Reporter: Jiten Bhagat Assignee: Jiten Bhagat When viewing a service, should be able to see the full list of changelogs for that service. Ensure that: - Must explain that any changes recorded in the SOAP service changelog may be from updates in the actual WSDL OR from things that we are now able to parse from the WSDL. - It is clarified that info from SoapServiceChange is specifically about the SOAP/WSDL based service. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:49:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:49:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-323) In listings, show archived things in greyed out box and text (and possibly collapsed) In-Reply-To: <13694223.7.1273598836996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4494680.69.1273668557030.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-323?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-323: -------------------------------- Summary: In listings, show archived things in greyed out box and text (and possibly collapsed) (was: Show archived things in greyed out box and text (and possibly collapsed)) > In listings, show archived things in greyed out box and text (and possibly collapsed) > ------------------------------------------------------------------------------------- > > Key: BIOCAT-323 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-323 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 hours > Remaining Estimate: 3 hours > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:49:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:49:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-323) In listings, show archived things in greyed out box and text (and possibly collapsed) In-Reply-To: <13694223.7.1273598836996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9471306.70.1273668558000.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-323?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-323 started by Jiten Bhagat. > In listings, show archived things in greyed out box and text (and possibly collapsed) > ------------------------------------------------------------------------------------- > > Key: BIOCAT-323 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-323 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 hours > Remaining Estimate: 3 hours > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:49:19 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:49:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-323) In listings, show archived things in greyed out box and text (and possibly collapsed) In-Reply-To: <13694223.7.1273598836996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32311202.71.1273668559178.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-323?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-323 stopped by Jiten Bhagat. > In listings, show archived things in greyed out box and text (and possibly collapsed) > ------------------------------------------------------------------------------------- > > Key: BIOCAT-323 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-323 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 hours > Remaining Estimate: 3 hours > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:49:20 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:49:20 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-323) In listings, show archived things in greyed out box and text (and possibly collapsed) In-Reply-To: <13694223.7.1273598836996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18523803.72.1273668560119.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-323?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10322 ] Jiten Bhagat logged work on BIOCAT-323: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-12 13:48 Start Date: 2010-05-12 13:48 Worklog Time Spent: 1 hour Issue Time Tracking ------------------- Remaining Estimate: 2 hours (was: 3 hours) Time Spent: 1 hour > In listings, show archived things in greyed out box and text (and possibly collapsed) > ------------------------------------------------------------------------------------- > > Key: BIOCAT-323 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-323 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 hours > Time Spent: 1 hour > Remaining Estimate: 2 hours > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:53:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:53:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-326) Implement option in services listing to ignore archived services In-Reply-To: <14174500.60.1273658418251.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10233885.73.1273668797034.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-326?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-326: -------------------------------- Component/s: Web Interface Original Estimate: 3 hours Remaining Estimate: 3 hours > Implement option in services listing to ignore archived services > ---------------------------------------------------------------- > > Key: BIOCAT-326 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-326 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 hours > Remaining Estimate: 3 hours > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:53:18 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:53:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-325) Implement filter for "Archived Services" In-Reply-To: <2148229.59.1273658417012.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23874356.74.1273668798539.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-325?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-325: -------------------------------- Component/s: Search / Filtering / Browsing Web Interface > Implement filter for "Archived Services" > ---------------------------------------- > > Key: BIOCAT-325 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-325 > Project: BioCatalogue > Issue Type: Sub-task > Components: Search / Filtering / Browsing, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 hours > Remaining Estimate: 3 hours > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:53:19 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:53:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-327) Implement option in search results to ignore archived items In-Reply-To: <20298642.61.1273658419378.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24502797.75.1273668799831.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-327?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-327: -------------------------------- Original Estimate: 3 hours Remaining Estimate: 3 hours Component/s: Web Interface > Implement option in search results to ignore archived items > ----------------------------------------------------------- > > Key: BIOCAT-327 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-327 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 hours > Remaining Estimate: 3 hours > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 08:53:21 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 13:53:21 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-329) Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI In-Reply-To: <18542635.64.1273667839433.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18200583.76.1273668801168.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-329: -------------------------------- Original Estimate: 5 hours Remaining Estimate: 5 hours Component/s: Web Interface > Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI > ---------------------------------------------------------------------------------- > > Key: BIOCAT-329 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 5 hours > Remaining Estimate: 5 hours > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Wed May 12 08:54:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 08:54:02 -0400 (EDT) Subject: [BioCatalogue-developers] [1937] branches/service-updates-and-curation: [BIOCAT-323] Archived Services and SoapOperations are now shown in grey and collapsed in listings . Message-ID: <20100512125402.899B21D799C9@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed May 12 09:01:26 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 09:01:26 -0400 (EDT) Subject: [BioCatalogue-developers] [1938] branches/service-updates-and-curation: Consolidated some of the styling for the archived styles. Message-ID: <20100512130126.925991858345@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed May 12 09:14:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 09:14:14 -0400 (EDT) Subject: [BioCatalogue-developers] [1939] branches/service-updates-and-curation/public/stylesheets/styles.css: Tightened up the listing_item style. Message-ID: <20100512131414.CBB631858316@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed May 12 09:17:24 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 09:17:24 -0400 (EDT) Subject: [BioCatalogue-developers] [1940] branches/service-updates-and-curation/app: [BIOCAT-329] Show " archived operations" as a separate list in the operations tab. Message-ID: <20100512131724.BD12A1858317@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed May 12 09:18:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 14:18:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-329) Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI In-Reply-To: <18542635.64.1273667839433.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <510031.77.1273670297002.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10323 ] Jiten Bhagat logged work on BIOCAT-329: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-12 14:17 Start Date: 2010-05-12 14:16 Worklog Time Spent: 1 hour Work Description: [Rev 1940] A separate "archived operations" list is show in the operations tab. Issue Time Tracking ------------------- Remaining Estimate: 4 hours (was: 5 hours) Time Spent: 1 hour > Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI > ---------------------------------------------------------------------------------- > > Key: BIOCAT-329 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 5 hours > Time Spent: 1 hour > Remaining Estimate: 4 hours > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 09:38:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 14:38:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-329) Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI In-Reply-To: <18542635.64.1273667839433.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23024916.78.1273671497005.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10324 ] Jiten Bhagat logged work on BIOCAT-329: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-12 14:37 Start Date: 2010-05-12 14:37 Worklog Time Spent: 30 minutes Issue Time Tracking ------------------- Remaining Estimate: 3 hours, 30 minutes (was: 4 hours) Time Spent: 1 hour, 30 minutes (was: 1 hour) > Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI > ---------------------------------------------------------------------------------- > > Key: BIOCAT-329 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 5 hours > Time Spent: 1 hour, 30 minutes > Remaining Estimate: 3 hours, 30 minutes > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Wed May 12 09:38:28 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 09:38:28 -0400 (EDT) Subject: [BioCatalogue-developers] [1941] branches/service-updates-and-curation: [BIOCAT-329] Archived operations on the 'show' operation page are shown in a separate collection and greyed out. Message-ID: <20100512133828.DFF2E1D799C9@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed May 12 09:56:16 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 09:56:16 -0400 (EDT) Subject: [BioCatalogue-developers] [1942] branches/service-updates-and-curation/app/views/soap_services/ _show_service_tabs.html.erb: Added an info icon with tooltip next to the " archived operations" header to explain what they are. Message-ID: <20100512135616.C184E1858310@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed May 12 10:16:20 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 10:16:20 -0400 (EDT) Subject: [BioCatalogue-developers] [1943] branches/service-updates-and-curation: [BIOCAT-328] Added an archived status banner for archived services / SOAP operation pages. Message-ID: <20100512141620.8CABD1858335@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed May 12 10:18:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 15:18:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-328) For items that are archived add a "this is archived" message at the top of the 'show' page for the item In-Reply-To: <17913058.63.1273667836992.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29889040.86.1273673897006.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-328?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10325 ] Jiten Bhagat logged work on BIOCAT-328: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-12 15:18 Start Date: 2010-05-12 15:18 Worklog Time Spent: 1 hour Issue Time Tracking ------------------- Remaining Estimate: 0 minutes (was: 1 hour) Time Spent: 1 hour > For items that are archived add a "this is archived" message at the top of the 'show' page for the item > ------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-328 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-328 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 1 hour > Time Spent: 1 hour > Remaining Estimate: 0 minutes > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 10:20:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 15:20:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-329) Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI In-Reply-To: <18542635.64.1273667839433.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7118363.87.1273674017000.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10326 ] Jiten Bhagat logged work on BIOCAT-329: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-12 15:18 Start Date: 2010-05-12 14:18 Worklog Time Spent: 30 minutes Issue Time Tracking ------------------- Remaining Estimate: 3 hours (was: 3 hours, 30 minutes) Time Spent: 2 hours (was: 1 hour, 30 minutes) > Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI > ---------------------------------------------------------------------------------- > > Key: BIOCAT-329 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 5 hours > Time Spent: 2 hours > Remaining Estimate: 3 hours > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Wed May 12 10:44:38 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 10:44:38 -0400 (EDT) Subject: [BioCatalogue-developers] [1944] branches/service-updates-and-curation: Nicer styling for the " actions" drop down menu, and moved it to the left hand side where users usually look for such a thing . Message-ID: <20100512144438.290B5185834E@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed May 12 11:00:48 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 11:00:48 -0400 (EDT) Subject: [BioCatalogue-developers] [1945] branches/service-updates-and-curation/app/views/search/show.html.erb : Fixed a usability issue with the search page (as reported by Alan) whereby the "next page" button is first on the right then moves to the left when paging occurs, which was confusing. Message-ID: <20100512150049.0EF361858343@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed May 12 11:18:05 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 11:18:05 -0400 (EDT) Subject: [BioCatalogue-developers] [1946] branches/service-updates-and-curation: Tweaks to the h4 style. Message-ID: <20100512151805.E91AF1858344@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed May 12 11:42:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 16:42:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-332) Allow linking to alternative services Message-ID: <2571312.89.1273678937001.JavaMail.jira@rosalind.cs.man.ac.uk> Allow linking to alternative services ------------------------------------- Key: BIOCAT-332 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-332 Project: BioCatalogue Issue Type: New Feature Components: Service Container, Web Interface Reporter: Paul Gordon Assignee: Jiten Bhagat Especially in cases of archived services where it would make sense to point to an alternative that isn't deprecated/archived. Paul's original email: --- Hi Jits, I like the idea or "archiving", because then you could point people to working equivalents if they exist...if you plan on doing that, it might make sense to also link to the alternatives on those screens. My $0.02, Paul --- -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 12 12:03:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 12 May 2010 17:03:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-329) Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI In-Reply-To: <18542635.64.1273667839433.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16717945.90.1273680197017.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10327 ] Jiten Bhagat logged work on BIOCAT-329: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-12 17:02 Start Date: 2010-05-12 15:02 Worklog Time Spent: 2 hours Issue Time Tracking ------------------- Remaining Estimate: 1 hour (was: 3 hours) Time Spent: 4 hours (was: 2 hours) > Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI > ---------------------------------------------------------------------------------- > > Key: BIOCAT-329 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 5 hours > Time Spent: 4 hours > Remaining Estimate: 1 hour > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Wed May 12 12:14:31 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 12:14:31 -0400 (EDT) Subject: [BioCatalogue-developers] [1947] branches/service-updates-and-curation: [BIOCAT-329] Archived inputs and outputs are now shown as separate collections. Message-ID: <20100512161431.2BA981678217@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed May 12 12:17:45 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 12:17:45 -0400 (EDT) Subject: [BioCatalogue-developers] [1948] branches/service-updates-and-curation: simple spreadsheet export implementation Message-ID: <20100512161745.638101858344@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed May 12 12:31:03 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 12:31:03 -0400 (EDT) Subject: [BioCatalogue-developers] [1949] branches/service-updates-and-curation/vendor/gems/spreadsheet-0.6.4. 1/.specification: Updated specs for spreadsheet gem Message-ID: <20100512163103.A15811D799CB@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed May 12 12:46:04 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 12:46:04 -0400 (EDT) Subject: [BioCatalogue-developers] [1950] branches/service-updates-and-curation: Added missing ruby-ole gem ( that is required by the spreadsheet gem). Message-ID: <20100512164604.ED2601D799CB@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed May 12 13:06:52 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 12 May 2010 13:06:52 -0400 (EDT) Subject: [BioCatalogue-developers] [1951] branches/service-updates-and-curation/app/models/soap_service.rb: Bugfixes for the WSDL sync method. Message-ID: <20100512170652.624DB1858351@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed May 12 20:43:53 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 13 May 2010 01:43:53 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:getEntryFromHSSP' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:getEntryFromHSSP' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1045 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 May 12 22:54:49 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 13 May 2010 03:54:49 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPSIBlastpFromAminoAcidSequence' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPSIBlastpFromAminoAcidSequence' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1006 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu May 13 00:31:39 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 13 May 2010 05:31:39 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPSIBlastpFromAminoAcidSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPSIBlastpFromAminoAcidSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1006 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Thu May 13 01:00:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 13 May 2010 06:00:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-333) paging does not work when a providers services are listed from service show page Message-ID: <7774406.91.1273726817082.JavaMail.jira@rosalind.cs.man.ac.uk> paging does not work when a providers services are listed from service show page -------------------------------------------------------------------------------- Key: BIOCAT-333 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-333 Project: BioCatalogue Issue Type: Bug Components: Web Interface Reporter: Eric Nzuobontane Assignee: Jiten Bhagat When a provider link is clicked from a service show page, the provider profile is shown with all the providers services. If provider has several pages of services, then clicking next or page number take you back to provider profile. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu May 13 01:06:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 13 May 2010 06:06:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-316) url checker should follow redirects Message-ID: <7104649.92.1273727177017.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-316?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-316 started by Eric Nzuobontane. > url checker should follow redirects > ------------------------------------ > > Key: BIOCAT-316 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-316 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > URL checker( for wsdls and other urls) should follow a few (1, 2, 3 ?) redirects as there may be permanent redirects to temporal redirects... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu May 13 01:16:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 13 May 2010 06:16:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-316) url checker should follow redirects Message-ID: <30067343.93.1273727777020.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-316?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14914#action_14914 ] Eric Nzuobontane commented on BIOCAT-316: ----------------------------------------- A default maximum of three redirects can be followed. The expectation is that this will cover 99 percent of the cases. Since the number of redirects to follow is configurable, this default can be changed if need be. > url checker should follow redirects > ------------------------------------ > > Key: BIOCAT-316 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-316 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > URL checker( for wsdls and other urls) should follow a few (1, 2, 3 ?) redirects as there may be permanent redirects to temporal redirects... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Thu May 13 02:38:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 13 May 2010 07:38:06 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parseFeatureAASequenceFromPMUTText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parseFeatureAASequenceFromPMUTText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/997 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 May 13 04:37:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 13 May 2010 04:37:09 -0400 (EDT) Subject: [BioCatalogue-developers] [1952] trunk/lib/bio_catalogue: Moved the checking of urls & endpoints to it own module and implemented following redirects for URL checks . Message-ID: <20100513083709.654E6185831A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 13 04:55:19 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 13 May 2010 04:55:19 -0400 (EDT) Subject: [BioCatalogue-developers] [1953] trunk/lib/bio_catalogue: follow convention for naming modules Message-ID: <20100513085519.7E77A1858321@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu May 13 07:34:20 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 13 May 2010 12:34:20 +0100 Subject: [BioCatalogue-developers] Removing the Rubyforge tasks list Message-ID: <4BEBE3BC.8050805@cs.man.ac.uk> Hi guys, I would like to delete the Rubyforge tasks list (http://rubyforge.org/pm/task.php?group_id=6901&group_project_id=12540) as it is still showing up on Google etc. Any objections? Jits From ericnzuo at ebi.ac.uk Thu May 13 07:52:43 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 13 May 2010 12:52:43 +0100 Subject: [BioCatalogue-developers] Removing the Rubyforge tasks list In-Reply-To: <4BEBE3BC.8050805@cs.man.ac.uk> References: <4BEBE3BC.8050805@cs.man.ac.uk> Message-ID: <4BEBE80B.3010003@ebi.ac.uk> All the tasks are in Jira, so that should be fine. Eric Jiten Bhagat wrote: > Hi guys, > > I would like to delete the Rubyforge tasks list > (http://rubyforge.org/pm/task.php?group_id=6901&group_project_id=12540) > as it is still showing up on Google etc. > > Any objections? > > Jits > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Thu May 13 09:39:20 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 13 May 2010 14:39:20 +0100 Subject: [BioCatalogue-developers] Latest service annotation report Message-ID: <4BEC0108.7020708@cs.man.ac.uk> Hi Franck, I've run the annotation report generator on the database snapshot from 11th May and this is what I get: Total SOAP Services: 1583 A. How many SOAP Services have a description? 1431 B. How many SOAP Services have a description AND a documentation URL? 877 C. How many SOAP Services have a description AND all operations have a description? 1095 D. How many SOAP Services have a description AND all operations have a description and ALL inputs/outputs have a description? 38 E. How many SOAP Services have a description AND all operations have a description and ALL inputs/outputs have a description AND example data? 0 Jits From jits at cs.man.ac.uk Thu May 13 09:56:36 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 13 May 2010 14:56:36 +0100 Subject: [BioCatalogue-developers] Removing the Rubyforge tasks list In-Reply-To: <4BEBE3BC.8050805@cs.man.ac.uk> References: <4BEBE3BC.8050805@cs.man.ac.uk> Message-ID: <4BEC0514.8070703@cs.man.ac.uk> Done! Say goodbye to rubyforge tasks! Jits Jiten Bhagat wrote: > Hi guys, > > I would like to delete the Rubyforge tasks list > (http://rubyforge.org/pm/task.php?group_id=6901&group_project_id=12540) > as it is still showing up on Google etc. > > Any objections? > > Jits > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From ytanoh at cs.man.ac.uk Thu May 13 09:58:24 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 13 May 2010 14:58:24 +0100 Subject: [BioCatalogue-developers] Latest service annotation report In-Reply-To: <4BEC0108.7020708@cs.man.ac.uk> References: <4BEC0108.7020708@cs.man.ac.uk> Message-ID: Hi Jits, Thanks for the report ... I can see some improvements. But I don't understand why 'E' is still 0. the following service for example is fully annotated so we have at least 1: http://www.biocatalogue.org/services/70 Franck On 13 May 2010 14:39, Jiten Bhagat wrote: > Hi Franck, > > I've run the annotation report generator on the database snapshot from > 11th May and this is what I get: > > Total SOAP Services: 1583 > A. How many SOAP Services have a description? 1431 > B. How many SOAP Services have a description AND a documentation URL? 877 > C. How many SOAP Services have a description AND all operations have a > description? 1095 > D. How many SOAP Services have a description AND all operations have a > description and ALL inputs/outputs have a description? 38 > E. How many SOAP Services have a description AND all operations have a > description and ALL inputs/outputs have a description AND example data? 0 > > Jits > > > -- "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 May 13 10:16:48 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 13 May 2010 15:16:48 +0100 Subject: [BioCatalogue-developers] Latest service annotation report In-Reply-To: References: <4BEC0108.7020708@cs.man.ac.uk> Message-ID: <4BEC09D0.2050108@cs.man.ac.uk> Interesting! I'll take a closer look at the script. Thanks! Jits Franck Tanoh wrote: > Hi Jits, > > Thanks for the report ... I can see some improvements. > But I don't understand why 'E' is still 0. the following service for > example is fully annotated so we have at least 1: > http://www.biocatalogue.org/services/70 > > Franck > > On 13 May 2010 14:39, Jiten Bhagat wrote: > >> Hi Franck, >> >> I've run the annotation report generator on the database snapshot from >> 11th May and this is what I get: >> >> Total SOAP Services: 1583 >> A. How many SOAP Services have a description? 1431 >> B. How many SOAP Services have a description AND a documentation URL? 877 >> C. How many SOAP Services have a description AND all operations have a >> description? 1095 >> D. How many SOAP Services have a description AND all operations have a >> description and ALL inputs/outputs have a description? 38 >> E. How many SOAP Services have a description AND all operations have a >> description and ALL inputs/outputs have a description AND example data? 0 >> >> Jits >> >> >> >> > > > > From jits at cs.man.ac.uk Thu May 13 11:05:55 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 13 May 2010 16:05:55 +0100 Subject: [BioCatalogue-developers] Latest service annotation report In-Reply-To: <4BEC09D0.2050108@cs.man.ac.uk> References: <4BEC0108.7020708@cs.man.ac.uk> <4BEC09D0.2050108@cs.man.ac.uk> Message-ID: <4BEC1553.7050303@cs.man.ac.uk> Well spotted Franck. I had forgotten to update the annotation attribute "example" to "example_data" :-( New results: Total SOAP Services: 1583 A. How many SOAP Services have a description? 1431 B. How many SOAP Services have a description AND a documentation URL? 877 C. How many SOAP Services have a description AND all operations have a description? 1095 D. How many SOAP Services have a description AND all operations have a description and ALL inputs/outputs have a description? 38 E. How many SOAP Services have a description AND all operations have a description and ALL inputs/outputs have a description AND example data? 10 Service IDs for E - 2, 20, 27, 30, 36, 37, 41, 70, 2172, and 2173 Jits Jiten Bhagat wrote: > Interesting! I'll take a closer look at the script. Thanks! > > Jits > > > Franck Tanoh wrote: > >> Hi Jits, >> >> Thanks for the report ... I can see some improvements. >> But I don't understand why 'E' is still 0. the following service for >> example is fully annotated so we have at least 1: >> http://www.biocatalogue.org/services/70 >> >> Franck >> >> On 13 May 2010 14:39, Jiten Bhagat wrote: >> >> >>> Hi Franck, >>> >>> I've run the annotation report generator on the database snapshot from >>> 11th May and this is what I get: >>> >>> Total SOAP Services: 1583 >>> A. How many SOAP Services have a description? 1431 >>> B. How many SOAP Services have a description AND a documentation URL? 877 >>> C. How many SOAP Services have a description AND all operations have a >>> description? 1095 >>> D. How many SOAP Services have a description AND all operations have a >>> description and ALL inputs/outputs have a description? 38 >>> E. How many SOAP Services have a description AND all operations have a >>> description and ALL inputs/outputs have a description AND example data? 0 >>> >>> Jits >>> >>> >>> >>> >>> >> >> >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From ytanoh at cs.man.ac.uk Thu May 13 11:29:59 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 13 May 2010 16:29:59 +0100 Subject: [BioCatalogue-developers] Latest service annotation report In-Reply-To: <4BEC1553.7050303@cs.man.ac.uk> References: <4BEC0108.7020708@cs.man.ac.uk> <4BEC09D0.2050108@cs.man.ac.uk> <4BEC1553.7050303@cs.man.ac.uk> Message-ID: Encouraging results but still some way to go.... Thanks Franck On 13 May 2010 16:05, Jiten Bhagat wrote: > Well spotted Franck. > > I had forgotten to update the annotation attribute "example" to > "example_data" :-( > > New results: > > Total SOAP Services: 1583 > A. How many SOAP Services have a description? 1431 > B. How many SOAP Services have a description AND a documentation URL? 877 > C. How many SOAP Services have a description AND all operations have a > description? 1095 > D. How many SOAP Services have a description AND all operations have a > description and ALL inputs/outputs have a description? 38 > E. How many SOAP Services have a description AND all operations have a > description and ALL inputs/outputs have a description AND example data? 10 > Service IDs for E - 2, 20, 27, 30, 36, 37, 41, 70, 2172, and 2173 > > Jits > > > > Jiten Bhagat wrote: >> Interesting! I'll take a closer look at the script. Thanks! >> >> Jits >> >> >> Franck Tanoh wrote: >> >>> Hi Jits, >>> >>> Thanks for the report ... I can see some improvements. >>> But I don't understand why 'E' is still 0. the following service for >>> example is fully annotated so we have at least 1: >>> http://www.biocatalogue.org/services/70 >>> >>> Franck >>> >>> On 13 May 2010 14:39, Jiten Bhagat wrote: >>> >>> >>>> Hi Franck, >>>> >>>> I've run the annotation report generator on the database snapshot from >>>> 11th May and this is what I get: >>>> >>>> Total SOAP Services: 1583 >>>> A. How many SOAP Services have a description? 1431 >>>> B. How many SOAP Services have a description AND a documentation URL? 877 >>>> C. How many SOAP Services have a description AND all operations have a >>>> description? 1095 >>>> D. How many SOAP Services have a description AND all operations have a >>>> description and ALL inputs/outputs have a description? 38 >>>> E. How many SOAP Services have a description AND all operations have a >>>> description and ALL inputs/outputs have a description AND example data? 0 >>>> >>>> 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 ericnzuo at ebi.ac.uk Thu May 13 11:42:10 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 13 May 2010 16:42:10 +0100 Subject: [BioCatalogue-developers] Latest service annotation report In-Reply-To: References: <4BEC0108.7020708@cs.man.ac.uk> <4BEC09D0.2050108@cs.man.ac.uk> <4BEC1553.7050303@cs.man.ac.uk> Message-ID: <4BEC1DD2.4090802@ebi.ac.uk> It will be interesting to know how many of those descriptions come from providers. I believe providers know best what their services are about. Eric Franck Tanoh wrote: > Encouraging results but still some way to go.... > > Thanks > Franck > > On 13 May 2010 16:05, Jiten Bhagat wrote: > >> Well spotted Franck. >> >> I had forgotten to update the annotation attribute "example" to >> "example_data" :-( >> >> New results: >> >> Total SOAP Services: 1583 >> A. How many SOAP Services have a description? 1431 >> B. How many SOAP Services have a description AND a documentation URL? 877 >> C. How many SOAP Services have a description AND all operations have a >> description? 1095 >> D. How many SOAP Services have a description AND all operations have a >> description and ALL inputs/outputs have a description? 38 >> E. How many SOAP Services have a description AND all operations have a >> description and ALL inputs/outputs have a description AND example data? 10 >> Service IDs for E - 2, 20, 27, 30, 36, 37, 41, 70, 2172, and 2173 >> >> Jits >> >> >> >> Jiten Bhagat wrote: >> >>> Interesting! I'll take a closer look at the script. Thanks! >>> >>> Jits >>> >>> >>> Franck Tanoh wrote: >>> >>> >>>> Hi Jits, >>>> >>>> Thanks for the report ... I can see some improvements. >>>> But I don't understand why 'E' is still 0. the following service for >>>> example is fully annotated so we have at least 1: >>>> http://www.biocatalogue.org/services/70 >>>> >>>> Franck >>>> >>>> On 13 May 2010 14:39, Jiten Bhagat wrote: >>>> >>>> >>>> >>>>> Hi Franck, >>>>> >>>>> I've run the annotation report generator on the database snapshot from >>>>> 11th May and this is what I get: >>>>> >>>>> Total SOAP Services: 1583 >>>>> A. How many SOAP Services have a description? 1431 >>>>> B. How many SOAP Services have a description AND a documentation URL? 877 >>>>> C. How many SOAP Services have a description AND all operations have a >>>>> description? 1095 >>>>> D. How many SOAP Services have a description AND all operations have a >>>>> description and ALL inputs/outputs have a description? 38 >>>>> E. How many SOAP Services have a description AND all operations have a >>>>> description and ALL inputs/outputs have a description AND example data? 0 >>>>> >>>>> Jits >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>> _______________________________________________ >>> 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 Thu May 13 12:35:49 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 13 May 2010 17:35:49 +0100 Subject: [BioCatalogue-developers] Latest service annotation report In-Reply-To: <4BEC1DD2.4090802@ebi.ac.uk> References: <4BEC0108.7020708@cs.man.ac.uk> <4BEC09D0.2050108@cs.man.ac.uk> <4BEC1553.7050303@cs.man.ac.uk> <4BEC1DD2.4090802@ebi.ac.uk> Message-ID: That can be tricky to find unless you define provider description as descriptions from the WSDL which is only half true. For example James built and submitted the following service to the BioCatalogue: http://www.biocatalogue.org/services/2173 There are no descriptions in the WSDL but he later manually added descriptions to the service. As far as i'm concerned those descriptions are from the providers. There are several example like that. Franck On 13 May 2010 16:42, Eric Nzuobontane wrote: > It will be interesting to know how many of those descriptions come from > providers. I believe providers know best what their services are about. > > Eric > > > Franck Tanoh wrote: >> >> Encouraging results but still some way to go.... >> >> Thanks >> Franck >> >> On 13 May 2010 16:05, Jiten Bhagat wrote: >> >>> >>> Well spotted Franck. >>> >>> I had forgotten to update the annotation attribute "example" to >>> "example_data" :-( >>> >>> New results: >>> >>> Total SOAP Services: 1583 >>> A. How many SOAP Services have a description? 1431 >>> B. How many SOAP Services have a description AND a documentation URL? 877 >>> C. How many SOAP Services have a description AND all operations have a >>> description? 1095 >>> D. How many SOAP Services have a description AND all operations have a >>> description and ALL inputs/outputs have a description? 38 >>> E. How many SOAP Services have a description AND all operations have a >>> description and ALL inputs/outputs have a description AND example data? >>> 10 >>> Service IDs for E - 2, 20, 27, 30, 36, 37, 41, 70, 2172, and 2173 >>> >>> Jits >>> >>> >>> >>> Jiten Bhagat wrote: >>> >>>> >>>> Interesting! I'll take a closer look at the script. Thanks! >>>> >>>> Jits >>>> >>>> >>>> Franck Tanoh wrote: >>>> >>>> >>>>> >>>>> Hi Jits, >>>>> >>>>> Thanks for the report ... I can see some improvements. >>>>> But I don't understand why 'E' is still 0. the following service for >>>>> example is fully annotated so we have at least 1: >>>>> http://www.biocatalogue.org/services/70 >>>>> >>>>> Franck >>>>> >>>>> On 13 May 2010 14:39, Jiten Bhagat wrote: >>>>> >>>>> >>>>> >>>>>> >>>>>> Hi Franck, >>>>>> >>>>>> I've run the annotation report generator on the database snapshot from >>>>>> 11th May and this is what I get: >>>>>> >>>>>> Total SOAP Services: 1583 >>>>>> A. How many SOAP Services have a description? 1431 >>>>>> B. How many SOAP Services have a description AND a documentation URL? >>>>>> 877 >>>>>> C. How many SOAP Services have a description AND all operations have a >>>>>> description? 1095 >>>>>> D. How many SOAP Services have a description AND all operations have a >>>>>> description and ALL inputs/outputs have a description? 38 >>>>>> E. How many SOAP Services have a description AND all operations have a >>>>>> description and ALL inputs/outputs have a description AND example >>>>>> data? 0 >>>>>> >>>>>> Jits >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> 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 Thu May 13 20:02:03 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 14 May 2010 01:02:03 +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 issues at mygrid.org.uk Fri May 14 04:34:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 14 May 2010 09:34:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-334) Monitor example endpoints for REST services Message-ID: <13728321.108.1273826057119.JavaMail.jira@rosalind.cs.man.ac.uk> Monitor example endpoints for REST services ------------------------------------------- Key: BIOCAT-334 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-334 Project: BioCatalogue Issue Type: Refinement Components: Service Monitoring Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Base endpoints for REST services do often point to valid resources or resolve to valid urls. Instead of attempting to monitor these automatically, we monitor the example endpoints instead, which are provided as annotations on the services. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 14 04:34:20 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 14 May 2010 09:34:20 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-334) Monitor example endpoints for REST services In-Reply-To: <13728321.108.1273826057119.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26389675.109.1273826060529.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-334?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-334 started by Eric Nzuobontane. > Monitor example endpoints for REST services > ------------------------------------------- > > Key: BIOCAT-334 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-334 > Project: BioCatalogue > Issue Type: Refinement > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Base endpoints for REST services do often point to valid resources or resolve to valid urls. Instead of attempting to monitor these automatically, we monitor the example endpoints instead, which are provided as annotations on the services. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 14 04:38:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 14 May 2010 09:38:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-335) Allow enabling/disabling of availability checks from UI Message-ID: <23903801.110.1273826297000.JavaMail.jira@rosalind.cs.man.ac.uk> Allow enabling/disabling of availability checks from UI ------------------------------------------------------- Key: BIOCAT-335 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-335 Project: BioCatalogue Issue Type: Refinement Components: Service Monitoring Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Provide UI to enable disable availability checks so that admins can temporarily or permanently removes checks from the monitoring. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri May 14 07:05:49 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 07:05:49 -0400 (EDT) Subject: [BioCatalogue-developers] [1954] branches/service-updates-and-curation: [BIOCAT-307] More fixes for the SoapService wsdl sync method. Message-ID: <20100514110549.C54911858344@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri May 14 07:12:21 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 14 May 2010 12:12:21 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromFASTAToDNASequenceCollection' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromFASTAToDNASequenceCollection' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/786 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 May 14 07:28:25 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 14 May 2010 12:28:25 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parseMultipleAlignFromBLASTText' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parseMultipleAlignFromBLASTText' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/989 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri May 14 08:05:06 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 08:05:06 -0400 (EDT) Subject: [BioCatalogue-developers] [1955] trunk/test: REST support test updates Message-ID: <20100514120506.5E4391678217@rubyforge.org> An HTML attachment was scrubbed... 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URL: From noreply at rubyforge.org Fri May 14 09:35:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 09:35:09 -0400 (EDT) Subject: [BioCatalogue-developers] [1958] trunk: enable activation/ de-activation of availability checks from UI and monitor example endpoints for rest services Message-ID: <20100514133509.6D5B81858346@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 14 09:45:00 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 09:45:00 -0400 (EDT) Subject: [BioCatalogue-developers] [1959] branches/service-updates-and-curation/vendor/plugins/annotations: Updated annotations plugin to latest. Message-ID: <20100514134500.1F52D1678217@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 14 09:47:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 09:47:47 -0400 (EDT) Subject: [BioCatalogue-developers] [1960] branches/service-updates-and-curation/config/routes.rb: Changed route for curation controller to be more restful Message-ID: <20100514134747.B907C1858346@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri May 14 10:06:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 14 May 2010 15:06:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-336) Implement a bulk create Annotations API endpoint for the curation by spreadsheets app Message-ID: <25706594.147.1273845976997.JavaMail.jira@rosalind.cs.man.ac.uk> Implement a bulk create Annotations API endpoint for the curation by spreadsheets app ------------------------------------------------------------------------------------- Key: BIOCAT-336 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-336 Project: BioCatalogue Issue Type: New Feature Components: REST API Reporter: Jiten Bhagat Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 14 10:10:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 14 May 2010 15:10:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-336) Implement a bulk create Annotations API endpoint for the curation by spreadsheets app In-Reply-To: <25706594.147.1273845976997.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31327152.148.1273846217008.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-336?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-336: -------------------------------- Description: The curation by spreadsheets feature needs to be built over the API as it cannot be built within the codebase due to the ruby 'spreadsheet' gem being GPL licensed. Therefore Mannie will be building a desktop app for this, which needs to interact with the BioCatalogue via the API. This will then > Implement a bulk create Annotations API endpoint for the curation by spreadsheets app > ------------------------------------------------------------------------------------- > > Key: BIOCAT-336 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-336 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > The curation by spreadsheets feature needs to be built over the API as it cannot be built within the codebase due to the ruby 'spreadsheet' gem being GPL licensed. > Therefore Mannie will be building a desktop app for this, which needs to interact with the BioCatalogue via the API. This will then -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 14 10:10:18 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 14 May 2010 15:10:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-337) Implement an object_for_uri method that finds the object referred to by a URI in the REST API Message-ID: <7716562.149.1273846218900.JavaMail.jira@rosalind.cs.man.ac.uk> Implement an object_for_uri method that finds the object referred to by a URI in the REST API --------------------------------------------------------------------------------------------- Key: BIOCAT-337 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-337 Project: BioCatalogue Issue Type: Task Components: Performance / Optimisations Reporter: Jiten Bhagat Assignee: Jiten Bhagat Currently we can generate URIs for internal objects in the system. We now need to do the opposite. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 14 10:23:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 14 May 2010 15:23:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-337) Implement an object_for_uri method that finds the object referred to by a URI in the REST API In-Reply-To: <7716562.149.1273846218900.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5570867.150.1273846997004.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-337?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-337: -------------------------------- Component/s: REST API (was: Performance / Optimisations) > Implement an object_for_uri method that finds the object referred to by a URI in the REST API > --------------------------------------------------------------------------------------------- > > Key: BIOCAT-337 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-337 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Remaining Estimate: 2 hours > > Currently we can generate URIs for internal objects in the system. We now need to do the opposite. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri May 14 10:33:57 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 10:33:57 -0400 (EDT) Subject: [BioCatalogue-developers] [1961] branches/service-updates-and-curation/lib/bio_catalogue/util.rb: Added a generic way of logging exceptions. Message-ID: <20100514143357.93DE61858345@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 14 10:38:28 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 10:38:28 -0400 (EDT) Subject: [BioCatalogue-developers] [1962] branches/service-updates-and-curation/lib/bio_catalogue/util.rb: Improved the log_exception method to be able to log as errors, warnings or just info. Message-ID: <20100514143828.9C504185834B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 14 10:39:39 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 10:39:39 -0400 (EDT) Subject: [BioCatalogue-developers] [1963] branches/service-updates-and-curation/lib/bio_catalogue/api.rb: [ BIOCAT-337] Implemented an object_for_uri method that finds the object referred to by a URI in the REST API . Message-ID: <20100514143939.91D2C1858350@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri May 14 10:41:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 14 May 2010 15:41:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-337) Implement an object_for_uri method that finds the object referred to by a URI in the REST API In-Reply-To: <7716562.149.1273846218900.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3700494.174.1273848077081.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-337?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10328 ] Jiten Bhagat logged work on BIOCAT-337: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-14 15:40 Start Date: 2010-05-14 14:39 Worklog Time Spent: 1 hour Issue Time Tracking ------------------- Remaining Estimate: 0 minutes (was: 2 hours) Time Spent: 1 hour > Implement an object_for_uri method that finds the object referred to by a URI in the REST API > --------------------------------------------------------------------------------------------- > > Key: BIOCAT-337 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-337 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 1 hour > Remaining Estimate: 0 minutes > > Currently we can generate URIs for internal objects in the system. We now need to do the opposite. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 14 10:41:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 14 May 2010 15:41:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-337) Implement an object_for_uri method that finds the object referred to by a URI in the REST API In-Reply-To: <7716562.149.1273846218900.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5833550.175.1273848077994.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-337?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-337. --------------------------------- Resolution: Fixed Done in revision 1963 > Implement an object_for_uri method that finds the object referred to by a URI in the REST API > --------------------------------------------------------------------------------------------- > > Key: BIOCAT-337 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-337 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 1 hour > Remaining Estimate: 0 minutes > > Currently we can generate URIs for internal objects in the system. We now need to do the opposite. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri May 14 11:12:43 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 11:12:43 -0400 (EDT) Subject: [BioCatalogue-developers] [1964] branches/service-updates-and-curation: removed spreadsheet work from the codebase Message-ID: <20100514151243.B225E16782A0@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri May 14 11:39:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 14 May 2010 16:39:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-338) fix rake task to check wsdl parsing Message-ID: <31790990.448.1273851557004.JavaMail.jira@rosalind.cs.man.ac.uk> fix rake task to check wsdl parsing ----------------------------------- Key: BIOCAT-338 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-338 Project: BioCatalogue Issue Type: Bug Components: Misc Codebase Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Fix the rake task which checks whether WSDLs parse and make it configurable. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 14 11:42:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 14 May 2010 16:42:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-338) fix rake task to check wsdl parsing In-Reply-To: <31790990.448.1273851557004.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26460903.449.1273851737000.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-338?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14920#action_14920 ] Jiten Bhagat commented on BIOCAT-338: ------------------------------------- This needs to take into account the WSDL parsing refactorings that are currently in the service-updates-and-curation branch > fix rake task to check wsdl parsing > ----------------------------------- > > Key: BIOCAT-338 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-338 > Project: BioCatalogue > Issue Type: Bug > Components: Misc Codebase > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Fix the rake task which checks whether WSDLs parse and make it configurable. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri May 14 12:24:51 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 12:24:51 -0400 (EDT) Subject: [BioCatalogue-developers] [1965] branches/service-updates-and-curation: [BIOCAT-336] Initial work on the /annotations/bulk_create endpoint. Message-ID: <20100514162452.16D1F1858350@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 14 12:32:57 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 12:32:57 -0400 (EDT) Subject: [BioCatalogue-developers] [1966] branches/service-updates-and-curation/app/controllers/ annotations_controller.rb: [BIOCAT-336] Added more documentation to the / annotations/bulk_create method. Message-ID: <20100514163257.E628B1858353@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri May 14 12:35:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 14 May 2010 17:35:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-336) Implement a bulk create Annotations API endpoint for the curation by spreadsheets app In-Reply-To: <25706594.147.1273845976997.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1635712.475.1273854917006.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-336?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10336 ] Jiten Bhagat logged work on BIOCAT-336: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-14 17:33 Start Date: 2010-05-14 15:33 Worklog Time Spent: 3 hours Work Description: Initial implementation in revision 1965 Issue Time Tracking ------------------- Remaining Estimate: 1 hour (was: 4 hours) Time Spent: 3 hours > Implement a bulk create Annotations API endpoint for the curation by spreadsheets app > ------------------------------------------------------------------------------------- > > Key: BIOCAT-336 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-336 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 4 hours > Time Spent: 3 hours > Remaining Estimate: 1 hour > > The curation by spreadsheets feature needs to be built over the API as it cannot be built within the codebase due to the ruby 'spreadsheet' gem being GPL licensed. > Therefore Mannie will be building a desktop app for this, which needs to interact with the BioCatalogue via the API. This will then -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri May 14 12:46:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 12:46:14 -0400 (EDT) Subject: [BioCatalogue-developers] [1967] branches/service-updates-and-curation: [BIOCAT-336] Refactored the bulk_create mechanism to the BioCatalogue:: Annotations module so that it can be used in other places easily. Message-ID: <20100514164615.0AB871678312@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 14 12:52:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 12:52:42 -0400 (EDT) Subject: [BioCatalogue-developers] [1968] branches/service-updates-and-curation/test/unit/lib/bio_catalogue/ annotations_test.rb: Prepared a test file for the BioCatalogue: Annotations module. Message-ID: <20100514165242.E72DD16782A0@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 14 13:06:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 13:06:02 -0400 (EDT) Subject: [BioCatalogue-developers] [1969] branches/service-updates-and-curation/app/controllers/ annotations_controller.rb: [BIOCAT-336] Allow admins to do bulk_create of annotations too. Message-ID: <20100514170602.D9D1F1858351@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 14 13:06:20 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 13:06:20 -0400 (EDT) Subject: [BioCatalogue-developers] [1970] branches/service-updates-and-curation/app/controllers/ application_controller.rb: Basic authentication for JSON too. Message-ID: <20100514170620.233351858353@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 14 13:09:21 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 13:09:21 -0400 (EDT) Subject: [BioCatalogue-developers] [1971] branches/service-updates-and-curation/lib/bio_catalogue/annotations. rb: Fixed typo in a comment Message-ID: <20100514170921.2F0F31858351@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 14 13:09:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 13:09:42 -0400 (EDT) Subject: [BioCatalogue-developers] [1972] branches/service-updates-and-curation/app/controllers/ annotations_controller.rb: [BIOCAT-336] Actually allow the bulk_create action through! Message-ID: <20100514170942.39FB41858351@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 14 13:20:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 13:20:22 -0400 (EDT) Subject: [BioCatalogue-developers] [1973] trunk/lib/tasks/check_wsdl_parse.rake: fix for wsdl parse task Message-ID: <20100514172022.B01AC1858356@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri May 14 13:39:07 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 14 May 2010 18:39:07 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPHDFromFASTA' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPHDFromFASTA' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/999 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri May 14 13:40:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 14 May 2010 13:40:14 -0400 (EDT) Subject: [BioCatalogue-developers] [1974] branches/service-updates-and-curation: [BIOCAT-336] Refactored the way the BioCatalogue: Annotations works and how the XML and JSON results are generated, so that things are simpler. Message-ID: <20100514174014.6DF271858346@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri May 14 19:09:07 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 15 May 2010 00:09:07 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runFlexibilityPhysicalProperties' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runFlexibilityPhysicalProperties' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1017 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri May 14 23:55:52 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 15 May 2010 04:55:52 +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 Sat May 15 03:00:52 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 15 May 2010 08:00:52 +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 Sat May 15 18:50:36 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 15 May 2010 23:50:36 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runMBFromMSF' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runMBFromMSF' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1078 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 May 16 03:29:32 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 16 May 2010 08:29:32 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runGeneIDGFF' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runGeneIDGFF' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/769 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun May 16 08:08:16 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 16 May 2010 13:08:16 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMultiPairwiseMetaAlignmentGFF' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMultiPairwiseMetaAlignmentGFF' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/783 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Sun May 16 11:38:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Sun, 16 May 2010 16:38:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-339) Convert INBTester.pl templates to URL checks Message-ID: <12638841.476.1274024297139.JavaMail.jira@rosalind.cs.man.ac.uk> Convert INBTester.pl templates to URL checks --------------------------------------------- Key: BIOCAT-339 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-339 Project: BioCatalogue Issue Type: Refinement Components: Service Monitoring Reporter: Eric Nzuobontane Assignee: Jiten Bhagat INBTester.pl scripts basically contruct a URL and parse the output from that URL. That can be converted to URL checks which would make them runnable on the main servers. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Sun May 16 12:13:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Sun, 16 May 2010 17:13:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-339) Convert INBTester.pl templates to URL checks In-Reply-To: <12638841.476.1274024297139.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3448952.477.1274026397010.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-339?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-339: --------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > Convert INBTester.pl templates to URL checks > --------------------------------------------- > > Key: BIOCAT-339 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-339 > Project: BioCatalogue > Issue Type: Refinement > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > INBTester.pl scripts basically contruct a URL and parse the output from that URL. That can be converted to URL checks which would make them runnable on the main servers. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Mon May 17 00:49:09 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 17 May 2010 05:49:09 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMetaAlignmentGFF' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMetaAlignmentGFF' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/781 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Mon May 17 05:03:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 17 May 2010 10:03:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-340) For failing tests(checks) indicate for how long they have been failing Message-ID: <9779773.478.1274086997118.JavaMail.jira@rosalind.cs.man.ac.uk> For failing tests(checks) indicate for how long they have been failing ---------------------------------------------------------------------- Key: BIOCAT-340 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-340 Project: BioCatalogue Issue Type: Task Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Show in the UI how long a particular test/check has been failing. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Mon May 17 05:10:03 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 17 May 2010 10:10:03 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: Question on local set up] Message-ID: <4BF107EB.10604@cs.man.ac.uk> FYI -------- Original Message -------- Subject: Re: Question on local set up Date: Fri, 14 May 2010 10:53:12 -0400 From: Jackson, Tod To: Jiten Bhagat Hello Jits! Good to hear from you. Actually, there are a few things I was planning on sending you at some point in the not to distant future. As far as basic installation, I think it was pretty straight forward. The developer guide/setup instructions you put out there are very helpful. Of course, depending on the platform you?re targeting, things can be slightly different. I?ve performed the setup on Ubuntu, Fedora and now RHEL4. All have had their little ?surprises? for me but there?s not a lot the BioCatalogue product itself can really do about that. Here are a few high-level items I was going to mention, note most of these are related to the goal of being able to keep up with any changes you may make to the code base (i.e., being able to deploy a new version of the product with minimal effort). This is becoming even more important because we?re also considering the potential use of the BioCatalogue product internally at Emory (i.e., another distinct deployment of the product). Perhaps, we can work together on some of these? * Product name ? you call it the BioCatalogue and we?re going to refer to it as the EdUnify Registry (and eventually the ?Emory Web Service Registry? as well). Ideally, I?d like to be able to ?re-brand? the product without having to change any more code than necessary. To that end, I?ve introduced an external variable called PRODUCT_NAME that I?ve added to biocat_local.rb. Then, I added appropriate references to that variable in the various places where I thought it made sense. I?ve had mixed success with this approach. In some cases, the variable gets resolved to the value I?ve specified but in some cases it just shows up as ?PRODUCT_NAME? so I must be referring to it incorrectly or something. I haven?t had a chance to dig into it much. As I?ve mentioned, I?m still muddling my way through the Ruby on Rails platform...I did develop a potentially useful utility for this work (and the re-branding in general) that allows me to do prompted search and replaces of various varieties. Grep wasn?t quite what I needed so I did something in Java that I?ve been using. * Partner images ? I think it might be cool to put all ?partner? images in a subdirectory under images and just pull them all in dynamically instead of linking them statically in index.html.erb. This would allow anyone using the product to just dump their partner images in that directory and link them in automatically (again, less maintenance for me during re-branding :) ). * Wiki ? so far, I?ve just taken the wiki content from the BioCatalogue wiki and replicated it in a local DokuWiki installation. I?m not too thrilled with that approach because it makes it kind of hard to maintain etc. Ideally, I?d like to separate the wiki from the ?product? just a bit more and make it stand on it?s own a bit more. I?d thought about just linking off to the BioCatalogue wiki but thought it might get confusing for our users going from a product referred to as the ?EdUnify Registry? to a wiki that talks about the BioCatalogue. I?ve got several detailed thoughts about this that I will try to send you more about. I see two main components to this, and most things like this. First, there?s the ?product.? This product can be used by various ?projects.? Ideally, I think we?d have a wiki that focuses on the product that would be very general and just talk about how to use it etc. The content associated to this wiki would be very similar if not identical regardless of the project it was associated to. The only real difference would be the wiki ?branding.? i.e., the name of the product. Then, there might be a ?project? wiki that talks more about the specific context in which the product is being used. This could vary from project to project. For example, EdUnify is going to be using it in the context of ?web services for higher education? and the BioCatalogue project uses it in the context of ?life sciences.? So, there could be vastly different documentation associated to those uses of the product maintained by these projects independently. The first wiki I refer to here though might be shared between the two because it?s really just general documentation about how to use the product and what web services are etc. Sorry, I?m probably rambling a bit. I?ll try to send a better explanation. * One of our users ran into an issue with searching by tags. He added a tag to an operation. Then, he followed the Services link from the main page. Then, he clicked on the tag he?d added to the operation. When you do that, it doesn?t quite return what you?d expect. I tracked it down and thought I had it fixed but then I realized that there doesn?t appear to be a way to link an annotation to the actual service it?s associated to unless the annotation was made on the service itself. The tweaking I did was in tags.rb in the get_service_ids_for_tag(tag_name) method. Initially, I thought I had it figured out but once I was dealing with an instance that had more than one service, I realized it was a ?false fix.? I?m going to look at it some more and will try to send you a better explanation if that doesn?t make sense. I think if you just try it (add a tag to an operation and try to drill down on it as I?ve described here, you?ll see what I?m talking about) * Shibboleth ? the scenarios in which we?ll be using the product are still being fleshed out but it seems as though some sort of trusted federated authentication approach might be needed. So, we?re getting ready to start seeing if we can hook things up with Shibboleth. If you?d done anything along these lines yet (or have any thoughts or references I could look at) I?d appreciate hearing about them. Like I said, we?re in the early stages of this so I?ll send you more information as we move forward. * Deployment ? currently, we?re running things under Apache using the passenger phusion (a.k.a. mod_rails/mod_rack). This is all working fine but ideally, I?d like to deploy to an application server (like Tomcat or Jboss). I?ve been trying to get it working off and on for the past few weeks and haven?t had much luck at all. I?ve been trying to use warbler to create .war file and then deploy that to my app server. The war gets created but the app server isn?t liking it. I?ve been trying it with a very simple RoR app (not BioCatalogue) because I figured there might be some trial and error required. So far, I haven?t had much luck even with my very simple app. I?m not sure if you?ve ever tried doing anything like this? I don?t expect you to answer anything for me here, I?m just trying to give you an idea as to where I?m heading. The reason I?m going down this path is again related to the main goal I mentioned above. Typically, for each given ?project? that?s using the ?product? we?ve got at least two environments deployed (dev and demo). Ultimately, we?ll have three probably (prod). The way I?m doing it now, I have to maintain the actual code base in all environments (add another ?project? to the mix and it becomes even more challenging). So, my hope is that once I get this working, I can maintain the code base in on place and just deploy the war to the appropriate target environment when needed. We also typically use SVN for deployment as well as source code version control. I haven?t done that yet even for what we?re doing now so that would simplify things a bit but ultimately, I?d like to go down the app server route if possible. Again, I?m just letting you know where I?m trying to go, please let me know if you have any thoughts or recommendations related to this. * Terms of use ? this is another area we?ll probably need to talk about at some point because I?m not sure how that all needs to work. There may be multiple ?terms of use? depending on the project using the product. I?m just throwing this out there as something to think about. In general, I think it may just boil down to modeling the documentation (wiki stuff) with a little more thought towards the potential of multiple ?projects? using the same basic ?product.? I?ll try to send some more details regarding this as well in the near future. There are probably more things I?d love to discuss with you but I?ll leave it at these for now. We?re really excited about the potential of the various efforts we have that are trying to use BioCatalogue and I look forward to working more closely with you as we move forward. So far, I?ve just been muddling my way through trying to get things to a point where more eyes and minds can think about some of these things. I suspect in the coming weeks and months, we?ll have many more thoughts from various people to add to the mix. Thanks again for all your help! Tod On 5/14/10 5:05 AM, "Jiten Bhagat" wrote: Hi Tod, I just came across your BioCat installation this morning - https://demo.edunify.pesc.org/ - and I was impressed by how customised you were able to make it. It's our goal to package up the BioCatalogue as an easily installable and configurable product and your efforts here are very useful to us. Is there anything we can do to help with your demo? Many thanks, Jits Jackson, Tod wrote: > > Greetings, > > I and some colleagues from Emory University have been working on > getting an instance of the Biocatalogue application deployed locally > in hopes that it might be useful in a project we?re participating in > called EdUnify (_http://www.pesc.org/interior.php?page_id=204_) which > is sponsored by the PESC organization (_http://www.pesc.org/_). > > I?ve been working with Ruby 1.8.7 on Ubuntu 9.10. While I was able to > get it working, I had to make some modifications that I?m sure aren?t > correct so I thought I would post what I did here and see what I may > be missing. DISCLAIMER: I?m new to Ruby on Rails but do have a > strong development background especially in Java. Also, I did all of > this before the wiki > (_http://www.biocatalogue.org/wiki/doku.php?id=development:codebase_guidelines_) > was available so I will be checking that out to see if I could have > missed anything important with my trial and error approach. > > Here?s a high-level overview of the steps I took: > > - Exported the latest code base from the SVN repository to my > local environment (www/biocat) > > - Changed all the *.yml.pre to *.yml etc. > > - Ran a rake db:create/migrate > > - Installed a few missing gems > > - Once I got the basic environment where it needed to be in the > first 4 steps above, I ran it with the WEBrick app server > (script/server from my www/biocat directory) > > - Then, I tried to access the app by going to: > _http://localhost:3000/biocat/home_ > > Below is the stack trace that I got when I performed the basic steps > listed above. The error was ?wrong number of arguments (0 for 1)? > Based on the information in the stack trace, I found the code location > where I thought the error was occurring and it was this line in the > activity_feeds_helper.rb file: ?al_items = > Rails.cache.read(cach_key)? in my file it was line #44. So, to get > around this, I just commented out that line and replaced it with an > empty al_items = [ ]. Obviously, this is a hack but it did get me > around the error and allowed me to basically run the app locally. > Once I had it ?running? and accessible, I set up Passenger and was > able to run it via Apache as well. > > My question is what does this kind of error indicate? In the Java > world, I would probably lean toward a deprecated API or something like > that? i.e., perhaps this works with earlier versions but is no longer > supported in 1.8.7 or something like that? I haven?t dug into the > Rails.cache API so I?m not sure if my assessment is accurate or not so > I thought posting it here might be a good place to start while I look > into that a bit more myself. > > I thank you in advance for any help. > > Tod Jackson > [snip] ------------------------------------------------------------------------ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). From ericnzuo at ebi.ac.uk Mon May 17 05:36:03 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 17 May 2010 10:36:03 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: Question on local set up] In-Reply-To: <4BF107EB.10604@cs.man.ac.uk> References: <4BF107EB.10604@cs.man.ac.uk> Message-ID: <4BF10E03.1040001@ebi.ac.uk> Hi Jits, This is very interesting. It is true that whilst we have always wanted to make BioCatalogue customizable and easily installable in other environments, we have not really put effort into what bits of it should/could be made more generic & hence easily customizable. This experience is very very valuable. Eric Jiten Bhagat wrote: > FYI > > -------- Original Message -------- > Subject: Re: Question on local set up > Date: Fri, 14 May 2010 10:53:12 -0400 > From: Jackson, Tod > To: Jiten Bhagat > > > > Hello Jits! Good to hear from you. > > Actually, there are a few things I was planning on sending you at some > point in the not to distant future. As far as basic installation, I > think it was pretty straight forward. The developer guide/setup > instructions you put out there are very helpful. Of course, depending > on the platform you?re targeting, things can be slightly different. > I?ve performed the setup on Ubuntu, Fedora and now RHEL4. All have had > their little ?surprises? for me but there?s not a lot the BioCatalogue > product itself can really do about that. > > Here are a few high-level items I was going to mention, note most of > these are related to the goal of being able to keep up with any changes > you may make to the code base (i.e., being able to deploy a new version > of the product with minimal effort). This is becoming even more > important because we?re also considering the potential use of the > BioCatalogue product internally at Emory (i.e., another distinct > deployment of the product). Perhaps, we can work together on some of these? > > * Product name ? you call it the BioCatalogue and we?re going to > refer to it as the EdUnify Registry (and eventually the ?Emory Web > Service Registry? as well). Ideally, I?d like to be able to > ?re-brand? the product without having to change any more code than > necessary. To that end, I?ve introduced an external variable > called PRODUCT_NAME that I?ve added to biocat_local.rb. Then, I > added appropriate references to that variable in the various > places where I thought it made sense. I?ve had mixed success with > this approach. In some cases, the variable gets resolved to the > value I?ve specified but in some cases it just shows up as > ?PRODUCT_NAME? so I must be referring to it incorrectly or > something. I haven?t had a chance to dig into it much. As I?ve > mentioned, I?m still muddling my way through the Ruby on Rails > platform...I did develop a potentially useful utility for this > work (and the re-branding in general) that allows me to do > prompted search and replaces of various varieties. Grep wasn?t > quite what I needed so I did something in Java that I?ve been using. > * Partner images ? I think it might be cool to put all ?partner? > images in a subdirectory under images and just pull them all in > dynamically instead of linking them statically in index.html.erb. > This would allow anyone using the product to just dump their > partner images in that directory and link them in automatically > (again, less maintenance for me during re-branding :) ). > * Wiki ? so far, I?ve just taken the wiki content from the > BioCatalogue wiki and replicated it in a local DokuWiki > installation. I?m not too thrilled with that approach because it > makes it kind of hard to maintain etc. Ideally, I?d like to > separate the wiki from the ?product? just a bit more and make it > stand on it?s own a bit more. I?d thought about just linking off > to the BioCatalogue wiki but thought it might get confusing for > our users going from a product referred to as the ?EdUnify > Registry? to a wiki that talks about the BioCatalogue. I?ve got > several detailed thoughts about this that I will try to send you > more about. I see two main components to this, and most things > like this. First, there?s the ?product.? This product can be > used by various ?projects.? Ideally, I think we?d have a wiki > that focuses on the product that would be very general and just > talk about how to use it etc. The content associated to this wiki > would be very similar if not identical regardless of the project > it was associated to. The only real difference would be the wiki > ?branding.? i.e., the name of the product. Then, there might be > a ?project? wiki that talks more about the specific context in > which the product is being used. This could vary from project to > project. For example, EdUnify is going to be using it in the > context of ?web services for higher education? and the > BioCatalogue project uses it in the context of ?life sciences.? > So, there could be vastly different documentation associated to > those uses of the product maintained by these projects > independently. The first wiki I refer to here though might be > shared between the two because it?s really just general > documentation about how to use the product and what web services > are etc. Sorry, I?m probably rambling a bit. I?ll try to send a > better explanation. > * One of our users ran into an issue with searching by tags. He > added a tag to an operation. Then, he followed the Services link > from the main page. Then, he clicked on the tag he?d added to the > operation. When you do that, it doesn?t quite return what you?d > expect. I tracked it down and thought I had it fixed but then I > realized that there doesn?t appear to be a way to link an > annotation to the actual service it?s associated to unless the > annotation was made on the service itself. The tweaking I did was > in tags.rb in the get_service_ids_for_tag(tag_name) method. > Initially, I thought I had it figured out but once I was dealing > with an instance that had more than one service, I realized it was > a ?false fix.? I?m going to look at it some more and will try to > send you a better explanation if that doesn?t make sense. I think > if you just try it (add a tag to an operation and try to drill > down on it as I?ve described here, you?ll see what I?m talking about) > * Shibboleth ? the scenarios in which we?ll be using the product are > still being fleshed out but it seems as though some sort of > trusted federated authentication approach might be needed. So, > we?re getting ready to start seeing if we can hook things up with > Shibboleth. If you?d done anything along these lines yet (or have > any thoughts or references I could look at) I?d appreciate hearing > about them. Like I said, we?re in the early stages of this so > I?ll send you more information as we move forward. > * Deployment ? currently, we?re running things under Apache using > the passenger phusion (a.k.a. mod_rails/mod_rack). This is all > working fine but ideally, I?d like to deploy to an application > server (like Tomcat or Jboss). I?ve been trying to get it working > off and on for the past few weeks and haven?t had much luck at > all. I?ve been trying to use warbler to create .war file and then > deploy that to my app server. The war gets created but the app > server isn?t liking it. I?ve been trying it with a very simple > RoR app (not BioCatalogue) because I figured there might be some > trial and error required. So far, I haven?t had much luck even > with my very simple app. I?m not sure if you?ve ever tried doing > anything like this? I don?t expect you to answer anything for me > here, I?m just trying to give you an idea as to where I?m heading. > The reason I?m going down this path is again related to the main > goal I mentioned above. Typically, for each given ?project? > that?s using the ?product? we?ve got at least two environments > deployed (dev and demo). Ultimately, we?ll have three probably > (prod). The way I?m doing it now, I have to maintain the actual > code base in all environments (add another ?project? to the mix > and it becomes even more challenging). So, my hope is that once I > get this working, I can maintain the code base in on place and > just deploy the war to the appropriate target environment when > needed. We also typically use SVN for deployment as well as > source code version control. I haven?t done that yet even for > what we?re doing now so that would simplify things a bit but > ultimately, I?d like to go down the app server route if possible. > Again, I?m just letting you know where I?m trying to go, please > let me know if you have any thoughts or recommendations related to > this. > * Terms of use ? this is another area we?ll probably need to talk > about at some point because I?m not sure how that all needs to > work. There may be multiple ?terms of use? depending on the > project using the product. I?m just throwing this out there as > something to think about. In general, I think it may just boil > down to modeling the documentation (wiki stuff) with a little more > thought towards the potential of multiple ?projects? using the > same basic ?product.? I?ll try to send some more details > regarding this as well in the near future. > > > There are probably more things I?d love to discuss with you but I?ll > leave it at these for now. We?re really excited about the potential of > the various efforts we have that are trying to use BioCatalogue and I > look forward to working more closely with you as we move forward. So > far, I?ve just been muddling my way through trying to get things to a > point where more eyes and minds can think about some of these things. I > suspect in the coming weeks and months, we?ll have many more thoughts > from various people to add to the mix. > > Thanks again for all your help! > Tod > > On 5/14/10 5:05 AM, "Jiten Bhagat" wrote: > > Hi Tod, > > I just came across your BioCat installation this morning - > https://demo.edunify.pesc.org/ - and I was impressed by how > customised you were able to make it. > > It's our goal to package up the BioCatalogue as an easily installable > and configurable product and your efforts here are very useful to us. > > Is there anything we can do to help with your demo? > > Many thanks, > Jits > > > > Jackson, Tod wrote: > > > > Greetings, > > > > I and some colleagues from Emory University have been working on > > getting an instance of the Biocatalogue application deployed locally > > in hopes that it might be useful in a project we?re participating in > > called EdUnify (_http://www.pesc.org/interior.php?page_id=204_) which > > is sponsored by the PESC organization (_http://www.pesc.org/_). > > > > I?ve been working with Ruby 1.8.7 on Ubuntu 9.10. While I was able to > > get it working, I had to make some modifications that I?m sure aren?t > > correct so I thought I would post what I did here and see what I may > > be missing. DISCLAIMER: I?m new to Ruby on Rails but do have a > > strong development background especially in Java. Also, I did all of > > this before the wiki > > (_http://www.biocatalogue.org/wiki/doku.php?id=development:codebase_guidelines_) > > was available so I will be checking that out to see if I could have > > missed anything important with my trial and error approach. > > > > Here?s a high-level overview of the steps I took: > > > > - Exported the latest code base from the SVN repository to my > > local environment (www/biocat) > > > > - Changed all the *.yml.pre to *.yml etc. > > > > - Ran a rake db:create/migrate > > > > - Installed a few missing gems > > > > - Once I got the basic environment where it needed to be in the > > first 4 steps above, I ran it with the WEBrick app server > > (script/server from my www/biocat directory) > > > > - Then, I tried to access the app by going to: > > _http://localhost:3000/biocat/home_ > > > > Below is the stack trace that I got when I performed the basic steps > > listed above. The error was ?wrong number of arguments (0 for 1)? > > Based on the information in the stack trace, I found the code location > > where I thought the error was occurring and it was this line in the > > activity_feeds_helper.rb file: ?al_items = > > Rails.cache.read(cach_key)? in my file it was line #44. So, to get > > around this, I just commented out that line and replaced it with an > > empty al_items = [ ]. Obviously, this is a hack but it did get me > > around the error and allowed me to basically run the app locally. > > Once I had it ?running? and accessible, I set up Passenger and was > > able to run it via Apache as well. > > > > My question is what does this kind of error indicate? In the Java > > world, I would probably lean toward a deprecated API or something like > > that? i.e., perhaps this works with earlier versions but is no longer > > supported in 1.8.7 or something like that? I haven?t dug into the > > Rails.cache API so I?m not sure if my assessment is accurate or not so > > I thought posting it here might be a good place to start while I look > > into that a bit more myself. > > > > I thank you in advance for any help. > > > > Tod Jackson > > > > [snip] > > > > ------------------------------------------------------------------------ > This e-mail message (including any attachments) is for the sole use of > the intended recipient(s) and may contain confidential and privileged > information. If the reader of this message is not the intended > recipient, you are hereby notified that any dissemination, distribution > or copying of this message (including any attachments) is strictly > prohibited. > > If you have received this message in error, please contact > the sender by reply e-mail message and destroy all copies of the > original message (including attachments). > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Mon May 17 05:43:50 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 17 May 2010 10:43:50 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: Question on local set up] In-Reply-To: <4BF10E03.1040001@ebi.ac.uk> References: <4BF107EB.10604@cs.man.ac.uk> <4BF10E03.1040001@ebi.ac.uk> Message-ID: <4BF10FD6.90001@cs.man.ac.uk> Eric, Absolutely! It's deja-vu for me since we had exactly the same experience with myExperiment - which is now a lot more customisable. It's actually not that difficult to do so (thanks to Ruby) but just time consuming. May I recommend you have a look at the Sysmo-db's (another RoR project here in Manchester) install guide - http://sysmo-db.googlecode.com/hg/doc/seek/files/doc/INSTALL.html We need something similar for us too. Cheers, Jits Eric Nzuobontane wrote: > Hi Jits, > This is very interesting. It is true that whilst we have always wanted > to make BioCatalogue customizable and easily installable in other > environments, we have not really put effort into what bits of it > should/could be made more generic & hence easily customizable. This > experience is very very valuable. > > Eric > > Jiten Bhagat wrote: >> FYI >> >> -------- Original Message -------- >> Subject: Re: Question on local set up >> Date: Fri, 14 May 2010 10:53:12 -0400 >> From: Jackson, Tod >> To: Jiten Bhagat >> >> >> >> Hello Jits! Good to hear from you. >> >> Actually, there are a few things I was planning on sending you at some >> point in the not to distant future. As far as basic installation, I >> think it was pretty straight forward. The developer guide/setup >> instructions you put out there are very helpful. Of course, depending >> on the platform you?re targeting, things can be slightly different. >> I?ve performed the setup on Ubuntu, Fedora and now RHEL4. All have had >> their little ?surprises? for me but there?s not a lot the BioCatalogue >> product itself can really do about that. >> >> Here are a few high-level items I was going to mention, note most of >> these are related to the goal of being able to keep up with any changes >> you may make to the code base (i.e., being able to deploy a new version >> of the product with minimal effort). This is becoming even more >> important because we?re also considering the potential use of the >> BioCatalogue product internally at Emory (i.e., another distinct >> deployment of the product). Perhaps, we can work together on some of >> these? >> >> * Product name ? you call it the BioCatalogue and we?re going to >> refer to it as the EdUnify Registry (and eventually the ?Emory Web >> Service Registry? as well). Ideally, I?d like to be able to >> ?re-brand? the product without having to change any more code than >> necessary. To that end, I?ve introduced an external variable >> called PRODUCT_NAME that I?ve added to biocat_local.rb. Then, I >> added appropriate references to that variable in the various >> places where I thought it made sense. I?ve had mixed success with >> this approach. In some cases, the variable gets resolved to the >> value I?ve specified but in some cases it just shows up as >> ?PRODUCT_NAME? so I must be referring to it incorrectly or >> something. I haven?t had a chance to dig into it much. As I?ve >> mentioned, I?m still muddling my way through the Ruby on Rails >> platform...I did develop a potentially useful utility for this >> work (and the re-branding in general) that allows me to do >> prompted search and replaces of various varieties. Grep wasn?t >> quite what I needed so I did something in Java that I?ve been >> using. >> * Partner images ? I think it might be cool to put all ?partner? >> images in a subdirectory under images and just pull them all in >> dynamically instead of linking them statically in index.html.erb. >> This would allow anyone using the product to just dump their >> partner images in that directory and link them in automatically >> (again, less maintenance for me during re-branding :) ). >> * Wiki ? so far, I?ve just taken the wiki content from the >> BioCatalogue wiki and replicated it in a local DokuWiki >> installation. I?m not too thrilled with that approach because it >> makes it kind of hard to maintain etc. Ideally, I?d like to >> separate the wiki from the ?product? just a bit more and make it >> stand on it?s own a bit more. I?d thought about just linking off >> to the BioCatalogue wiki but thought it might get confusing for >> our users going from a product referred to as the ?EdUnify >> Registry? to a wiki that talks about the BioCatalogue. I?ve got >> several detailed thoughts about this that I will try to send you >> more about. I see two main components to this, and most things >> like this. First, there?s the ?product.? This product can be >> used by various ?projects.? Ideally, I think we?d have a wiki >> that focuses on the product that would be very general and just >> talk about how to use it etc. The content associated to this wiki >> would be very similar if not identical regardless of the project >> it was associated to. The only real difference would be the wiki >> ?branding.? i.e., the name of the product. Then, there might be >> a ?project? wiki that talks more about the specific context in >> which the product is being used. This could vary from project to >> project. For example, EdUnify is going to be using it in the >> context of ?web services for higher education? and the >> BioCatalogue project uses it in the context of ?life sciences.? >> So, there could be vastly different documentation associated to >> those uses of the product maintained by these projects >> independently. The first wiki I refer to here though might be >> shared between the two because it?s really just general >> documentation about how to use the product and what web services >> are etc. Sorry, I?m probably rambling a bit. I?ll try to send a >> better explanation. >> * One of our users ran into an issue with searching by tags. He >> added a tag to an operation. Then, he followed the Services link >> from the main page. Then, he clicked on the tag he?d added to the >> operation. When you do that, it doesn?t quite return what you?d >> expect. I tracked it down and thought I had it fixed but then I >> realized that there doesn?t appear to be a way to link an >> annotation to the actual service it?s associated to unless the >> annotation was made on the service itself. The tweaking I did was >> in tags.rb in the get_service_ids_for_tag(tag_name) method. >> Initially, I thought I had it figured out but once I was dealing >> with an instance that had more than one service, I realized it was >> a ?false fix.? I?m going to look at it some more and will try to >> send you a better explanation if that doesn?t make sense. I think >> if you just try it (add a tag to an operation and try to drill >> down on it as I?ve described here, you?ll see what I?m talking >> about) >> * Shibboleth ? the scenarios in which we?ll be using the product are >> still being fleshed out but it seems as though some sort of >> trusted federated authentication approach might be needed. So, >> we?re getting ready to start seeing if we can hook things up with >> Shibboleth. If you?d done anything along these lines yet (or have >> any thoughts or references I could look at) I?d appreciate hearing >> about them. Like I said, we?re in the early stages of this so >> I?ll send you more information as we move forward. >> * Deployment ? currently, we?re running things under Apache using >> the passenger phusion (a.k.a. mod_rails/mod_rack). This is all >> working fine but ideally, I?d like to deploy to an application >> server (like Tomcat or Jboss). I?ve been trying to get it working >> off and on for the past few weeks and haven?t had much luck at >> all. I?ve been trying to use warbler to create .war file and then >> deploy that to my app server. The war gets created but the app >> server isn?t liking it. I?ve been trying it with a very simple >> RoR app (not BioCatalogue) because I figured there might be some >> trial and error required. So far, I haven?t had much luck even >> with my very simple app. I?m not sure if you?ve ever tried doing >> anything like this? I don?t expect you to answer anything for me >> here, I?m just trying to give you an idea as to where I?m heading. >> The reason I?m going down this path is again related to the main >> goal I mentioned above. Typically, for each given ?project? >> that?s using the ?product? we?ve got at least two environments >> deployed (dev and demo). Ultimately, we?ll have three probably >> (prod). The way I?m doing it now, I have to maintain the actual >> code base in all environments (add another ?project? to the mix >> and it becomes even more challenging). So, my hope is that once I >> get this working, I can maintain the code base in on place and >> just deploy the war to the appropriate target environment when >> needed. We also typically use SVN for deployment as well as >> source code version control. I haven?t done that yet even for >> what we?re doing now so that would simplify things a bit but >> ultimately, I?d like to go down the app server route if possible. >> Again, I?m just letting you know where I?m trying to go, please >> let me know if you have any thoughts or recommendations related to >> this. >> * Terms of use ? this is another area we?ll probably need to talk >> about at some point because I?m not sure how that all needs to >> work. There may be multiple ?terms of use? depending on the >> project using the product. I?m just throwing this out there as >> something to think about. In general, I think it may just boil >> down to modeling the documentation (wiki stuff) with a little more >> thought towards the potential of multiple ?projects? using the >> same basic ?product.? I?ll try to send some more details >> regarding this as well in the near future. >> >> >> There are probably more things I?d love to discuss with you but I?ll >> leave it at these for now. We?re really excited about the potential of >> the various efforts we have that are trying to use BioCatalogue and I >> look forward to working more closely with you as we move forward. So >> far, I?ve just been muddling my way through trying to get things to a >> point where more eyes and minds can think about some of these things. I >> suspect in the coming weeks and months, we?ll have many more thoughts >> from various people to add to the mix. >> >> Thanks again for all your help! >> Tod >> >> On 5/14/10 5:05 AM, "Jiten Bhagat" wrote: >> >> Hi Tod, >> >> I just came across your BioCat installation this morning - >> https://demo.edunify.pesc.org/ - and I was impressed by how >> customised you were able to make it. >> >> It's our goal to package up the BioCatalogue as an easily >> installable >> and configurable product and your efforts here are very useful to >> us. >> >> Is there anything we can do to help with your demo? >> >> Many thanks, >> Jits >> >> >> >> Jackson, Tod wrote: >> > >> > Greetings, >> > >> > I and some colleagues from Emory University have been working on >> > getting an instance of the Biocatalogue application deployed >> locally >> > in hopes that it might be useful in a project we?re >> participating in >> > called EdUnify (_http://www.pesc.org/interior.php?page_id=204_) >> which >> > is sponsored by the PESC organization (_http://www.pesc.org/_). >> > >> > I?ve been working with Ruby 1.8.7 on Ubuntu 9.10. While I was >> able to >> > get it working, I had to make some modifications that I?m sure >> aren?t >> > correct so I thought I would post what I did here and see what >> I may >> > be missing. DISCLAIMER: I?m new to Ruby on Rails but do have a >> > strong development background especially in Java. Also, I did >> all of >> > this before the wiki >> > >> (_http://www.biocatalogue.org/wiki/doku.php?id=development:codebase_guidelines_) >> >> > was available so I will be checking that out to see if I could >> have >> > missed anything important with my trial and error approach. >> > >> > Here?s a high-level overview of the steps I took: >> > >> > - Exported the latest code base from the SVN repository >> to my >> > local environment (www/biocat) >> > >> > - Changed all the *.yml.pre to *.yml etc. >> > >> > - Ran a rake db:create/migrate >> > >> > - Installed a few missing gems >> > >> > - Once I got the basic environment where it needed to be >> in the >> > first 4 steps above, I ran it with the WEBrick app server >> > (script/server from my www/biocat directory) >> > >> > - Then, I tried to access the app by going to: >> > _http://localhost:3000/biocat/home_ >> > >> > Below is the stack trace that I got when I performed the basic >> steps >> > listed above. The error was ?wrong number of arguments (0 for 1)? >> > Based on the information in the stack trace, I found the code >> location >> > where I thought the error was occurring and it was this line in >> the >> > activity_feeds_helper.rb file: ?al_items = >> > Rails.cache.read(cach_key)? in my file it was line #44. So, to >> get >> > around this, I just commented out that line and replaced it >> with an >> > empty al_items = [ ]. Obviously, this is a hack but it did get me >> > around the error and allowed me to basically run the app locally. >> > Once I had it ?running? and accessible, I set up Passenger and was >> > able to run it via Apache as well. >> > >> > My question is what does this kind of error indicate? In the Java >> > world, I would probably lean toward a deprecated API or >> something like >> > that? i.e., perhaps this works with earlier versions but is no >> longer >> > supported in 1.8.7 or something like that? I haven?t dug into the >> > Rails.cache API so I?m not sure if my assessment is accurate or >> not so >> > I thought posting it here might be a good place to start while >> I look >> > into that a bit more myself. >> > >> > I thank you in advance for any help. >> > >> > Tod Jackson >> > >> >> [snip] >> >> >> >> ------------------------------------------------------------------------ >> This e-mail message (including any attachments) is for the sole use of >> the intended recipient(s) and may contain confidential and privileged >> information. If the reader of this message is not the intended >> recipient, you are hereby notified that any dissemination, distribution >> or copying of this message (including any attachments) is strictly >> prohibited. >> >> If you have received this message in error, please contact >> the sender by reply e-mail message and destroy all copies of the >> original message (including attachments). >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > > From noreply at rubyforge.org Mon May 17 06:02:37 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 17 May 2010 06:02:37 -0400 (EDT) Subject: [BioCatalogue-developers] [1975] branches/service-updates-and-curation/app/models/soap_service.rb: [ BIOCAT-307] Bugfix for the WSDL sync - endpoint was not being parsed correctly. Message-ID: <20100517100237.C556E16782AB@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 17 07:35:01 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 17 May 2010 07:35:01 -0400 (EDT) Subject: [BioCatalogue-developers] [1976] branches/service-updates-and-curation/app/models/soap_service.rb: [ BIOCAT-307] More fixes for the WSDL sync, and added namespace to solr indexing. Message-ID: <20100517113501.B7F631858358@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Mon May 17 08:11:23 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 17 May 2010 13:11:23 +0100 Subject: [BioCatalogue-developers] Service update checker - examples of the kinds of changelogs I am seeing... Message-ID: <4BF1326B.8030102@cs.man.ac.uk> I ran it against the first 30 SOAP services in the BioCatalogue and the attached file shows the changelogs I got. How does look Franck, Eric? Jits -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: soap_service_changelog_examples.txt URL: From jits at cs.man.ac.uk Mon May 17 08:13:12 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 17 May 2010 13:13:12 +0100 Subject: [BioCatalogue-developers] Service update checker - examples of the kinds of changelogs I am seeing... In-Reply-To: <4BF1326B.8030102@cs.man.ac.uk> References: <4BF1326B.8030102@cs.man.ac.uk> Message-ID: <4BF132D8.6060601@cs.man.ac.uk> Attached is the PDF version (in case the text file is not viewable properly for some). Jits Jiten Bhagat wrote: > I ran it against the first 30 SOAP services in the BioCatalogue and the > attached file shows the changelogs I got. > > How does look Franck, Eric? > > Jits > > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers -------------- next part -------------- A non-text attachment was scrubbed... Name: soap_service_changelog_examples.pdf Type: application/pdf Size: 27849 bytes Desc: not available URL: From noreply at rubyforge.org Mon May 17 08:30:32 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 17 May 2010 08:30:32 -0400 (EDT) Subject: [BioCatalogue-developers] [1977] branches/service-updates-and-curation/app/models/soap_service.rb: [ BIOCAT-307] Better handling of SoapOperations with the same names but for different ports . Message-ID: <20100517123032.C429F1678314@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon May 17 08:31:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 17 May 2010 13:31:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-307) Implement SoapService WSDL sync process Message-ID: <18470713.493.1274099477051.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-307?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10337 ] Jiten Bhagat logged work on BIOCAT-307: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-17 13:30 Start Date: 2010-05-17 11:30 Worklog Time Spent: 2 hours Issue Time Tracking ------------------- Remaining Estimate: 6 hours (was: 1 day) Time Spent: 2 days, 2 hours (was: 2 days) > Implement SoapService WSDL sync process > --------------------------------------- > > Key: BIOCAT-307 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-307 > Project: BioCatalogue > Issue Type: Sub-task > Components: SOAP Services Support > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Original Estimate: 3 days > Time Spent: 2 days, 2 hours > Remaining Estimate: 6 hours > > As part of the service update checker work, the SoapService model needs to have a special update method that syncs the current model state with the latest WSDL. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon May 17 09:08:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 17 May 2010 14:08:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-336) Implement a bulk create Annotations API endpoint for the curation by spreadsheets app In-Reply-To: <25706594.147.1273845976997.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29827512.501.1274101697024.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-336?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14921#action_14921 ] Jiten Bhagat commented on BIOCAT-336: ------------------------------------- Initial implementation done. Awaiting testing and usage. > Implement a bulk create Annotations API endpoint for the curation by spreadsheets app > ------------------------------------------------------------------------------------- > > Key: BIOCAT-336 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-336 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 4 hours > Time Spent: 3 hours > Remaining Estimate: 1 hour > > The curation by spreadsheets feature needs to be built over the API as it cannot be built within the codebase due to the ruby 'spreadsheet' gem being GPL licensed. > Therefore Mannie will be building a desktop app for this, which needs to interact with the BioCatalogue via the API. This will then -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon May 17 09:10:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 17 May 2010 09:10:07 -0400 (EDT) Subject: [BioCatalogue-developers] [1978] branches/service-updates-and-curation: updated service provider merging to take migrate the annotations as well Message-ID: <20100517131007.9C2681858345@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 17 09:36:46 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 17 May 2010 09:36:46 -0400 (EDT) Subject: [BioCatalogue-developers] [1979] branches/service-updates-and-curation/app/models/soap_service.rb: Use standard exception logging. Message-ID: <20100517133647.3AF741858356@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 17 09:42:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 17 May 2010 09:42:42 -0400 (EDT) Subject: [BioCatalogue-developers] [1980] branches/service-updates-and-curation/lib: [BIOCAT-308] Intial work on implementing the jobs and rake task for running the service update checker . Message-ID: <20100517134243.01056185832C@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Mon May 17 09:43:00 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 17 May 2010 14:43:00 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:cnio.es:runOFunCUT' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:cnio.es:runOFunCUT' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/973 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Mon May 17 09:49:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 17 May 2010 09:49:07 -0400 (EDT) Subject: [BioCatalogue-developers] [1981] branches/service-updates-and-curation/lib/bio_catalogue/jobs/ run_service_updater.rb: Bugfix for RunServiceUpdater job. Message-ID: <20100517134907.98DF41858345@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon May 17 09:51:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 17 May 2010 14:51:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-308) Implement background job(s) for running the service update checker Message-ID: <31163473.502.1274104276998.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-308?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10338 ] Jiten Bhagat logged work on BIOCAT-308: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-17 14:49 Start Date: 2010-05-17 13:10 Worklog Time Spent: 1 hour, 30 minutes Work Description: Initial work completed in revision 1980 Issue Time Tracking ------------------- Remaining Estimate: 30 minutes (was: 2 hours) Time Spent: 1 hour, 30 minutes > Implement background job(s) for running the service update checker > ------------------------------------------------------------------ > > Key: BIOCAT-308 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-308 > Project: BioCatalogue > Issue Type: Sub-task > Components: Background Processing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 1 hour, 30 minutes > Remaining Estimate: 30 minutes > > Implement the necessary background jobs and rake tasks required to perform the update checking asynchronously. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Mon May 17 11:08:20 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 17 May 2010 16:08:20 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: Services dead?] Message-ID: <4BF15BE4.30507@ebi.ac.uk> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== -------------- next part -------------- An embedded message was scrubbed... From: Christophe Blanchet Subject: Re: Services dead? Date: Mon, 17 May 2010 16:49:44 +0200 Size: 4097 URL: From issues at mygrid.org.uk Mon May 17 11:45:16 2010 From: issues at mygrid.org.uk (Franck Tanoh (JIRA)) Date: Mon, 17 May 2010 16:45:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-341) Possibility to harvest soaplab service description during submission Message-ID: <9661112.503.1274111116993.JavaMail.jira@rosalind.cs.man.ac.uk> Possibility to harvest soaplab service description during submission -------------------------------------------------------------------- Key: BIOCAT-341 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-341 Project: BioCatalogue Issue Type: Task Components: Content Acquisition, Service Monitoring Reporter: Franck Tanoh Assignee: Eric Nzuobontane Priority: Critical We need to automatically harvest annotation for soaplab service during submission. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon May 17 11:57:17 2010 From: issues at mygrid.org.uk (Franck Tanoh (JIRA)) Date: Mon, 17 May 2010 16:57:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-341) Possibility to harvest soaplab service description during submission In-Reply-To: <9661112.503.1274111116993.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2670724.504.1274111837020.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-341?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Franck Tanoh updated BIOCAT-341: -------------------------------- Component/s: Service Submission (was: Service Monitoring) > Possibility to harvest soaplab service description during submission > -------------------------------------------------------------------- > > Key: BIOCAT-341 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-341 > Project: BioCatalogue > Issue Type: Task > Components: Content Acquisition, Service Submission > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > Priority: Critical > > We need to automatically harvest annotation for soaplab service during submission. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon May 17 12:25:38 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 17 May 2010 12:25:38 -0400 (EDT) Subject: [BioCatalogue-developers] [1982] branches/service-updates-and-curation/lib/bio_catalogue/delayed_jobs .rb: Enhanced the job_exists? method to allow you to check for actual fields, like "service_id: 9" etc. Message-ID: <20100517162538.C3A5B1858356@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 17 12:37:26 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 17 May 2010 12:37:26 -0400 (EDT) Subject: [BioCatalogue-developers] [1983] branches/service-updates-and-curation: [BIOCAT-309] Implemented " Check for Updates" button on service show page. Message-ID: <20100517163726.8DCAC185835B@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon May 17 12:38:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 17 May 2010 17:38:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-309) Add "Check for Updates" button to service show page Message-ID: <579814.505.1274114296995.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-309?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10339 ] Jiten Bhagat logged work on BIOCAT-309: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-17 17:38 Start Date: 2010-05-17 15:15 Worklog Time Spent: 2 hours Issue Time Tracking ------------------- Remaining Estimate: 1 hour (was: 3 hours) Time Spent: 2 hours > Add "Check for Updates" button to service show page > --------------------------------------------------- > > Key: BIOCAT-309 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-309 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 hours > Time Spent: 2 hours > Remaining Estimate: 1 hour > > This should submit a job to run the update checker for the service. > This should only show for SOAP services at the moment. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon May 17 12:56:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 17 May 2010 12:56:09 -0400 (EDT) Subject: [BioCatalogue-developers] [1984] branches/service-updates-and-curation/app: [BIOCAT-310] Submit a job to run the update checker after a user tries to submit a service that already exists in the catalogue . Message-ID: <20100517165609.539E11678312@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon May 17 12:58:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 17 May 2010 17:58:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-310) Run update checker after a user tries to submit a duplicate service Message-ID: <6433888.506.1274115497055.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-310?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10340 ] Jiten Bhagat logged work on BIOCAT-310: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-17 17:56 Start Date: 2010-05-17 17:15 Worklog Time Spent: 30 minutes Issue Time Tracking ------------------- Remaining Estimate: 0 minutes (was: 2 hours) Time Spent: 30 minutes > Run update checker after a user tries to submit a duplicate service > ------------------------------------------------------------------- > > Key: BIOCAT-310 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-310 > Project: BioCatalogue > Issue Type: Sub-task > Components: Service Submission > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 30 minutes > Remaining Estimate: 0 minutes > > At SOAP service submission time, if a service already exists, submit a job to run the update checker and inform the user that the service has been found and an update check has been scheduled for it. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon May 17 12:58:19 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 17 May 2010 17:58:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-310) Run update checker after a user tries to submit a duplicate service Message-ID: <12050347.507.1274115499851.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-310?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-310. --------------------------------- Resolution: Fixed > Run update checker after a user tries to submit a duplicate service > ------------------------------------------------------------------- > > Key: BIOCAT-310 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-310 > Project: BioCatalogue > Issue Type: Sub-task > Components: Service Submission > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 30 minutes > Remaining Estimate: 0 minutes > > At SOAP service submission time, if a service already exists, submit a job to run the update checker and inform the user that the service has been found and an update check has been scheduled for it. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon May 17 12:58:21 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 17 May 2010 17:58:21 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-308) Implement background job(s) for running the service update checker Message-ID: <25194377.508.1274115501486.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-308?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-308. --------------------------------- Resolution: Fixed Awaiting testing and final integration > Implement background job(s) for running the service update checker > ------------------------------------------------------------------ > > Key: BIOCAT-308 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-308 > Project: BioCatalogue > Issue Type: Sub-task > Components: Background Processing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 1 hour, 30 minutes > Remaining Estimate: 30 minutes > > Implement the necessary background jobs and rake tasks required to perform the update checking asynchronously. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon May 17 12:58:22 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 17 May 2010 17:58:22 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-307) Implement SoapService WSDL sync process Message-ID: <7423702.509.1274115502998.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-307?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-307. --------------------------------- Remaining Estimate: 2 hours (was: 6 hours) Resolution: Fixed Awaiting testing and final integration > Implement SoapService WSDL sync process > --------------------------------------- > > Key: BIOCAT-307 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-307 > Project: BioCatalogue > Issue Type: Sub-task > Components: SOAP Services Support > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Original Estimate: 3 days > Time Spent: 2 days, 2 hours > Remaining Estimate: 2 hours > > As part of the service update checker work, the SoapService model needs to have a special update method that syncs the current model state with the latest WSDL. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon May 17 12:58:24 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 17 May 2010 17:58:24 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-311) Implement a mechanism to record changes made to SOAP services Message-ID: <25242257.510.1274115504534.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-311?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-311. --------------------------------- Remaining Estimate: 0 minutes (was: 2 hours) Resolution: Fixed Awaiting testing and final integration > Implement a mechanism to record changes made to SOAP services > ------------------------------------------------------------- > > Key: BIOCAT-311 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-311 > Project: BioCatalogue > Issue Type: Sub-task > Components: SOAP Services Support > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 4 hours > Time Spent: 2 hours > Remaining Estimate: 0 minutes > > Need a way of recording the changelog, when changes have been found in a WSDL (or if better WSDL parsing results in more information found). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon May 17 12:58:26 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 17 May 2010 17:58:26 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-309) Add "Check for Updates" button to service show page Message-ID: <24453684.511.1274115506065.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-309?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-309. --------------------------------- Remaining Estimate: 30 minutes (was: 1 hour) Resolution: Fixed Awaiting testing and final integration > Add "Check for Updates" button to service show page > --------------------------------------------------- > > Key: BIOCAT-309 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-309 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 hours > Time Spent: 2 hours > Remaining Estimate: 30 minutes > > This should submit a job to run the update checker for the service. > This should only show for SOAP services at the moment. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon May 17 13:08:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 17 May 2010 18:08:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-328) For items that are archived add a "this is archived" message at the top of the 'show' page for the item In-Reply-To: <17913058.63.1273667836992.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15437478.512.1274116097001.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-328?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-328. --------------------------------- Resolution: Fixed > For items that are archived add a "this is archived" message at the top of the 'show' page for the item > ------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-328 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-328 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 1 hour > Time Spent: 1 hour > Remaining Estimate: 0 minutes > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue May 18 02:55:18 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 02:55:18 -0400 (EDT) Subject: [BioCatalogue-developers] [1985] branches/web-service-ownership/app/models/user_mailer.rb: use sender email constant for as return address for BioCatalogue emails Message-ID: <20100518065518.2A5A11858361@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue May 18 04:53:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 18 May 2010 09:53:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-336) Implement a bulk create Annotations API endpoint for the curation by spreadsheets app In-Reply-To: <25706594.147.1273845976997.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10432143.513.1274172797168.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-336?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-336. --------------------------------- Resolution: Fixed > Implement a bulk create Annotations API endpoint for the curation by spreadsheets app > ------------------------------------------------------------------------------------- > > Key: BIOCAT-336 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-336 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 4 hours > Time Spent: 3 hours > Remaining Estimate: 1 hour > > The curation by spreadsheets feature needs to be built over the API as it cannot be built within the codebase due to the ruby 'spreadsheet' gem being GPL licensed. > Therefore Mannie will be building a desktop app for this, which needs to interact with the BioCatalogue via the API. This will then -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue May 18 04:53:58 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 04:53:58 -0400 (EDT) Subject: [BioCatalogue-developers] [1986] branches/service-updates-and-curation: [BIOCAT-330] Implemented " archive" and "unarchive" functionality in the UI to allow admins, curators and service submitters to archive/unarchive services. Message-ID: <20100518085359.D2D0D1858332@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue May 18 04:57:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 18 May 2010 09:57:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-330) Implement button to allow curators/admins to mark a service as archived In-Reply-To: <17543975.65.1273667956999.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <601079.514.1274173037049.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-330?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10341 ] Jiten Bhagat logged work on BIOCAT-330: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-18 09:57 Start Date: 2010-05-17 17:45 Worklog Time Spent: 2 hours Work Description: Initial work done in revision 1986 Issue Time Tracking ------------------- Remaining Estimate: 1 hour (was: 3 hours) Time Spent: 2 hours > Implement button to allow curators/admins to mark a service as archived > ----------------------------------------------------------------------- > > Key: BIOCAT-330 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-330 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 hours > Time Spent: 2 hours > Remaining Estimate: 1 hour > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue May 18 04:57:18 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 18 May 2010 09:57:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-330) Implement button to allow curators/admins to mark a service as archived In-Reply-To: <17543975.65.1273667956999.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29344144.515.1274173038395.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-330?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-330. --------------------------------- Resolution: Fixed Awaiting full testing > Implement button to allow curators/admins to mark a service as archived > ----------------------------------------------------------------------- > > Key: BIOCAT-330 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-330 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 hours > Time Spent: 2 hours > Remaining Estimate: 1 hour > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue May 18 06:14:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 18 May 2010 11:14:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-342) Infinitely recursive validates_associated in ServiceTest and TestScript cause failures in save Message-ID: <26987327.516.1274177657019.JavaMail.jira@rosalind.cs.man.ac.uk> Infinitely recursive validates_associated in ServiceTest and TestScript cause failures in save ---------------------------------------------------------------------------------------------- Key: BIOCAT-342 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-342 Project: BioCatalogue Issue Type: Bug Components: Service Monitoring Environment: Ruby, Rails, ActiveRecord Reporter: Jiten Bhagat Assignee: Eric Nzuobontane In app/models/service_test.rb: validates_associated :test In app/models/test_script.rb: validates_associated :service_test, :message => " is invalid. Creation of associated service test probably failed" This causes an infinite loop (and therefore a "stack level too deep" exception) when saving (because each model in turn will call each other recursively). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue May 18 06:16:37 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 06:16:37 -0400 (EDT) Subject: [BioCatalogue-developers] [1987] branches/service-updates-and-curation/app/views/layouts/_flashes. html.erb: Slightly better styling for the notice flash Message-ID: <20100518101638.0D8B13C8042@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 18 06:18:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 06:18:07 -0400 (EDT) Subject: [BioCatalogue-developers] [1988] branches/service-updates-and-curation: When archiving, should set the updated_at field for the object too. Message-ID: <20100518101807.E51D53C8042@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue May 18 06:28:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 18 May 2010 11:28:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-331) Show changelogs on service show page as part of the "Activity" tab In-Reply-To: <29588368.68.1273668436995.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23719082.519.1274178497018.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-331?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-331: -------------------------------- Summary: Show changelogs on service show page as part of the "Activity" tab (was: Show changelogs on service show page) > Show changelogs on service show page as part of the "Activity" tab > ------------------------------------------------------------------ > > Key: BIOCAT-331 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-331 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 5 hours > Remaining Estimate: 5 hours > > When viewing a service, should be able to see the full list of changelogs for that service. > Ensure that: > - Must explain that any changes recorded in the SOAP service changelog may be from updates in the actual WSDL OR from things that we are now able to parse from the WSDL. > - It is clarified that info from SoapServiceChange is specifically about the SOAP/WSDL based service. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue May 18 06:24:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 18 May 2010 11:24:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-342) Infinitely recursive validates_associated in ServiceTest and TestScript cause failures in save In-Reply-To: <26987327.516.1274177657019.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7898848.517.1274178257018.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-342?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14927#action_14927 ] Eric Nzuobontane commented on BIOCAT-342: ----------------------------------------- this was fixed and should be available in trunk > Infinitely recursive validates_associated in ServiceTest and TestScript cause failures in save > ---------------------------------------------------------------------------------------------- > > Key: BIOCAT-342 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-342 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring > Environment: Ruby, Rails, ActiveRecord > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > > In app/models/service_test.rb: > validates_associated :test > In app/models/test_script.rb: > validates_associated :service_test, :message => " is invalid. Creation of associated service test probably failed" > This causes an infinite loop (and therefore a "stack level too deep" exception) when saving (because each model in turn will call each other recursively). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue May 18 06:31:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 18 May 2010 11:31:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-343) Implement an "Activity" tab on a service's page Message-ID: <29654500.520.1274178676994.JavaMail.jira@rosalind.cs.man.ac.uk> Implement an "Activity" tab on a service's page ----------------------------------------------- Key: BIOCAT-343 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343 Project: BioCatalogue Issue Type: New Feature Components: Activity Logging / Feeds / Notifications, Web Interface Reporter: Jiten Bhagat Assignee: Jiten Bhagat This should show a full activity list/feed for the service -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue May 18 06:33:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 18 May 2010 11:33:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-342) Infinitely recursive validates_associated in ServiceTest and TestScript cause failures in save In-Reply-To: <26987327.516.1274177657019.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20872066.521.1274178797014.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-342?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-342 started by Eric Nzuobontane. > Infinitely recursive validates_associated in ServiceTest and TestScript cause failures in save > ---------------------------------------------------------------------------------------------- > > Key: BIOCAT-342 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-342 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring > Environment: Ruby, Rails, ActiveRecord > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > > In app/models/service_test.rb: > validates_associated :test > In app/models/test_script.rb: > validates_associated :service_test, :message => " is invalid. Creation of associated service test probably failed" > This causes an infinite loop (and therefore a "stack level too deep" exception) when saving (because each model in turn will call each other recursively). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue May 18 06:26:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 18 May 2010 11:26:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-233) Need to take into account old/deprecated/deleted services Message-ID: <30333566.518.1274178377015.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-233?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10342 ] Jiten Bhagat logged work on BIOCAT-233: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-18 11:25 Start Date: 2010-05-18 11:25 Worklog Time Spent: 2 hours Work Description: More work spent on the acts_as_archived mechanism Issue Time Tracking ------------------- Remaining Estimate: 0 minutes (was: 2 days, 2 hours) Time Spent: 1 day (was: 6 hours) > Need to take into account old/deprecated/deleted services > --------------------------------------------------------- > > Key: BIOCAT-233 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-233 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 days > Time Spent: 1 day > Remaining Estimate: 0 minutes > > From Steve: > "Perhaps a wikipedia-like approach, where something gets marked for > deletion and gets a big warning badge in the meantime, giving people a > chance to comment / complain before it goes in the bin. " -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue May 18 06:36:37 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 06:36:37 -0400 (EDT) Subject: [BioCatalogue-developers] [1989] branches/rest-write-api/: Removing old branch as it is now stale ( a new branch for the REST write API will be created at a later stage) Message-ID: <20100518103637.278633C8042@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 18 06:37:48 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 06:37:48 -0400 (EDT) Subject: [BioCatalogue-developers] [1990] branches/service-provider-mapping/: Removing unused branch ( to avoid confusion) as the service provider mapping work was done in service-updates-and-curation . Message-ID: <20100518103748.CB3DE3C8045@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue May 18 06:42:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 18 May 2010 11:42:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-342) Infinitely recursive validates_associated in ServiceTest and TestScript cause failures in save In-Reply-To: <26987327.516.1274177657019.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17511032.522.1274179336998.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-342?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-342. ------------------------------------- Resolution: Implemented Fix for this issue is already available in trunk > Infinitely recursive validates_associated in ServiceTest and TestScript cause failures in save > ---------------------------------------------------------------------------------------------- > > Key: BIOCAT-342 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-342 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring > Environment: Ruby, Rails, ActiveRecord > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > > In app/models/service_test.rb: > validates_associated :test > In app/models/test_script.rb: > validates_associated :service_test, :message => " is invalid. Creation of associated service test probably failed" > This causes an infinite loop (and therefore a "stack level too deep" exception) when saving (because each model in turn will call each other recursively). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue May 18 06:46:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 18 May 2010 11:46:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-344) Update soaplab services descriptions by calling the describe method Message-ID: <7031632.523.1274179577000.JavaMail.jira@rosalind.cs.man.ac.uk> Update soaplab services descriptions by calling the describe method ------------------------------------------------------------------- Key: BIOCAT-344 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-344 Project: BioCatalogue Issue Type: Task Components: Content Acquisition Environment: SAOP, Soaplab, soapclients Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Call the describe method for the soaplab services and add the content to the service description -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue May 18 07:22:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 18 May 2010 12:22:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-345) update the annotations counts mechanism to take into account these new fields Message-ID: <32597963.524.1274181737002.JavaMail.jira@rosalind.cs.man.ac.uk> update the annotations counts mechanism to take into account these new fields ----------------------------------------------------------------------------- Key: BIOCAT-345 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-345 Project: BioCatalogue Issue Type: Refinement Components: Annotations (in App) Reporter: Eric Nzuobontane Assignee: Jiten Bhagat update the annotations counts mechanism to take into account these new fields (like soaplab_description and namespace) -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue May 18 07:59:26 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 07:59:26 -0400 (EDT) Subject: [BioCatalogue-developers] [1991] branches/service-updates-and-curation/app/models/soap_service.rb: [ BIOCAT-307] Bugfixes for the handling of inputs and outputs in the WSDL sync method. Message-ID: <20100518115927.087821858354@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue May 18 08:03:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 18 May 2010 13:03:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-307) Implement SoapService WSDL sync process Message-ID: <29893282.525.1274184197016.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-307?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10343 ] Jiten Bhagat logged work on BIOCAT-307: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-18 13:02 Start Date: 2010-05-18 12:59 Worklog Time Spent: 30 minutes Work Description: Bugfixes for the handling of inputs and outputs in the WSDL sync method. Revision 1991. Issue Time Tracking ------------------- Remaining Estimate: 1 hour, 30 minutes (was: 2 hours) Time Spent: 2 days, 2 hours, 30 minutes (was: 2 days, 2 hours) > Implement SoapService WSDL sync process > --------------------------------------- > > Key: BIOCAT-307 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-307 > Project: BioCatalogue > Issue Type: Sub-task > Components: SOAP Services Support > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Original Estimate: 3 days > Time Spent: 2 days, 2 hours, 30 minutes > Remaining Estimate: 1 hour, 30 minutes > > As part of the service update checker work, the SoapService model needs to have a special update method that syncs the current model state with the latest WSDL. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue May 18 08:44:36 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 08:44:36 -0400 (EDT) Subject: [BioCatalogue-developers] [1992] branches/service-updates-and-curation/app/models/soap_service.rb: [ BIOCAT-307] Another bugfix for the handling of inputs and outputs in the WSDL sync method . Message-ID: <20100518124436.8059D1858360@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 18 09:00:27 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 09:00:27 -0400 (EDT) Subject: [BioCatalogue-developers] [1993] trunk/config/environments/production.rb: By default, disable the rotating of logs. Message-ID: <20100518130027.99AAC3C8042@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 18 09:01:04 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 09:01:04 -0400 (EDT) Subject: [BioCatalogue-developers] [1994] trunk/script/biocatalogue/service_annotation_report.rb: Bugfix for the example data annotations check. Message-ID: <20100518130104.5DA771858364@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue May 18 09:27:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 18 May 2010 14:27:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-343) Implement an "News" tab on a service's page In-Reply-To: <29654500.520.1274178676994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32140651.526.1274189237004.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-343: -------------------------------- Summary: Implement an "News" tab on a service's page (was: Implement an "Activity" tab on a service's page) Original Estimate: 2 days (was: 1 day) Remaining Estimate: 2 days (was: 1 day) Description: This should show a full activity list/feed for the service, showing events that have happened, like new annotations, WSDL changes, etc. Maybe have the WSDL changes in a separate column on the right hand side? was:This should show a full activity list/feed for the service > Implement an "News" tab on a service's page > ------------------------------------------- > > Key: BIOCAT-343 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 days > Remaining Estimate: 2 days > > This should show a full activity list/feed for the service, showing events that have happened, like new annotations, WSDL changes, etc. > Maybe have the WSDL changes in a separate column on the right hand side? -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue May 18 09:33:26 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 09:33:26 -0400 (EDT) Subject: [BioCatalogue-developers] [1995] branches/service-updates-and-curation/app/views: Moved the activity UI partial into the shared folder ( in preparation for usage in other parts of the UI). Message-ID: <20100518133326.519BD3C804A@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue May 18 09:43:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 18 May 2010 14:43:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-331) Show changelogs on service show page as part of the "News" tab In-Reply-To: <29588368.68.1273668436995.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <586740.527.1274190197008.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-331?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-331: -------------------------------- Summary: Show changelogs on service show page as part of the "News" tab (was: Show changelogs on service show page as part of the "Activity" tab) > Show changelogs on service show page as part of the "News" tab > -------------------------------------------------------------- > > Key: BIOCAT-331 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-331 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 5 hours > Remaining Estimate: 5 hours > > When viewing a service, should be able to see the full list of changelogs for that service. > Ensure that: > - Must explain that any changes recorded in the SOAP service changelog may be from updates in the actual WSDL OR from things that we are now able to parse from the WSDL. > - It is clarified that info from SoapServiceChange is specifically about the SOAP/WSDL based service. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue May 18 09:43:18 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 18 May 2010 14:43:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-346) Add entries to the homepage activity feed for when changes have been found Message-ID: <12074178.528.1274190198761.JavaMail.jira@rosalind.cs.man.ac.uk> Add entries to the homepage activity feed for when changes have been found -------------------------------------------------------------------------- Key: BIOCAT-346 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-346 Project: BioCatalogue Issue Type: Sub-task Components: Activity Logging / Feeds / Notifications, Web Interface Reporter: Jiten Bhagat Assignee: Jiten Bhagat Look for ActivityLog events with the action 'create' and activity_loggable_type 'SoapServiceChange'. Make sure to link to the actual changelog (eg: /services/8#soap_service_change_10) -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue May 18 09:51:45 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 09:51:45 -0400 (EDT) Subject: [BioCatalogue-developers] [1996] trunk: minor changes to service monitoring work and initial work soaplab service description call Message-ID: <20100518135145.DB9233C804A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 18 10:48:36 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 10:48:36 -0400 (EDT) Subject: [BioCatalogue-developers] [1997] trunk: bugfix test_script model and fix of related tests Message-ID: <20100518144836.BA7F13C8042@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 18 11:57:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 11:57:47 -0400 (EDT) Subject: [BioCatalogue-developers] [1998] branches/service-updates-and-curation: [BIOCAT-331] Initial work on the new "News" tab on the service page. Message-ID: <20100518155748.1378816782A0@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 18 11:59:34 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 11:59:34 -0400 (EDT) Subject: [BioCatalogue-developers] [1999] trunk: merged web-service-ownership branch into trunk Message-ID: <20100518155935.14E7916782A0@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 18 12:10:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 12:10:42 -0400 (EDT) Subject: [BioCatalogue-developers] [2000] branches/service-updates-and-curation: Refactored the tabber startup code - moved into a non-obtrusive JS way. Message-ID: <20100518161042.E3F693C804B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 18 12:12:18 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 12:12:18 -0400 (EDT) Subject: [BioCatalogue-developers] [2001] branches/service-updates-and-curation/app/controllers/ services_controller.rb: Updated the text for flash messages when an update check has been requested for a service . Message-ID: <20100518161218.AFDAD16782AB@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue May 18 12:17:02 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 18 May 2010 17:17:02 +0100 Subject: [BioCatalogue-developers] info from the web-service-ownership merge into trunck Message-ID: <4BF2BD7E.6020607@ebi.ac.uk> merge -r 1758:1985 svn+ssh://ebontane at rubyforge.org/var/svn/biocatalogue/branches/web-service-ownership /local/copy --- Merging r1758 through r1985 into /Users/ericnzuobontane/Documents/workspace/biocatalogue/trunk Merge complete. ===== File Statistics: ===== Added: 32 Updated: 11 ==== Conflict Statistics: ===== File conflicts: 1 resolve --accept=working /Users/ericnzuobontane/Documents/workspace/biocatalogue/trunk/db/schema.rb Committed revision 1999. -- 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 May 18 13:11:49 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 18 May 2010 18:11:49 +0100 Subject: [BioCatalogue-developers] Confusion on service responsibility Message-ID: <4BF2CA55.3060103@cs.man.ac.uk> Hi Eric, Whilst merging I came across some confusion in the UI. In app/views/services/show.html.erb there is: <% if BioCatalogue::Auth.allow_user_to_claim_thing?(current_user, @service) %>
  • <%= link_to(image_tag(icon_filename_for(:curator)) + content_tag(:span, ' Take Responsibility'), new_responsibility_request_url(:service_id => @service.id)) -%>
    • <% end %> Is this the same as requesting responsibility? In which case, the check for "BioCatalogue::Auth.allow_user_to_claim_thing?" doesn't make sense to me. Jits From noreply at rubyforge.org Tue May 18 13:13:31 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 13:13:31 -0400 (EDT) Subject: [BioCatalogue-developers] [2002] trunk: Merged revisions 1817:2001 from 'service-updates-and-curation ' to trunk. Message-ID: <20100518171332.A913316782A0@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 18 13:20:04 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 18 May 2010 13:20:04 -0400 (EDT) Subject: [BioCatalogue-developers] [2003] trunk/app/views/soap_operations/_listing.html.erb: Style fixes for the SOAP operations partial Message-ID: <20100518172004.F38B91858346@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue May 18 20:22:56 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 19 May 2010 01:22:56 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromFASTAToDNASequence' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromFASTAToDNASequence' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/784 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed May 19 05:03:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 19 May 2010 05:03:14 -0400 (EDT) Subject: [BioCatalogue-developers] [2004] trunk/app/views/services/show.html.erb: Fixes for the actions dropdown menu for the Service page. Message-ID: <20100519090314.25ABE1858345@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Wed May 19 06:04:18 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 19 May 2010 11:04:18 +0100 Subject: [BioCatalogue-developers] Running the Service Provider Clustering Script In-Reply-To: <84A2C27D-6E45-4C73-BE9C-AE618D3E59F6@mygrid.org.uk> References: <84A2C27D-6E45-4C73-BE9C-AE618D3E59F6@mygrid.org.uk> Message-ID: <4BF3B7A2.4030906@ebi.ac.uk> Thanks Mannie! One thing I note is that for the scripts we have in /scripts we have different ways of passing arguments to them. We need to adopt one style and make all scripts consistent with that style. Eric Mannie T wrote: > Hi Eric, > > This is to outline the few steps needed in order to run the script to > cluster service providers. > > Assuming Solr is already running: > 1. Run the migrations (the service_provider_hostnames table is needed!!!) > 2. Copy the attached CSV file into the data folder for the Rails app. > This CSV file contains the the Service Provider clustering > information. Be sure to keep the name as is... > 3. Run the command: > ruby script/biocatalogue/cluster_service_providers_apr10.rb > Running the script without having provided any arguments will run it > in "development". For production mode, run: > ruby script/biocatalogue/cluster_service_providers_apr10.rb production > > A log is created and is name following > format: update_service_providers_{date}_{time}.log > > Regards, > Mannie > > > > ------------------------------------------------------------------------ > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From issues at mygrid.org.uk Wed May 19 06:16:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 19 May 2010 11:16:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-347) Deploy new release on the test server Message-ID: <28020018.568.1274264177087.JavaMail.jira@rosalind.cs.man.ac.uk> Deploy new release on the test server ------------------------------------- Key: BIOCAT-347 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-347 Project: BioCatalogue Issue Type: Task Components: Server Management Environment: Apache, mod_rails, RoR, CentOS Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Deploy the new codebase onto the test server -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 19 06:20:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 19 May 2010 11:20:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-348) Create release notes for new code base deployment Message-ID: <13638682.569.1274264416998.JavaMail.jira@rosalind.cs.man.ac.uk> Create release notes for new code base deployment ------------------------------------------------- Key: BIOCAT-348 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-348 Project: BioCatalogue Issue Type: Sub-task Components: Wiki Environment: Wiki Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Create a page for release instructions, testing script and major features for the release -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Wed May 19 06:23:34 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 19 May 2010 11:23:34 +0100 Subject: [BioCatalogue-developers] Running the Service Provider Clustering Script In-Reply-To: <4BF3B7A2.4030906@ebi.ac.uk> References: <84A2C27D-6E45-4C73-BE9C-AE618D3E59F6@mygrid.org.uk> <4BF3B7A2.4030906@ebi.ac.uk> Message-ID: <4BF3BC26.9060600@cs.man.ac.uk> Agreed. Unfortunately things have evolved in different ways with those scripts. We have different ways to: - log - pass arguments - determine whether it's a one off (eg: xxx_apr10) - etc Need to consolidate if we can. Jits Eric Nzuobontane wrote: > Thanks Mannie! > One thing I note is that for the scripts we have in /scripts we have > different ways of passing arguments to them. We need to adopt one > style and make all scripts consistent with that style. > > Eric > > > > Mannie T wrote: >> Hi Eric, >> >> This is to outline the few steps needed in order to run the script to >> cluster service providers. >> >> Assuming Solr is already running: >> 1. Run the migrations (the service_provider_hostnames table is >> needed!!!) >> 2. Copy the attached CSV file into the data folder for the Rails app. >> This CSV file contains the the Service Provider clustering >> information. Be sure to keep the name as is... >> 3. Run the command: ruby >> script/biocatalogue/cluster_service_providers_apr10.rb >> Running the script without having provided any arguments will run it >> in "development". For production mode, run: >> ruby script/biocatalogue/cluster_service_providers_apr10.rb production >> >> A log is created and is name following format: >> update_service_providers_{date}_{time}.log >> >> Regards, >> Mannie >> >> >> >> ------------------------------------------------------------------------ >> > > From issues at mygrid.org.uk Wed May 19 09:42:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 19 May 2010 14:42:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-348) Create release notes for new code base deployment In-Reply-To: <13638682.569.1274264416998.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30151692.1026.1274276537013.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-348?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-348 started by Eric Nzuobontane. > Create release notes for new code base deployment > ------------------------------------------------- > > Key: BIOCAT-348 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-348 > Project: BioCatalogue > Issue Type: Sub-task > Components: Wiki > Environment: Wiki > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 2 hours > Remaining Estimate: 2 hours > > Create a page for release instructions, testing script and major features for the release -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Wed May 19 11:01:06 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 19 May 2010 16:01:06 +0100 Subject: [BioCatalogue-developers] pre-release notes Message-ID: <4BF3FD32.9090606@ebi.ac.uk> Hi Guys, Could you please update the page which I created here? Especially the included in this release and to be tested sections. Franck you please add your DRAMA thing to the to be tested section? http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes Another thing is whether we should make an announcement for the release. It would be better if we did as I will be the one to be crucified should anything go wrong. I do not expect much to go wrong but you never know. 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 Wed May 19 11:04:37 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 19 May 2010 16:04:37 +0100 Subject: [BioCatalogue-developers] pre-release notes In-Reply-To: <4BF3FD32.9090606@ebi.ac.uk> References: <4BF3FD32.9090606@ebi.ac.uk> Message-ID: <4BF3FE05.3090708@cs.man.ac.uk> Eric Nzuobontane wrote: > Hi Guys, > Could you please update the page which I created here? Especially the > included in this release and to be tested sections. Franck you please > add your DRAMA thing to the to be tested section? > http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes > I've added some stuff. > > Another thing is whether we should make an announcement for the > release. It would be better if we did as I will be the one to be > crucified should anything go wrong. I do not expect much to go wrong > but you never know. Could do, but it's not certain to me when the update will go ahead. It really depends on our initial testing today (if there are any show stopping errors then we would need to postpone the release). > > Eric Jits From jits at cs.man.ac.uk Wed May 19 11:15:55 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 19 May 2010 16:15:55 +0100 Subject: [BioCatalogue-developers] pre-release notes In-Reply-To: <4BF3FE05.3090708@cs.man.ac.uk> References: <4BF3FD32.9090606@ebi.ac.uk> <4BF3FE05.3090708@cs.man.ac.uk> Message-ID: <4BF400AB.3070109@cs.man.ac.uk> Also, did you find out what was causing the service deletion timeout errors? Jits Jiten Bhagat wrote: > Eric Nzuobontane wrote: > >> Hi Guys, >> Could you please update the page which I created here? Especially the >> included in this release and to be tested sections. Franck you please >> add your DRAMA thing to the to be tested section? >> http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes >> >> > > I've added some stuff. > > > >> Another thing is whether we should make an announcement for the >> release. It would be better if we did as I will be the one to be >> crucified should anything go wrong. I do not expect much to go wrong >> but you never know. >> > > Could do, but it's not certain to me when the update will go ahead. It > really depends on our initial testing today (if there are any show > stopping errors then we would need to postpone the release). > > >> Eric >> > > Jits > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From ericnzuo at ebi.ac.uk Wed May 19 11:24:12 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 19 May 2010 16:24:12 +0100 Subject: [BioCatalogue-developers] pre-release notes In-Reply-To: <4BF400AB.3070109@cs.man.ac.uk> References: <4BF3FD32.9090606@ebi.ac.uk> <4BF3FE05.3090708@cs.man.ac.uk> <4BF400AB.3070109@cs.man.ac.uk> Message-ID: <4BF4029C.6080809@ebi.ac.uk> No unfortunately, but now that the release is under test, I should finally get to that one. Eric Jiten Bhagat wrote: > Also, did you find out what was causing the service deletion timeout errors? > > Jits > > > Jiten Bhagat wrote: > >> Eric Nzuobontane wrote: >> >> >>> Hi Guys, >>> Could you please update the page which I created here? Especially the >>> included in this release and to be tested sections. Franck you please >>> add your DRAMA thing to the to be tested section? >>> http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes >>> >>> >>> >> I've added some stuff. >> >> >> >> >>> Another thing is whether we should make an announcement for the >>> release. It would be better if we did as I will be the one to be >>> crucified should anything go wrong. I do not expect much to go wrong >>> but you never know. >>> >>> >> Could do, but it's not certain to me when the update will go ahead. It >> really depends on our initial testing today (if there are any show >> stopping errors then we would need to postpone the release). >> >> >> >>> Eric >>> >>> >> Jits >> >> _______________________________________________ >> 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 May 19 12:11:30 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 19 May 2010 17:11:30 +0100 Subject: [BioCatalogue-developers] pre-release notes In-Reply-To: <4BF3FD32.9090606@ebi.ac.uk> References: <4BF3FD32.9090606@ebi.ac.uk> Message-ID: >Franck you please add your DRAMA thing to the to be tested section? Added but not yet completed > Another thing is whether we should make an announcement for the release. if it's a small update without any major changes or disruptions no need for a pre-announcement (isn't what we're usually doing?) We can do the announcement on the friend list once the update is completed. Franck On 19 May 2010 16:01, Eric Nzuobontane wrote: > Hi Guys, > Could you please update the page which I created here? Especially the > included in this release and to be tested sections. Franck you please add > your DRAMA thing to the to be tested section? > http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes > > Another thing is whether we should make an announcement for the release. It > would be better if we did as I will be the one to be crucified should > anything go wrong. I do not expect much to go wrong but you never know. > > 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 jits at cs.man.ac.uk Wed May 19 12:17:44 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 19 May 2010 17:17:44 +0100 Subject: [BioCatalogue-developers] pre-release notes In-Reply-To: References: <4BF3FD32.9090606@ebi.ac.uk> Message-ID: <4BF40F28.3000109@cs.man.ac.uk> Hmm... given the size of the update (LOTS of new features) I think it's best if we do announce it beforehand. The only thing is we need to agree on a time slot for the final release, and stick to it. This all depends on how the service update checker run that Eric is doing now finishes. If it goes ahead with no errors (on ALL the SOAP services in the catalogue) then we're good to go. Otherwise we need to rethink. I will also be doing the news feed stuff on Friday in my branch and merge back if all goes well. Jits Franck Tanoh wrote: >> Franck you please add your DRAMA thing to the to be tested section? >> > Added but not yet completed > > >> Another thing is whether we should make an announcement for the release. >> > if it's a small update without any major changes or disruptions no > need for a pre-announcement (isn't what we're usually doing?) > We can do the announcement on the friend list once the update is completed. > > Franck > > On 19 May 2010 16:01, Eric Nzuobontane wrote: > >> Hi Guys, >> Could you please update the page which I created here? Especially the >> included in this release and to be tested sections. Franck you please add >> your DRAMA thing to the to be tested section? >> http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes >> >> Another thing is whether we should make an announcement for the release. It >> would be better if we did as I will be the one to be crucified should >> anything go wrong. I do not expect much to go wrong but you never know. >> >> 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 >> >> > > > > From ytanoh at cs.man.ac.uk Wed May 19 12:29:55 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 19 May 2010 17:29:55 +0100 Subject: [BioCatalogue-developers] pre-release notes In-Reply-To: <4BF40F28.3000109@cs.man.ac.uk> References: <4BF3FD32.9090606@ebi.ac.uk> <4BF40F28.3000109@cs.man.ac.uk> Message-ID: >I think it's best if we do announce it beforehand. In that case, we may not be able to do the release next week. From what I gathered from last big update we need to display the banner on top of the main site for about a week or so before such updates. We'll put ourselves in the fire line if we announce it without showing the banner on the site.... So if we're going to announce the release let's display the banner today or tomorrow, it'll give have the time to do the release on Wed or Thurs next week. Franck On 19 May 2010 17:17, Jiten Bhagat wrote: > Hmm... given the size of the update (LOTS of new features) I think it's > best if we do announce it beforehand. The only thing is we need to agree > on a time slot for the final release, and stick to it. This all depends > on how the service update checker run that Eric is doing now finishes. > If it goes ahead with no errors (on ALL the SOAP services in the > catalogue) then we're good to go. Otherwise we need to rethink. > > I will also be doing the news feed stuff on Friday in my branch and > merge back if all goes well. > > Jits > > > > Franck Tanoh wrote: >>> Franck you please add your DRAMA thing to the to be tested section? >>> >> Added but not yet completed >> >> >>> Another thing is whether we should make an announcement for the release. >>> >> if it's a small update without any major changes or disruptions no >> need for a pre-announcement (isn't what we're usually doing?) >> We can do the announcement on the friend list once the update is completed. >> >> Franck >> >> On 19 May 2010 16:01, Eric Nzuobontane wrote: >> >>> Hi Guys, >>> Could you please update the page which I created here? Especially the >>> included in this release and to be tested sections. Franck you please add >>> your DRAMA thing to the to be tested section? >>> http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes >>> >>> Another thing is whether we should make an announcement for the release. It >>> would be better if we did as I will be the one to be crucified should >>> anything go wrong. I do not expect much to go wrong but you never know. >>> >>> 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 twitter-follow-biocatalogue-developers=rubyforge.org at postmaster.twitter.com Wed May 19 14:15:59 2010 From: twitter-follow-biocatalogue-developers=rubyforge.org at postmaster.twitter.com (Twitter) Date: Wed, 19 May 2010 18:15:59 +0000 Subject: [BioCatalogue-developers] Jeff Rogers is now following you on Twitter! Message-ID: <4bf42adfe0e61_261866792a0902512@mx004.twitter.com.tmail> Hi, BioCatalogue Test (biocat_test). Jeff Rogers (meetjeffrogers) is now following your tweets on Twitter. Check out Jeff Rogers's profile here: http://twitter.com/meetjeffrogers You may follow Jeff Rogers as well by clicking on the "follow" button. Jeff Rogers may not appear in your follower list. Jeff Rogers may have decided to stop following you, or the account may have been suspended for a Terms of Service violation. If you believe Jeff Rogers is engaging in abusive behavior on Twitter, you may report Jeff Rogers for spam (http://twitter.com/user_spam_reports/biocat_test/confirm/meetjeffrogers?token=iqubpwVHI2ZgbR2bn4Igl%2BXGDlJpwKbSx34sWFyVhxEVcflGmbeoBU6myM9KAPG9zdtFB69r68reV1dNZcYwqH60a3O9wlFZJOy%2FLmhX1Y1e7g0UYRl3Sg%3D%3D&utm_medium=email&utm_content=block&evid=E9TFsI4xHF0Cr1EAaToPgngAqk32uKgtyBbkTmjhKbo%3D&utm_source=follow&utm_campaign=twitter20080331162631). Best, Twitter -- If you'd rather not receive follow notification emails from Twitter, you can unsubscribe immediately. To resubscribe or change other Twitter email preferences, visit your account settings to manage email notices. Unsubscribe: http://twitter.com/account/unsubscribe?code=YSlaCzjGdvoZcrlfVh97oa%2BYGDfTIfHzHvSuGoY7f508V9Q3yhtvdw%3D%3D&utm_medium=email&utm_content=unsubscribe&evid=E9TFsI4xHF0Cr1EAaToPgngAqk32uKgtyBbkTmjhKbo%3D&t=follow&utm_source=follow&utm_campaign=twitter20080331162631 -------------- next part -------------- An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed May 19 14:54:38 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 19 May 2010 19:54:38 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEntryFromFSSP' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEntryFromFSSP' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/790 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 Thu May 20 04:17:11 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 20 May 2010 09:17:11 +0100 Subject: [BioCatalogue-developers] pre-release notes In-Reply-To: References: <4BF3FD32.9090606@ebi.ac.uk> Message-ID: <4BF4F007.9060404@ebi.ac.uk> >> Another thing is whether we should make an announcement for the release. >> > if it's a small update without any major changes or disruptions no > need for a pre-announcement (isn't what we're usually doing?) > We can do the announcement on the friend list once the update is completed. > Well, that is what has been happening yes. But it is me stupidly risking my head in order not to get bugged down in what is not the most unworkable policy. And if you remember the case that caused the biggest problems last time, I sent that mail just after a meeting in which we all agreed to do the update. Yet it was me under attack as having taken stupid unilateral decision to bring a service down. I just do not want that to happen again. Eric > Franck > > On 19 May 2010 16:01, Eric Nzuobontane wrote: > >> Hi Guys, >> Could you please update the page which I created here? Especially the >> included in this release and to be tested sections. Franck you please add >> your DRAMA thing to the to be tested section? >> http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes >> >> Another thing is whether we should make an announcement for the release. It >> would be better if we did as I will be the one to be crucified should >> anything go wrong. I do not expect much to go wrong but you never know. >> >> 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 >> >> > > > > -- 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 Thu May 20 04:27:55 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 20 May 2010 09:27:55 +0100 Subject: [BioCatalogue-developers] pre-release notes In-Reply-To: References: <4BF3FD32.9090606@ebi.ac.uk> <4BF40F28.3000109@cs.man.ac.uk> Message-ID: <4BF4F28B.2060501@cs.man.ac.uk> Franck Tanoh wrote: >> I think it's best if we do announce it beforehand. >> > In that case, we may not be able to do the release next week. From > what I gathered from last big update we need to display the banner on > top of the main site for about a week or so before such updates. We'll > put ourselves in the fire line if we announce it without showing the > banner on the site.... > So if we're going to announce the release let's display the banner > today or tomorrow, it'll give have the time to do the release on Wed > or Thurs next week. > Yeap, I was thinking along the same lines as this as well. Jits > Franck > > On 19 May 2010 17:17, Jiten Bhagat wrote: > >> Hmm... given the size of the update (LOTS of new features) I think it's >> best if we do announce it beforehand. The only thing is we need to agree >> on a time slot for the final release, and stick to it. This all depends >> on how the service update checker run that Eric is doing now finishes. >> If it goes ahead with no errors (on ALL the SOAP services in the >> catalogue) then we're good to go. Otherwise we need to rethink. >> >> I will also be doing the news feed stuff on Friday in my branch and >> merge back if all goes well. >> >> Jits >> >> >> >> Franck Tanoh wrote: >> >>>> Franck you please add your DRAMA thing to the to be tested section? >>>> >>>> >>> Added but not yet completed >>> >>> >>> >>>> Another thing is whether we should make an announcement for the release. >>>> >>>> >>> if it's a small update without any major changes or disruptions no >>> need for a pre-announcement (isn't what we're usually doing?) >>> We can do the announcement on the friend list once the update is completed. >>> >>> Franck >>> >>> On 19 May 2010 16:01, Eric Nzuobontane wrote: >>> >>> >>>> Hi Guys, >>>> Could you please update the page which I created here? Especially the >>>> included in this release and to be tested sections. Franck you please add >>>> your DRAMA thing to the to be tested section? >>>> http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes >>>> >>>> Another thing is whether we should make an announcement for the release. It >>>> would be better if we did as I will be the one to be crucified should >>>> anything go wrong. I do not expect much to go wrong but you never know. >>>> >>>> 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 >>>> >>>> >>>> >>> >>> >>> >> > > > > From jits at cs.man.ac.uk Thu May 20 04:46:49 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 20 May 2010 09:46:49 +0100 Subject: [BioCatalogue-developers] pre-release notes In-Reply-To: <4BF4F007.9060404@ebi.ac.uk> References: <4BF3FD32.9090606@ebi.ac.uk> <4BF4F007.9060404@ebi.ac.uk> Message-ID: <4BF4F6F9.4090806@cs.man.ac.uk> Eric Nzuobontane wrote: > >>> Another thing is whether we should make an announcement for the >>> release. >>> >> if it's a small update without any major changes or disruptions no >> need for a pre-announcement (isn't what we're usually doing?) >> We can do the announcement on the friend list once the update is >> completed. >> > Well, that is what has been happening yes. But it is me stupidly > risking my head in order not to get bugged down in what is not the > most unworkable policy. And if you remember the case that caused the > biggest problems last time, I sent that mail just after a meeting in > which we all agreed to do the update. Yet it was me under attack as > having taken stupid unilateral decision to bring a service down. I > just do not want that to happen again. You sent the email to the main biocatalogue mailing list only, not to the friends list (nor anywhere external). Therefore no one else external to the project was informed. That was one of the main bones of contention as far as I remember. Secondly, we have no clue here what the policy is at the EBI. We expect you at meetings to tell us and let us know if any plans are not OK wrt to EBI policies (or even just general deployment policies). So if we say "we would like a release in 2 days time", you are well within your right to say "no, we need to announce it beforehand so can we do it a week later please?". Planning and agreeing a release is orthogonal to the procedures required to carry out the release. When I'm developing a new feature for Franck and something doesn't quite go right under the hood, then I take the blame for not implementing the feature correctly (or introducing bugs). You're absolutely within your right to say "I need 1 week advance notice before a release". Just make sure you say that when we are doing the *planning* so that we can factor these things in as early as possible. Jits > > Eric > > >> Franck >> >> On 19 May 2010 16:01, Eric Nzuobontane wrote: >> >>> Hi Guys, >>> Could you please update the page which I created here? Especially the >>> included in this release and to be tested sections. Franck you >>> please add >>> your DRAMA thing to the to be tested section? >>> http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes >>> >>> >>> Another thing is whether we should make an announcement for the >>> release. It >>> would be better if we did as I will be the one to be crucified should >>> anything go wrong. I do not expect much to go wrong but you never know. >>> >>> 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 >>> >>> >> >> >> >> > > From ericnzuo at ebi.ac.uk Thu May 20 05:05:00 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 20 May 2010 10:05:00 +0100 Subject: [BioCatalogue-developers] pre-release notes In-Reply-To: <4BF4F6F9.4090806@cs.man.ac.uk> References: <4BF3FD32.9090606@ebi.ac.uk> <4BF4F007.9060404@ebi.ac.uk> <4BF4F6F9.4090806@cs.man.ac.uk> Message-ID: <4BF4FB3C.6080409@ebi.ac.uk> Jiten Bhagat wrote: > Eric Nzuobontane wrote: > >>>> Another thing is whether we should make an announcement for the >>>> release. >>>> >>>> >>> if it's a small update without any major changes or disruptions no >>> need for a pre-announcement (isn't what we're usually doing?) >>> We can do the announcement on the friend list once the update is >>> completed. >>> >>> >> Well, that is what has been happening yes. But it is me stupidly >> risking my head in order not to get bugged down in what is not the >> most unworkable policy. And if you remember the case that caused the >> biggest problems last time, I sent that mail just after a meeting in >> which we all agreed to do the update. Yet it was me under attack as >> having taken stupid unilateral decision to bring a service down. I >> just do not want that to happen again. >> > > You sent the email to the main biocatalogue mailing list only, not to > the friends list (nor anywhere external). Therefore no one else external > to the project was informed. That was one of the main bones of > contention as far as I remember. > Secondly, we have no clue here what the policy is at the EBI. We expect > you at meetings to tell us and let us know if any plans are not OK wrt > to EBI policies (or even just general deployment policies). So if we say > "we would like a release in 2 days time", you are well within your right > to say "no, we need to announce it beforehand so can we do it a week > later please?". > That is very correct and I took the responsibility wholly. > Planning and agreeing a release is orthogonal to the procedures required > to carry out the release. > > When I'm developing a new feature for Franck and something doesn't quite > go right under the hood, then I take the blame for not implementing the > feature correctly (or introducing bugs). > > You're absolutely within your right to say "I need 1 week advance notice > before a release". Just make sure you say that when we are doing the > *planning* so that we can factor these things in as early as possible. > From the last case, I assume that we are now at least aware of the necessary notice banner & period. All I am saying is that we should follow it and I think we all agree. Eric > Jits > > > >> Eric >> >> >> >>> Franck >>> >>> On 19 May 2010 16:01, Eric Nzuobontane wrote: >>> >>> >>>> Hi Guys, >>>> Could you please update the page which I created here? Especially the >>>> included in this release and to be tested sections. Franck you >>>> please add >>>> your DRAMA thing to the to be tested section? >>>> http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes >>>> >>>> >>>> Another thing is whether we should make an announcement for the >>>> release. It >>>> would be better if we did as I will be the one to be crucified should >>>> anything go wrong. I do not expect much to go wrong but you never know. >>>> >>>> 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 >>>> >>>> >>>> >>> >>> >>> >> -- 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 Thu May 20 05:07:27 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 20 May 2010 10:07:27 +0100 Subject: [BioCatalogue-developers] pre-release notes In-Reply-To: <4BF4FB3C.6080409@ebi.ac.uk> References: <4BF3FD32.9090606@ebi.ac.uk> <4BF4F007.9060404@ebi.ac.uk> <4BF4F6F9.4090806@cs.man.ac.uk> <4BF4FB3C.6080409@ebi.ac.uk> Message-ID: <4BF4FBCF.9070909@cs.man.ac.uk> Cool :-) Eric Nzuobontane wrote: > Jiten Bhagat wrote: >> Eric Nzuobontane wrote: >> >>>>> Another thing is whether we should make an announcement for the >>>>> release. >>>>> >>>> if it's a small update without any major changes or disruptions no >>>> need for a pre-announcement (isn't what we're usually doing?) >>>> We can do the announcement on the friend list once the update is >>>> completed. >>>> >>> Well, that is what has been happening yes. But it is me stupidly >>> risking my head in order not to get bugged down in what is not the >>> most unworkable policy. And if you remember the case that caused the >>> biggest problems last time, I sent that mail just after a meeting in >>> which we all agreed to do the update. Yet it was me under attack as >>> having taken stupid unilateral decision to bring a service down. I >>> just do not want that to happen again. >>> >> >> You sent the email to the main biocatalogue mailing list only, not to >> the friends list (nor anywhere external). Therefore no one else external >> to the project was informed. That was one of the main bones of >> contention as far as I remember. >> Secondly, we have no clue here what the policy is at the EBI. We expect >> you at meetings to tell us and let us know if any plans are not OK wrt >> to EBI policies (or even just general deployment policies). So if we say >> "we would like a release in 2 days time", you are well within your right >> to say "no, we need to announce it beforehand so can we do it a week >> later please?". >> > That is very correct and I took the responsibility wholly. >> Planning and agreeing a release is orthogonal to the procedures required >> to carry out the release. >> >> When I'm developing a new feature for Franck and something doesn't quite >> go right under the hood, then I take the blame for not implementing the >> feature correctly (or introducing bugs). >> >> You're absolutely within your right to say "I need 1 week advance notice >> before a release". Just make sure you say that when we are doing the >> *planning* so that we can factor these things in as early as possible. >> > From the last case, I assume that we are now at least aware of the > necessary notice banner & period. All I am saying is that we should > follow it and I think we all agree. > > > Eric >> Jits >> >> >> >>> Eric >>> >>> >>> >>>> Franck >>>> >>>> On 19 May 2010 16:01, Eric Nzuobontane wrote: >>>> >>>> >>>>> Hi Guys, >>>>> Could you please update the page which I created here? Especially the >>>>> included in this release and to be tested sections. Franck you >>>>> please add >>>>> your DRAMA thing to the to be tested section? >>>>> http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes >>>>> >>>>> >>>>> >>>>> Another thing is whether we should make an announcement for the >>>>> release. It >>>>> would be better if we did as I will be the one to be crucified should >>>>> anything go wrong. I do not expect much to go wrong but you never >>>>> know. >>>>> >>>>> 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 >>>>> >>>>> >>>> >>>> >>> > > From noreply at rubyforge.org Thu May 20 05:53:41 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 20 May 2010 05:53:41 -0400 (EDT) Subject: [BioCatalogue-developers] [2005] trunk/app/models/soap_service.rb: Removed the read only constraint from the wsdl_files collection for SoapService as this was causing failure when running the update checker . Message-ID: <20100520095341.DD5F91858362@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 20 09:34:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 20 May 2010 09:34:42 -0400 (EDT) Subject: [BioCatalogue-developers] [2006] trunk: Fixes for the background jobs for the service updater. Message-ID: <20100520133442.C43871D799D2@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu May 20 09:59:40 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 20 May 2010 14:59:40 +0100 Subject: [BioCatalogue-developers] http://localhost:3000/announcements/14 Message-ID: <4BF5404C.1000903@ebi.ac.uk> Please have a look at this announcement http://localhost:3000/announcements/14 -- 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 Thu May 20 10:12:14 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 20 May 2010 15:12:14 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: EdUnify (BioCatalogue) flash demo] Message-ID: <4BF5433E.1020202@cs.man.ac.uk> FYI -------- Original Message -------- Subject: Re: EdUnify (BioCatalogue) flash demo Date: Thu, 20 May 2010 15:11:46 +0100 From: Jiten Bhagat To: Jackson, Tod CC: Wheat, Stephen References: Hi Todd, Thanks for sharing! That was a nice guide through the registry features. And it's great to see the registry software being re-purposed for your project. Do you mind if I share this with the rest of the team and wider audience here? One minor point - might be worth mentioning that operations, inputs and outputs will have descriptions if these are set in the WSDL document (therefore the emphasis is on the providers to give lots of metadata within the WSDL, which will get parsed out). There are a few new features in the next release (by end of next week) that might be useful to you: - Ability to describe the exact endpoints, parameters and representations of REST services. - SOAP operations and REST endpoints now get returned in search. - Ability to mark services as archived. - A full read REST API to the catalogue (so people can get programmatic access to your registry). - Ability for other users to request ownership/responsibility for services. - Ability to monitor changes in the WSDL and update the entries in the catalogue. As well as lots of UI tweaks and fixes. Let me know if any of these interest you and I'll help you get your instance updated after the release. I'd like to get your monitoring set up too at some point if you'd like? Please do keep me posted on these webinars and what people think of them. Regards, Jits Jackson, Tod wrote: > Hi Jits, > > I wanted to forward a link to you just in case you care to take a > look. It?s a flash production we put together for our EdUnify > community. We?re holding a couple webinars in June to try and > familiarize that group with our deployment of the BioCatalogue app (we > call it the ?EdUnify Registry?). We?re using this demo as a > pre-cursor to those webinars. This is the first in what will likely > be a series of demos we use for various purposes with that group. > This one focuses on simple service registration, annotating and > simple searches. > > https://demo.edunify.pesc.org/demo1/edunify-registry.html > > Feel free to provide comments or feedback. > > Best Regards, > Tod > ------------------------------------------------------------------------ > This e-mail message (including any attachments) is for the sole use of > the intended recipient(s) and may contain confidential and privileged > information. If the reader of this message is not the intended > recipient, you are hereby notified that any dissemination, distribution > or copying of this message (including any attachments) is strictly > prohibited. > > If you have received this message in error, please contact > the sender by reply e-mail message and destroy all copies of the > original message (including attachments). From ytanoh at cs.man.ac.uk Thu May 20 10:39:02 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 20 May 2010 15:39:02 +0100 Subject: [BioCatalogue-developers] http://localhost:3000/announcements/14 In-Reply-To: <4BF5404C.1000903@ebi.ac.uk> References: <4BF5404C.1000903@ebi.ac.uk> Message-ID: Localhost not accessible from here ... :-) On 20 May 2010 14:59, Eric Nzuobontane wrote: > Please have a look at this announcement > > http://localhost:3000/announcements/14 > > -- > 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 ericnzuo at ebi.ac.uk Thu May 20 10:42:16 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 20 May 2010 15:42:16 +0100 Subject: [BioCatalogue-developers] http://localhost:3000/announcements/14 In-Reply-To: References: <4BF5404C.1000903@ebi.ac.uk> Message-ID: <4BF54A48.1070301@ebi.ac.uk> local host moved http://test.biocatalogue.org/announcements/7 :) Franck Tanoh wrote: > Localhost not accessible from here ... :-) > > On 20 May 2010 14:59, Eric Nzuobontane wrote: > >> Please have a look at this announcement >> >> http://localhost:3000/announcements/14 >> >> -- >> 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 >> >> > > > > -- 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 May 20 10:53:53 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 20 May 2010 15:53:53 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: EdUnify (BioCatalogue) flash demo] In-Reply-To: <4BF5433E.1020202@cs.man.ac.uk> References: <4BF5433E.1020202@cs.man.ac.uk> Message-ID: <4BF54D01.5020401@ebi.ac.uk> I just listened to it. It is quite a nice intro to the catalogue. Eric Jiten Bhagat wrote: > FYI > > -------- Original Message -------- > Subject: Re: EdUnify (BioCatalogue) flash demo > Date: Thu, 20 May 2010 15:11:46 +0100 > From: Jiten Bhagat > To: Jackson, Tod > CC: Wheat, Stephen > References: > > > > Hi Todd, > > Thanks for sharing! That was a nice guide through the registry features. > And it's great to see the registry software being re-purposed for your > project. Do you mind if I share this with the rest of the team and wider > audience here? > > One minor point - might be worth mentioning that operations, inputs and > outputs will have descriptions if these are set in the WSDL document > (therefore the emphasis is on the providers to give lots of metadata > within the WSDL, which will get parsed out). > > There are a few new features in the next release (by end of next week) > that might be useful to you: > - Ability to describe the exact endpoints, parameters and > representations of REST services. > - SOAP operations and REST endpoints now get returned in search. > - Ability to mark services as archived. > - A full read REST API to the catalogue (so people can get programmatic > access to your registry). > - Ability for other users to request ownership/responsibility for services. > - Ability to monitor changes in the WSDL and update the entries in the > catalogue. > > As well as lots of UI tweaks and fixes. > > Let me know if any of these interest you and I'll help you get your > instance updated after the release. I'd like to get your monitoring set > up too at some point if you'd like? > > Please do keep me posted on these webinars and what people think of them. > > Regards, > Jits > > > Jackson, Tod wrote: > >> Hi Jits, >> >> I wanted to forward a link to you just in case you care to take a >> look. It?s a flash production we put together for our EdUnify >> community. We?re holding a couple webinars in June to try and >> familiarize that group with our deployment of the BioCatalogue app (we >> call it the ?EdUnify Registry?). We?re using this demo as a >> pre-cursor to those webinars. This is the first in what will likely >> be a series of demos we use for various purposes with that group. >> This one focuses on simple service registration, annotating and >> simple searches. >> >> https://demo.edunify.pesc.org/demo1/edunify-registry.html >> >> Feel free to provide comments or feedback. >> >> Best Regards, >> Tod >> ------------------------------------------------------------------------ >> This e-mail message (including any attachments) is for the sole use of >> the intended recipient(s) and may contain confidential and privileged >> information. If the reader of this message is not the intended >> recipient, you are hereby notified that any dissemination, distribution >> or copying of this message (including any attachments) is strictly >> prohibited. >> >> If you have received this message in error, please contact >> the sender by reply e-mail message and destroy all copies of the >> original message (including attachments). >> > > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Thu May 20 10:56:18 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 20 May 2010 15:56:18 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: EdUnify (BioCatalogue) flash demo] In-Reply-To: <4BF54D01.5020401@ebi.ac.uk> References: <4BF5433E.1020202@cs.man.ac.uk> <4BF54D01.5020401@ebi.ac.uk> Message-ID: <4BF54D92.5010207@cs.man.ac.uk> Indeed! We need a video like this on the homepage! Jits Eric Nzuobontane wrote: > I just listened to it. It is quite a nice intro to the catalogue. > > Eric > > > > Jiten Bhagat wrote: >> FYI >> >> -------- Original Message -------- >> Subject: Re: EdUnify (BioCatalogue) flash demo >> Date: Thu, 20 May 2010 15:11:46 +0100 >> From: Jiten Bhagat >> To: Jackson, Tod >> CC: Wheat, Stephen >> References: >> >> >> >> Hi Todd, >> >> Thanks for sharing! That was a nice guide through the registry features. >> And it's great to see the registry software being re-purposed for your >> project. Do you mind if I share this with the rest of the team and wider >> audience here? >> >> One minor point - might be worth mentioning that operations, inputs and >> outputs will have descriptions if these are set in the WSDL document >> (therefore the emphasis is on the providers to give lots of metadata >> within the WSDL, which will get parsed out). >> >> There are a few new features in the next release (by end of next week) >> that might be useful to you: >> - Ability to describe the exact endpoints, parameters and >> representations of REST services. >> - SOAP operations and REST endpoints now get returned in search. >> - Ability to mark services as archived. >> - A full read REST API to the catalogue (so people can get programmatic >> access to your registry). >> - Ability for other users to request ownership/responsibility for >> services. >> - Ability to monitor changes in the WSDL and update the entries in the >> catalogue. >> >> As well as lots of UI tweaks and fixes. >> >> Let me know if any of these interest you and I'll help you get your >> instance updated after the release. I'd like to get your monitoring set >> up too at some point if you'd like? >> >> Please do keep me posted on these webinars and what people think of >> them. >> >> Regards, >> Jits >> >> >> Jackson, Tod wrote: >> >>> Hi Jits, >>> >>> I wanted to forward a link to you just in case you care to take a >>> look. It?s a flash production we put together for our EdUnify >>> community. We?re holding a couple webinars in June to try and >>> familiarize that group with our deployment of the BioCatalogue app (we >>> call it the ?EdUnify Registry?). We?re using this demo as a >>> pre-cursor to those webinars. This is the first in what will likely >>> be a series of demos we use for various purposes with that group. >>> This one focuses on simple service registration, annotating and >>> simple searches. >>> >>> https://demo.edunify.pesc.org/demo1/edunify-registry.html >>> >>> Feel free to provide comments or feedback. >>> >>> Best Regards, >>> Tod >>> ------------------------------------------------------------------------ >>> >>> This e-mail message (including any attachments) is for the sole use of >>> the intended recipient(s) and may contain confidential and privileged >>> information. If the reader of this message is not the intended >>> recipient, you are hereby notified that any dissemination, distribution >>> or copying of this message (including any attachments) is strictly >>> prohibited. >>> >>> If you have received this message in error, please contact >>> the sender by reply e-mail message and destroy all copies of the >>> original message (including attachments). >>> >> >> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > > From utopia at cs.man.ac.uk Thu May 20 13:02:57 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 20 May 2010 18:02:57 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'BLASTatlas' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'BLASTatlas' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1690 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 May 21 02:24:40 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 21 May 2010 07:24:40 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:cnio.es:runISSComplete' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:cnio.es:runISSComplete' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/977 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Fri May 21 04:12:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 May 2010 09:12:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-349) Test the newly deployed code on biocatalogue test server Message-ID: <30589852.1187.1274429537097.JavaMail.jira@rosalind.cs.man.ac.uk> Test the newly deployed code on biocatalogue test server -------------------------------------------------------- Key: BIOCAT-349 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-349 Project: BioCatalogue Issue Type: Sub-task Components: Server Management Environment: RoR, Solr, Apache, Linux Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Test every major functionality in preparation for the live release on Wednesday afternoon -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 04:14:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 May 2010 09:14:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-349) Test the newly deployed code on biocatalogue test server In-Reply-To: <30589852.1187.1274429537097.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5468244.1188.1274429657030.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-349?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10346 ] Eric Nzuobontane logged work on BIOCAT-349: ------------------------------------------- Author: Eric Nzuobontane Created on: 2010-05-21 09:13 Start Date: 2010-05-21 09:11 Worklog Time Spent: 4 hours Issue Time Tracking ------------------- Remaining Estimate: 1 day, 4 hours (was: 2 days) Time Spent: 4 hours > Test the newly deployed code on biocatalogue test server > -------------------------------------------------------- > > Key: BIOCAT-349 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-349 > Project: BioCatalogue > Issue Type: Sub-task > Components: Server Management > Environment: RoR, Solr, Apache, Linux > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 2 days > Time Spent: 4 hours > Remaining Estimate: 1 day, 4 hours > > Test every major functionality in preparation for the live release on Wednesday afternoon -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 04:51:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 May 2010 09:51:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-350) investigate why soaplab autotagging failed during submission Message-ID: <24698088.1189.1274431876996.JavaMail.jira@rosalind.cs.man.ac.uk> investigate why soaplab autotagging failed during submission ------------------------------------------------------------ Key: BIOCAT-350 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350 Project: BioCatalogue Issue Type: Bug Components: Service Submission Reporter: Eric Nzuobontane Assignee: Jiten Bhagat Soaplab services are normally tagged with soaplab and tool group name at submission time. That process failed during the submission of these services http://www.biocatalogue.org/users/112#services -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 04:59:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 May 2010 09:59:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-350) investigate why soaplab autotagging failed during submission In-Reply-To: <24698088.1189.1274431876996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27405601.1190.1274432357019.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-350: --------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > investigate why soaplab autotagging failed during submission > ------------------------------------------------------------ > > Key: BIOCAT-350 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Soaplab services are normally tagged with soaplab and tool group name at submission time. That process failed during the submission of these services http://www.biocatalogue.org/users/112#services -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 05:07:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 May 2010 10:07:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-350) investigate why soaplab autotagging failed during submission In-Reply-To: <24698088.1189.1274431876996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16662759.1191.1274432837015.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14940#action_14940 ] Jiten Bhagat commented on BIOCAT-350: ------------------------------------- I don't think these services were submitted via the Soaplab server submission. Looks like they were individually submitted as SOAP services. > investigate why soaplab autotagging failed during submission > ------------------------------------------------------------ > > Key: BIOCAT-350 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Soaplab services are normally tagged with soaplab and tool group name at submission time. That process failed during the submission of these services http://www.biocatalogue.org/users/112#services -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 05:13:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 May 2010 10:13:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-349) Test the newly deployed code on biocatalogue test server In-Reply-To: <30589852.1187.1274429537097.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3546602.1193.1274433197000.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-349?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14942#action_14942 ] Jiten Bhagat commented on BIOCAT-349: ------------------------------------- Just noticed that it's a sub task. in which case adding the release info to the parent task only would be fine. > Test the newly deployed code on biocatalogue test server > -------------------------------------------------------- > > Key: BIOCAT-349 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-349 > Project: BioCatalogue > Issue Type: Sub-task > Components: Server Management > Environment: RoR, Solr, Apache, Linux > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 2 days > Time Spent: 4 hours > Remaining Estimate: 1 day, 4 hours > > Test every major functionality in preparation for the live release on Wednesday afternoon -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 05:15:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 May 2010 10:15:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-349) Test the newly deployed code [May 2010 Release] on biocatalogue test server In-Reply-To: <30589852.1187.1274429537097.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24792572.1194.1274433317025.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-349?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane updated BIOCAT-349: ------------------------------------ Summary: Test the newly deployed code [May 2010 Release] on biocatalogue test server (was: Test the newly deployed code on biocatalogue test server) > Test the newly deployed code [May 2010 Release] on biocatalogue test server > --------------------------------------------------------------------------- > > Key: BIOCAT-349 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-349 > Project: BioCatalogue > Issue Type: Sub-task > Components: Server Management > Environment: RoR, Solr, Apache, Linux > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 2 days > Time Spent: 4 hours > Remaining Estimate: 1 day, 4 hours > > Test every major functionality in preparation for the live release on Wednesday afternoon -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 05:17:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 May 2010 10:17:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-347) Deploy new release on the test server [May 2010 Release] In-Reply-To: <28020018.568.1274264177087.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29796122.1195.1274433437035.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-347?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane updated BIOCAT-347: ------------------------------------ Summary: Deploy new release on the test server [May 2010 Release] (was: Deploy new release on the test server) > Deploy new release on the test server [May 2010 Release] > -------------------------------------------------------- > > Key: BIOCAT-347 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-347 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Environment: Apache, mod_rails, RoR, CentOS > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 2 minutes > Remaining Estimate: 2 minutes > > Deploy the new codebase onto the test server -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 05:11:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 May 2010 10:11:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-349) Test the newly deployed code on biocatalogue test server In-Reply-To: <30589852.1187.1274429537097.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31105620.1192.1274433077001.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-349?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14941#action_14941 ] Jiten Bhagat commented on BIOCAT-349: ------------------------------------- This seems like a very generic task to be adding to JIRA. Please add an identifier to the title of this (and other similar tasks to do with depoloyments) otherwise in the future you'll have many tasks like this with similar names and it will be ambiguous. Maybe add something like "[Release May 2010]" or "[Release 3rd week May 2010]" to the title. OR assign it to a version. > Test the newly deployed code on biocatalogue test server > -------------------------------------------------------- > > Key: BIOCAT-349 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-349 > Project: BioCatalogue > Issue Type: Sub-task > Components: Server Management > Environment: RoR, Solr, Apache, Linux > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 2 days > Time Spent: 4 hours > Remaining Estimate: 1 day, 4 hours > > Test every major functionality in preparation for the live release on Wednesday afternoon -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 05:24:16 2010 From: issues at mygrid.org.uk (Franck Tanoh (JIRA)) Date: Fri, 21 May 2010 10:24:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-350) investigate why soaplab autotagging failed during submission In-Reply-To: <24698088.1189.1274431876996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2245466.1196.1274433856997.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Franck Tanoh updated BIOCAT-350: -------------------------------- Description: Soaplab services are normally tagged with soaplab and tool group name at submission time. That process failed during the submission of these services http://www.biocatalogue.org/users/112#services The following services are also no tagged as soaplab services: http://www.biocatalogue.org/service_providers/249#services was:Soaplab services are normally tagged with soaplab and tool group name at submission time. That process failed during the submission of these services http://www.biocatalogue.org/users/112#services > investigate why soaplab autotagging failed during submission > ------------------------------------------------------------ > > Key: BIOCAT-350 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Soaplab services are normally tagged with soaplab and tool group name at submission time. That process failed during the submission of these services http://www.biocatalogue.org/users/112#services > The following services are also no tagged as soaplab services: http://www.biocatalogue.org/service_providers/249#services -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 05:26:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 May 2010 10:26:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-343) Implement an "News" tab on a service's page In-Reply-To: <29654500.520.1274178676994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4132115.1197.1274433977041.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-343 started by Jiten Bhagat. > Implement an "News" tab on a service's page > ------------------------------------------- > > Key: BIOCAT-343 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 days > Remaining Estimate: 2 days > > This should show a full activity list/feed for the service, showing events that have happened, like new annotations, WSDL changes, etc. > Maybe have the WSDL changes in a separate column on the right hand side? -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 05:26:18 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 May 2010 10:26:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-343) Implement an "News" tab on a service's page In-Reply-To: <29654500.520.1274178676994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5316862.1198.1274433978469.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10347 ] Jiten Bhagat logged work on BIOCAT-343: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-21 10:25 Start Date: 2010-05-19 10:25 Worklog Time Spent: 1 hour Work Description: Initial work on the skeleton Issue Time Tracking ------------------- Remaining Estimate: 1 day, 7 hours (was: 2 days) Time Spent: 1 hour > Implement an "News" tab on a service's page > ------------------------------------------- > > Key: BIOCAT-343 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 days > Time Spent: 1 hour > Remaining Estimate: 1 day, 7 hours > > This should show a full activity list/feed for the service, showing events that have happened, like new annotations, WSDL changes, etc. > Maybe have the WSDL changes in a separate column on the right hand side? -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 05:28:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 May 2010 10:28:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-331) Show changelogs on service show page as part of the "News" tab In-Reply-To: <29588368.68.1273668436995.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11234298.1199.1274434097009.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-331?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10348 ] Jiten Bhagat logged work on BIOCAT-331: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-21 10:26 Start Date: 2010-05-19 10:26 Worklog Time Spent: 4 hours Work Description: Initial work done on this. Pending user feedback and more testing. Issue Time Tracking ------------------- Remaining Estimate: 1 hour (was: 5 hours) Time Spent: 4 hours > Show changelogs on service show page as part of the "News" tab > -------------------------------------------------------------- > > Key: BIOCAT-331 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-331 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 5 hours > Time Spent: 4 hours > Remaining Estimate: 1 hour > > When viewing a service, should be able to see the full list of changelogs for that service. > Ensure that: > - Must explain that any changes recorded in the SOAP service changelog may be from updates in the actual WSDL OR from things that we are now able to parse from the WSDL. > - It is clarified that info from SoapServiceChange is specifically about the SOAP/WSDL based service. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 05:44:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 May 2010 10:44:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-350) investigate why soaplab autotagging failed during submission In-Reply-To: <24698088.1189.1274431876996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22735977.1200.1274435057043.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-350. ------------------------------------- Resolution: Fixed Confirmed from the db that there is no soaplab server entry for these services in the database. The service were submitted through normal soap mechanism there would not be tagged automatically > investigate why soaplab autotagging failed during submission > ------------------------------------------------------------ > > Key: BIOCAT-350 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Soaplab services are normally tagged with soaplab and tool group name at submission time. That process failed during the submission of these services http://www.biocatalogue.org/users/112#services > The following services are also no tagged as soaplab services: http://www.biocatalogue.org/service_providers/249#services -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 05:44:18 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 May 2010 10:44:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Reopened: (BIOCAT-350) investigate why soaplab autotagging failed during submission In-Reply-To: <24698088.1189.1274431876996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15178579.1201.1274435058453.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reopened BIOCAT-350: ------------------------------------- > investigate why soaplab autotagging failed during submission > ------------------------------------------------------------ > > Key: BIOCAT-350 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Soaplab services are normally tagged with soaplab and tool group name at submission time. That process failed during the submission of these services http://www.biocatalogue.org/users/112#services > The following services are also no tagged as soaplab services: http://www.biocatalogue.org/service_providers/249#services -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 05:44:19 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 May 2010 10:44:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-350) investigate why soaplab autotagging failed during submission In-Reply-To: <24698088.1189.1274431876996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15284015.1202.1274435059467.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-350. ------------------------------------- Resolution: Not A Bug see previous comment > investigate why soaplab autotagging failed during submission > ------------------------------------------------------------ > > Key: BIOCAT-350 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Soaplab services are normally tagged with soaplab and tool group name at submission time. That process failed during the submission of these services http://www.biocatalogue.org/users/112#services > The following services are also no tagged as soaplab services: http://www.biocatalogue.org/service_providers/249#services -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 05:46:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 21 May 2010 10:46:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-350) investigate why soaplab autotagging failed during submission In-Reply-To: <24698088.1189.1274431876996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27949802.1203.1274435177032.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14943#action_14943 ] Eric Nzuobontane edited comment on BIOCAT-350 at 21/05/10 10:45: ----------------------------------------------------------------- Confirmed from the database that there is no soaplab server entry for these services. The services were submitted through normal soap mechanism therefore would not be tagged automatically was (Author: eric): Confirmed from the db that there is no soaplab server entry for these services in the database. The service were submitted through normal soap mechanism there would not be tagged automatically > investigate why soaplab autotagging failed during submission > ------------------------------------------------------------ > > Key: BIOCAT-350 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-350 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Soaplab services are normally tagged with soaplab and tool group name at submission time. That process failed during the submission of these services http://www.biocatalogue.org/users/112#services > The following services are also no tagged as soaplab services: http://www.biocatalogue.org/service_providers/249#services -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Fri May 21 05:56:43 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 21 May 2010 10:56:43 +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 noreply at rubyforge.org Fri May 21 06:51:51 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 21 May 2010 06:51:51 -0400 (EDT) Subject: [BioCatalogue-developers] [2007] trunk/script/biocatalogue/sanity_check.rb: Added check for orphaned Annotations, and some textual changes to the reporting. Message-ID: <20100521105151.EC47D1858345@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 21 07:15:17 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 21 May 2010 07:15:17 -0400 (EDT) Subject: [BioCatalogue-developers] [2008] trunk/app/models/service_provider.rb: - bugfix: ServiceProvider. merge_into now takes into account the annotations made by the service provider in addition to those made on the service provider Message-ID: <20100521111518.300281858341@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 21 08:14:28 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 21 May 2010 08:14:28 -0400 (EDT) Subject: [BioCatalogue-developers] [2009] trunk/app/models/test_result.rb: Fix for logging for status changes in ActivityLogs - the ActivityLog#referenced value should be the corresponding Service . Message-ID: <20100521121428.527F91858352@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 21 08:34:23 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 21 May 2010 08:34:23 -0400 (EDT) Subject: [BioCatalogue-developers] [2010] trunk: [BIOCAT-306] Added SoapServiceChange create events to the homepage activity list. Message-ID: <20100521123423.CB889185834B@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri May 21 08:38:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 May 2010 13:38:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-346) Add entries to the homepage activity feed for when changes have been found In-Reply-To: <12074178.528.1274190198761.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27725252.1326.1274445497014.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-346?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10349 ] Jiten Bhagat logged work on BIOCAT-346: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-21 13:37 Start Date: 2010-05-21 10:00 Worklog Time Spent: 4 hours Work Description: Done, in revision 2010. The additional hours were for adding favourites and monitoring status changes. Issue Time Tracking ------------------- Remaining Estimate: 0 minutes (was: 2 hours) Time Spent: 4 hours > Add entries to the homepage activity feed for when changes have been found > -------------------------------------------------------------------------- > > Key: BIOCAT-346 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-346 > Project: BioCatalogue > Issue Type: Sub-task > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 4 hours > Remaining Estimate: 0 minutes > > Look for ActivityLog events with the action 'create' and activity_loggable_type 'SoapServiceChange'. > Make sure to link to the actual changelog (eg: /services/8#soap_service_change_10) -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 08:38:18 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 May 2010 13:38:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-346) Add entries to the homepage activity feed for when changes have been found In-Reply-To: <12074178.528.1274190198761.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1334501.1327.1274445498349.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-346?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-346. --------------------------------- Resolution: Implemented > Add entries to the homepage activity feed for when changes have been found > -------------------------------------------------------------------------- > > Key: BIOCAT-346 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-346 > Project: BioCatalogue > Issue Type: Sub-task > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 4 hours > Remaining Estimate: 0 minutes > > Look for ActivityLog events with the action 'create' and activity_loggable_type 'SoapServiceChange'. > Make sure to link to the actual changelog (eg: /services/8#soap_service_change_10) -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri May 21 10:52:54 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 21 May 2010 10:52:54 -0400 (EDT) Subject: [BioCatalogue-developers] [2011] trunk/script/biocatalogue/sanity_check.rb: Added more sanity checks. Message-ID: <20100521145254.E50F2185835B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 21 11:37:29 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 21 May 2010 11:37:29 -0400 (EDT) Subject: [BioCatalogue-developers] [2012] trunk: Major refactoring into the way the Activity Feeds are generated. Message-ID: <20100521153729.AB2B81858348@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 21 11:58:51 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 21 May 2010 11:58:51 -0400 (EDT) Subject: [BioCatalogue-developers] [2013] trunk: Added "Monitoring Status Changes" box to the homepage and a " Monitoring" tab to the /latest page. Message-ID: <20100521155851.69E791D799D5@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 21 12:02:43 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 21 May 2010 12:02:43 -0400 (EDT) Subject: [BioCatalogue-developers] [2014] trunk/app/views/home/latest.html.erb: Rearranged tabs on the / latest page to Activity, Monitoring, Services, Contributors. Message-ID: <20100521160243.829791D799D7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 21 12:24:03 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 21 May 2010 12:24:03 -0400 (EDT) Subject: [BioCatalogue-developers] [2015] trunk: Favourite/Unfavourite added to the 'Actions' dropdown menu for service page. Message-ID: <20100521162403.9DEB41D799D8@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 21 12:57:40 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 21 May 2010 12:57:40 -0400 (EDT) Subject: [BioCatalogue-developers] [2016] trunk: Initial work on the Latest Activity for the News tab for each service. Message-ID: <20100521165740.8546D18582FF@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri May 21 12:58:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 May 2010 17:58:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-331) Show changelogs on service show page as part of the "News" tab In-Reply-To: <29588368.68.1273668436995.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24993977.1433.1274461097016.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-331?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-331. --------------------------------- Resolution: Fixed Initial work done. Awaiting user testing. > Show changelogs on service show page as part of the "News" tab > -------------------------------------------------------------- > > Key: BIOCAT-331 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-331 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 5 hours > Time Spent: 4 hours > Remaining Estimate: 1 hour > > When viewing a service, should be able to see the full list of changelogs for that service. > Ensure that: > - Must explain that any changes recorded in the SOAP service changelog may be from updates in the actual WSDL OR from things that we are now able to parse from the WSDL. > - It is clarified that info from SoapServiceChange is specifically about the SOAP/WSDL based service. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 12:58:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 May 2010 17:58:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-343) Implement a "News" tab on a service's page In-Reply-To: <29654500.520.1274178676994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23169557.1434.1274461097931.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-343: -------------------------------- Summary: Implement a "News" tab on a service's page (was: Implement an "News" tab on a service's page) > Implement a "News" tab on a service's page > ------------------------------------------ > > Key: BIOCAT-343 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 days > Time Spent: 1 hour > Remaining Estimate: 1 day, 7 hours > > This should show a full activity list/feed for the service, showing events that have happened, like new annotations, WSDL changes, etc. > Maybe have the WSDL changes in a separate column on the right hand side? -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 13:00:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 May 2010 18:00:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-343) Implement a "News" tab on a service's page In-Reply-To: <29654500.520.1274178676994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16962492.1435.1274461217011.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10350 ] Jiten Bhagat logged work on BIOCAT-343: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-21 17:58 Start Date: 2010-05-21 13:00 Worklog Time Spent: 6 hours Work Description: Initial work carried out, in revision 2016. Issue Time Tracking ------------------- Remaining Estimate: 1 day, 1 hour (was: 1 day, 7 hours) Time Spent: 7 hours (was: 1 hour) > Implement a "News" tab on a service's page > ------------------------------------------ > > Key: BIOCAT-343 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 days > Time Spent: 7 hours > Remaining Estimate: 1 day, 1 hour > > This should show a full activity list/feed for the service, showing events that have happened, like new annotations, WSDL changes, etc. > Maybe have the WSDL changes in a separate column on the right hand side? -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 13:00:18 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 May 2010 18:00:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-343) Implement a "News" tab on a service's page In-Reply-To: <29654500.520.1274178676994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27916982.1436.1274461218121.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14964#action_14964 ] Jiten Bhagat commented on BIOCAT-343: ------------------------------------- NOTE: this currently doesn't take into actions carried out on the underlying service structure (eg: annotations on operations/inputs/outputs, etc). > Implement a "News" tab on a service's page > ------------------------------------------ > > Key: BIOCAT-343 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 days > Time Spent: 7 hours > Remaining Estimate: 1 day, 1 hour > > This should show a full activity list/feed for the service, showing events that have happened, like new annotations, WSDL changes, etc. > Maybe have the WSDL changes in a separate column on the right hand side? -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri May 21 13:02:51 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 21 May 2010 13:02:51 -0400 (EDT) Subject: [BioCatalogue-developers] [2017] trunk/app/views/services/_news_tab.html.erb: Removed redundant heading. Message-ID: <20100521170251.29DA318582FF@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 21 13:22:25 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 21 May 2010 13:22:25 -0400 (EDT) Subject: [BioCatalogue-developers] [2018] trunk: Various fixes and tweaks to the activity feed on the service page. Message-ID: <20100521172225.3FE221858317@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 21 14:17:11 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 21 May 2010 14:17:11 -0400 (EDT) Subject: [BioCatalogue-developers] [2019] trunk: Enhancements to show more activity on the news tab of the service page. Message-ID: <20100521181711.2EB1C1D799DC@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri May 21 14:19:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 May 2010 19:19:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-343) Implement a "News" tab on a service's page In-Reply-To: <29654500.520.1274178676994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7592727.1437.1274465957013.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10351 ] Jiten Bhagat logged work on BIOCAT-343: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-21 19:18 Start Date: 2010-05-21 17:18 Worklog Time Spent: 2 hours Work Description: Enhancements to show more activity on the news tab of the service page. This now takes into account all annotations on the associated ServiceDeployment, ServiceVersion, SoapServices and RestServices of a service. Issue Time Tracking ------------------- Remaining Estimate: 7 hours (was: 1 day, 1 hour) Time Spent: 1 day, 1 hour (was: 7 hours) > Implement a "News" tab on a service's page > ------------------------------------------ > > Key: BIOCAT-343 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 days > Time Spent: 1 day, 1 hour > Remaining Estimate: 7 hours > > This should show a full activity list/feed for the service, showing events that have happened, like new annotations, WSDL changes, etc. > Maybe have the WSDL changes in a separate column on the right hand side? -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 21 14:19:18 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 21 May 2010 19:19:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-343) Implement a "News" tab on a service's page In-Reply-To: <29654500.520.1274178676994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6491548.1438.1274465958663.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14965#action_14965 ] Jiten Bhagat commented on BIOCAT-343: ------------------------------------- This now takes into account all annotations on the associated ServiceDeployment, ServiceVersion, SoapServices and RestServices of a service. > Implement a "News" tab on a service's page > ------------------------------------------ > > Key: BIOCAT-343 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 days > Time Spent: 1 day, 1 hour > Remaining Estimate: 7 hours > > This should show a full activity list/feed for the service, showing events that have happened, like new annotations, WSDL changes, etc. > Maybe have the WSDL changes in a separate column on the right hand side? -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Sat May 22 05:36:37 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 22 May 2010 10:36:37 +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 utopia at cs.man.ac.uk Sat May 22 12:31:26 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 22 May 2010 17:31:26 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:cnio.es:runNCut' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:cnio.es:runNCut' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/970 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 May 22 17:45:22 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 22 May 2010 22:45:22 +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 Sat May 22 19:34:16 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 23 May 2010 00:34:16 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromAminoAcidSequence' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromAminoAcidSequence' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1000 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun May 23 05:33:07 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 23 May 2010 10:33:07 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:showPMUTonStructure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:showPMUTonStructure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/995 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 May 23 09:29:36 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 23 May 2010 14:29:36 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getNucleotideSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getNucleotideSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/940 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 May 23 15:49:20 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 23 May 2010 20:49:20 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'WHAT IF Web Services' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'WHAT IF Web Services' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/2777 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun May 23 22:52:21 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 24 May 2010 03:52:21 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:cnio.es:runFASSFromClustalw' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:cnio.es:runFASSFromClustalw' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/979 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 May 24 04:58:41 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 04:58:41 -0400 (EDT) Subject: [BioCatalogue-developers] [2020] trunk/lib/bio_catalogue/monitoring.rb: bugfix for updating rest endpoints Message-ID: <20100524085841.B291A1858354@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 24 05:46:57 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 05:46:57 -0400 (EDT) Subject: [BioCatalogue-developers] [2021] trunk/app/models/annotation.rb: Added an after_destroy callback to the Annotation model to take care of cleaning up associated UrlMonitor /ServiceTest records on deletion. Message-ID: <20100524094657.4B6321858370@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 24 07:18:30 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 07:18:30 -0400 (EDT) Subject: [BioCatalogue-developers] [2022] trunk/lib/bio_catalogue/monitoring.rb: Fixes to the monitoring: Handling exceptions & limiting number of urls to monitored per service Message-ID: <20100524111830.7157E167829F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 24 08:06:50 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 08:06:50 -0400 (EDT) Subject: [BioCatalogue-developers] [2023] trunk/lib/bio_catalogue/monitoring.rb: fix typo Message-ID: <20100524120651.034A9185836A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 24 10:39:05 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 10:39:05 -0400 (EDT) Subject: [BioCatalogue-developers] [2024] trunk/app/views: Various fixes to the current ATOM feeds. Message-ID: <20100524143905.A6C681858350@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 24 12:10:04 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 12:10:04 -0400 (EDT) Subject: [BioCatalogue-developers] [2025] trunk/app/views/announcements/index.atom.builder: Turns out manually setting the feed entry updated is not required. Message-ID: <20100524161004.666461858369@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 24 12:40:31 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 12:40:31 -0400 (EDT) Subject: [BioCatalogue-developers] [2026] trunk: ATOM feeds for Latest Activity, Service Monitoring Status Changes and each individual Service' s Latest Activity / News. Message-ID: <20100524164031.C69291678217@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 24 12:43:27 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 12:43:27 -0400 (EDT) Subject: [BioCatalogue-developers] [2027] trunk/app/views/widgets/_action_bar.html.erb: Added the link to the "getting started" page on the drop down menu on the action bar ( after the Search By Data option). Message-ID: <20100524164328.0CAFA1858362@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon May 24 12:45:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 24 May 2010 17:45:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-227) Implement RSS/atom feeds for services and activity feeds Message-ID: <962012.1508.1274719517102.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-227?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10354 ] Jiten Bhagat logged work on BIOCAT-227: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-24 17:44 Start Date: 2010-05-24 23:43 Worklog Time Spent: 4 hours Work Description: Revision 2026 - ATOM feeds for Latest Activity, Service Monitoring Status Changes and each individual Service's Latest Activity / News. Issue Time Tracking ------------------- Remaining Estimate: 0 minutes Time Spent: 4 hours > Implement RSS/atom feeds for services and activity feeds > -------------------------------------------------------- > > Key: BIOCAT-227 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-227 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Time Spent: 4 hours > Remaining Estimate: 0 minutes > > Mainly for latest services -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon May 24 12:45:19 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 24 May 2010 17:45:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-227) Implement RSS/atom feeds for services and activity feeds Message-ID: <10194083.1509.1274719519996.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-227?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-227. --------------------------------- Resolution: Fixed > Implement RSS/atom feeds for services and activity feeds > -------------------------------------------------------- > > Key: BIOCAT-227 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-227 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Time Spent: 4 hours > Remaining Estimate: 0 minutes > > Mainly for latest services -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon May 24 12:48:27 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 12:48:27 -0400 (EDT) Subject: [BioCatalogue-developers] [2028] trunk/app: Added feed icon to the Service 'News' tab. Message-ID: <20100524164827.4BED51678217@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 24 12:53:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 12:53:42 -0400 (EDT) Subject: [BioCatalogue-developers] [2029] trunk/app/helpers/activity_feeds_helper.rb: Added more info to the activity feed entry for SoapServiceChanges. Message-ID: <20100524165342.4076D1678217@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 24 12:57:13 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 12:57:13 -0400 (EDT) Subject: [BioCatalogue-developers] [2030] trunk/lib/bio_catalogue/activity_feeds.rb: Added monitoring status changes to a Service's latest activity feed. Message-ID: <20100524165714.0129C1858366@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 24 13:05:36 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 13:05:36 -0400 (EDT) Subject: [BioCatalogue-developers] [2031] trunk/script/biocatalogue/fix_activity_logs_for_status_change_may10. rb: Fix to the ActivityLog records for 'status_change' events - previously the 'referenced' was not being set to the associated Service, so activity feeds could not pick them up. Message-ID: <20100524170536.B4806185835C@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon May 24 13:01:17 2010 From: issues at mygrid.org.uk (Franck Tanoh (JIRA)) Date: Mon, 24 May 2010 18:01:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-351) Icons of the 'Monitoring test changes' activity on the homepage should be the same as those use to monitor services (red, green, blue circle) Message-ID: <29412179.1510.1274720477015.JavaMail.jira@rosalind.cs.man.ac.uk> Icons of the 'Monitoring test changes' activity on the homepage should be the same as those use to monitor services (red, green, blue circle) --------------------------------------------------------------------------------------------------------------------------------------------- Key: BIOCAT-351 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-351 Project: BioCatalogue Issue Type: Refinement Components: Activity Logging / Feeds / Notifications Reporter: Franck Tanoh Assignee: Jiten Bhagat Icons of the 'Monitoring test changes' activity on the homepage should be the same as those use to monitor services (red, green, blue circle). It will help make them uniform and also possibly easy to get the message. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon May 24 13:10:50 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 13:10:50 -0400 (EDT) Subject: [BioCatalogue-developers] [2032] trunk/app: Status changes. Message-ID: <20100524171050.7A065185835C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 24 13:20:46 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 13:20:46 -0400 (EDT) Subject: [BioCatalogue-developers] [2033] trunk/app/views: use display names for objects in emails instead of urls Message-ID: <20100524172047.078EF185834F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon May 24 13:35:53 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 13:35:53 -0400 (EDT) Subject: [BioCatalogue-developers] [2034] trunk: [BIOCAT-351] Added appropriate monitoring icons next to the status change list. Message-ID: <20100524173553.3299A1858332@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon May 24 13:58:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 24 May 2010 18:58:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-227) Implement RSS/atom feeds for services and activity feeds Message-ID: <28784505.1511.1274723897012.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-227?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10355 ] Jiten Bhagat logged work on BIOCAT-227: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-24 18:58 Start Date: 2010-05-24 16:58 Worklog Time Spent: 2 hours Issue Time Tracking ------------------- Time Spent: 6 hours (was: 4 hours) > Implement RSS/atom feeds for services and activity feeds > -------------------------------------------------------- > > Key: BIOCAT-227 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-227 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Time Spent: 6 hours > Remaining Estimate: 0 minutes > > Mainly for latest services -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon May 24 14:00:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 24 May 2010 19:00:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-352) Make the Activity Feed in the Service 'News' tab load asynchronously Message-ID: <32673675.1512.1274724016992.JavaMail.jira@rosalind.cs.man.ac.uk> Make the Activity Feed in the Service 'News' tab load asynchronously -------------------------------------------------------------------- Key: BIOCAT-352 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-352 Project: BioCatalogue Issue Type: Sub-task Components: Web Interface Reporter: Jiten Bhagat Assignee: Jiten Bhagat For perf reasons... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon May 24 14:09:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 24 May 2010 14:09:14 -0400 (EDT) Subject: [BioCatalogue-developers] [2035] trunk/app/views/shared/_activity.atom.builder: Make things more " ATOM-friendly" in the activity entries ATOM partial. Message-ID: <20100524180914.9B6331858324@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue May 25 00:52:52 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 25 May 2010 05:52:52 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'CLUSTAL W multiple alignment (CNRS IBCP)' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'CLUSTAL W multiple alignment (CNRS IBCP)' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/91 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 May 25 04:58:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 04:58:22 -0400 (EDT) Subject: [BioCatalogue-developers] [2036] trunk/app/views: Fixes for some views. Message-ID: <20100525085822.7068F19780E6@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 25 05:26:59 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 05:26:59 -0400 (EDT) Subject: [BioCatalogue-developers] [2037] trunk/app/views/user_mailer: bugfix : Use fully qualified name for ' display_name' function i.e BioCatalogue::Util.display_name Message-ID: <20100525092659.C67C519780E6@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 25 06:07:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 06:07:07 -0400 (EDT) Subject: [BioCatalogue-developers] [2038] trunk/app/views/responsibility_requests/index.html.erb: use display name function instead of service.name directly Message-ID: <20100525100707.C764C19780E6@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue May 25 08:06:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 25 May 2010 13:06:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-351) Icons of the 'Monitoring test changes' activity on the homepage should be the same as those use to monitor services (red, green, blue circle) In-Reply-To: <29412179.1510.1274720477015.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28356604.1545.1274789176995.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-351?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-351. --------------------------------- Resolution: Implemented > Icons of the 'Monitoring test changes' activity on the homepage should be the same as those use to monitor services (red, green, blue circle) > --------------------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-351 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-351 > Project: BioCatalogue > Issue Type: Refinement > Components: Activity Logging / Feeds / Notifications > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > > Icons of the 'Monitoring test changes' activity on the homepage should be the same as those use to monitor services (red, green, blue circle). It will help make them uniform and also possibly easy to get the message. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue May 25 08:12:50 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 08:12:50 -0400 (EDT) Subject: [BioCatalogue-developers] [2039] trunk: Fix for authorisation of actions on things within a service ( eg: annotations) by people who are given responsibility. Message-ID: <20100525121251.5183B1858341@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 25 08:15:35 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 08:15:35 -0400 (EDT) Subject: [BioCatalogue-developers] [2040] trunk/lib/bio_catalogue/auth.rb: Refactoring to make things clearer. Message-ID: <20100525121536.5195418581FE@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 25 08:32:38 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 08:32:38 -0400 (EDT) Subject: [BioCatalogue-developers] [2041] trunk/app/helpers/activity_feeds_helper.rb: Fix for the activity logs for monitoring status change entries where there is no previous result because the service was unchecked . Message-ID: <20100525123239.127DA1858341@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue May 25 08:45:30 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 25 May 2010 13:45:30 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'ConsensusPathDB' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'ConsensusPathDB' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/188 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 May 25 08:46:01 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 25 May 2010 13:46:01 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'ConsensusPathDB' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'ConsensusPathDB' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/188 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 May 25 09:06:26 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 09:06:26 -0400 (EDT) Subject: [BioCatalogue-developers] [2042] trunk/app/views/responsibility_requests: UI cleanup. Message-ID: <20100525130626.3578A1858289@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 25 09:29:26 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 09:29:26 -0400 (EDT) Subject: [BioCatalogue-developers] [2043] trunk: Various UI improvements. Message-ID: <20100525132926.43CA0197828C@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue May 25 09:54:21 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 25 May 2010 14:54:21 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'ConsensusPathDB' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'ConsensusPathDB' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/188 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue May 25 09:54:26 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 25 May 2010 14:54:26 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'ConsensusPathDB' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'ConsensusPathDB' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/188 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue May 25 10:17:35 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 10:17:35 -0400 (EDT) Subject: [BioCatalogue-developers] [2044] trunk/app: moved the edit button for service provider, next to the provider name to make it more obvious what is being edited Message-ID: <20100525141735.DC2E5177993C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 25 10:29:16 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 10:29:16 -0400 (EDT) Subject: [BioCatalogue-developers] [2045] trunk: Various UI changes based on feedback from Paul and Franck. Message-ID: <20100525142918.63DE61858344@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 25 10:50:19 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 10:50:19 -0400 (EDT) Subject: [BioCatalogue-developers] [2046] trunk: Major refactoring of the Service show page 'News' tab - now the activity feed is lazy loaded in the background AFTER the page is loaded . Message-ID: <20100525145019.98BB3185834B@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue May 25 10:57:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 25 May 2010 15:57:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-227) Implement RSS/atom feeds for services and activity feeds Message-ID: <24466826.1546.1274799437084.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-227?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10359 ] Jiten Bhagat logged work on BIOCAT-227: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-25 15:55 Start Date: 2010-05-24 15:55 Worklog Time Spent: 4 hours Issue Time Tracking ------------------- Time Spent: 1 day, 2 hours (was: 6 hours) > Implement RSS/atom feeds for services and activity feeds > -------------------------------------------------------- > > Key: BIOCAT-227 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-227 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Time Spent: 1 day, 2 hours > Remaining Estimate: 0 minutes > > Mainly for latest services -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue May 25 10:57:19 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 25 May 2010 15:57:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-352) Make the Activity Feed in the Service 'News' tab load asynchronously In-Reply-To: <32673675.1512.1274724016992.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16561767.1547.1274799439541.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-352?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10360 ] Jiten Bhagat logged work on BIOCAT-352: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-25 15:55 Start Date: 2010-05-25 13:55 Worklog Time Spent: 2 hours Issue Time Tracking ------------------- Remaining Estimate: 1 hour (was: 3 hours) Time Spent: 2 hours > Make the Activity Feed in the Service 'News' tab load asynchronously > -------------------------------------------------------------------- > > Key: BIOCAT-352 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-352 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 3 hours > Time Spent: 2 hours > Remaining Estimate: 1 hour > > For perf reasons... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue May 25 11:24:18 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 11:24:18 -0400 (EDT) Subject: [BioCatalogue-developers] [2047] trunk/public/stylesheets/styles.css: Small style fix. Message-ID: <20100525152418.2F3BC185834B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 25 11:44:52 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 11:44:52 -0400 (EDT) Subject: [BioCatalogue-developers] [2048] trunk/lib/bio_catalogue/activity_feeds.rb: Minor enhancement to prevent SQL queries with duplicate values in the conditions . Message-ID: <20100525154452.A4A7D185834B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 25 12:00:27 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 12:00:27 -0400 (EDT) Subject: [BioCatalogue-developers] [2049] trunk/vendor/plugins/atom_feed_helper/: Removed the atom_feed_helper as this was overriding the built in Rails AtomFeedHelper , which is much better now. Message-ID: <20100525160027.352AF185835A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 25 12:05:01 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 12:05:01 -0400 (EDT) Subject: [BioCatalogue-developers] [2050] trunk/app/views/shared/_activity.atom.builder: Minor tweak to activity feed ATOM output. Message-ID: <20100525160501.827AE1858351@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue May 25 14:08:44 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 25 May 2010 14:08:44 -0400 (EDT) Subject: [BioCatalogue-developers] [2051] trunk/lib/bio_catalogue/monitoring.rb: only add example endpoints from submitters and admins to monitoring Message-ID: <20100525180844.BFB90177993C@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed May 26 02:30:52 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 26 May 2010 07:30:52 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'phosphoELMdb' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'phosphoELMdb' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/115 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 May 26 04:24:55 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 26 May 2010 09:24:55 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'phosphoELMdb' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'phosphoELMdb' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/115 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 Wed May 26 04:32:54 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 26 May 2010 09:32:54 +0100 Subject: [BioCatalogue-developers] Steps needed for the codebase update Message-ID: <4BFCDCB6.2090305@ebi.ac.uk> Hi Guys, Could you please have another look at what needs to be done to update the codebase? Please let me know if I have missed anything or included anything which is not necessary http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes cheers. -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Wed May 26 04:45:07 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 26 May 2010 09:45:07 +0100 Subject: [BioCatalogue-developers] Release notes wiki page Message-ID: <4BFCDF93.3060300@cs.man.ac.uk> Regarding this page... http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes - "service-provider.xml file" should be "service-provider.csv file" - Restart the memcache servers *before* restarting the app and any workers. The last time you did an update we had many errors to do with memcache, because if you restart the the memcache servers during the app/workers running it will cause the connections within the app/workers to be broken. Jits From issues at mygrid.org.uk Wed May 26 04:55:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 26 May 2010 09:55:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-349) Test the newly deployed code [May 2010 Release] on biocatalogue test server In-Reply-To: <30589852.1187.1274429537097.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3698374.1592.1274864117134.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-349?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14974#action_14974 ] Eric Nzuobontane commented on BIOCAT-349: ----------------------------------------- Following have been tested for this release : 1) service update checker 2) service provider clustering 3) service ownership/responsibility 4) services change & monitoring feeds 5) rest example endpoint addition to monitoring 6) archiving of services, operations, inputs and outputs 7) including rest endpoints in search 8) Many other minor changes & tweaks > Test the newly deployed code [May 2010 Release] on biocatalogue test server > --------------------------------------------------------------------------- > > Key: BIOCAT-349 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-349 > Project: BioCatalogue > Issue Type: Sub-task > Components: Server Management > Environment: RoR, Solr, Apache, Linux > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 2 days > Time Spent: 4 hours > Remaining Estimate: 1 day, 4 hours > > Test every major functionality in preparation for the live release on Wednesday afternoon -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 26 04:57:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 26 May 2010 09:57:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-349) Test the newly deployed code [May 2010 Release] on biocatalogue test server In-Reply-To: <30589852.1187.1274429537097.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19463991.1593.1274864237056.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-349?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-349. ------------------------------------- Remaining Estimate: 1 hour (was: 1 day, 4 hours) Resolution: Fixed > Test the newly deployed code [May 2010 Release] on biocatalogue test server > --------------------------------------------------------------------------- > > Key: BIOCAT-349 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-349 > Project: BioCatalogue > Issue Type: Sub-task > Components: Server Management > Environment: RoR, Solr, Apache, Linux > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 2 days > Time Spent: 4 hours > Remaining Estimate: 1 hour > > Test every major functionality in preparation for the live release on Wednesday afternoon -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 26 04:59:18 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 26 May 2010 09:59:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-335) Allow enabling/disabling of availability checks from UI In-Reply-To: <23903801.110.1273826297000.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3595475.1595.1274864358479.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-335?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-335. ------------------------------------- Resolution: Implemented Feature implemented and available on test site > Allow enabling/disabling of availability checks from UI > ------------------------------------------------------- > > Key: BIOCAT-335 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-335 > Project: BioCatalogue > Issue Type: Refinement > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Provide UI to enable disable availability checks so that admins can temporarily or permanently removes checks from the monitoring. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 26 04:59:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 26 May 2010 09:59:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-335) Allow enabling/disabling of availability checks from UI In-Reply-To: <23903801.110.1273826297000.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27290017.1594.1274864357035.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-335?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-335 started by Eric Nzuobontane. > Allow enabling/disabling of availability checks from UI > ------------------------------------------------------- > > Key: BIOCAT-335 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-335 > Project: BioCatalogue > Issue Type: Refinement > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Provide UI to enable disable availability checks so that admins can temporarily or permanently removes checks from the monitoring. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 26 05:01:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 26 May 2010 10:01:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-304) Investigate twittering failure on live site Message-ID: <7420707.1596.1274864477051.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-304?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-304 stopped by Eric Nzuobontane. > Investigate twittering failure on live site > ------------------------------------------- > > Key: BIOCAT-304 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-304 > Project: BioCatalogue > Issue Type: Bug > Components: Server Management > Environment: RoR > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Priority: Minor > > Tweets fail to be created/sent from the live site to the biocatalogue twitter account. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 26 05:03:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 26 May 2010 10:03:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-305) Allow users to take ownership/claim responsibility of services Message-ID: <1842428.1597.1274864597004.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-305?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-305. ------------------------------------- Resolution: Implemented Functionality implemented and available on the test site > Allow users to take ownership/claim responsibility of services > -------------------------------------------------------------- > > Key: BIOCAT-305 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-305 > Project: BioCatalogue > Issue Type: New Feature > Components: Service Container > Environment: RoR > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Allow people that did not submit services to the given the permissions to manage the service entries in BioCatalogue -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Wed May 26 05:09:43 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 26 May 2010 10:09:43 +0100 Subject: [BioCatalogue-developers] [2051] trunk/lib/bio_catalogue/monitoring.rb: only add example endpoints from submitters and admins to monitoring In-Reply-To: <20100525180844.BFB90177993C@rubyforge.org> References: <20100525180844.BFB90177993C@rubyforge.org> Message-ID: <4BFCE557.5020803@cs.man.ac.uk> 2 things: 1. For the method 'self.from_trusted_source?', why don't you use Service#all_responsibles like we do in the Auth, to keep things consistent? Right now your current code doesn't take into account example endpoints from curators (ie: role_id = 2) and other people responsible for a service (through your new responsibility mechanism). 2. Change this: Annotation.find(:all, :conditions => {:annotatable_type => "RestMethod"}).collect{|a| a if a.attribute.name=="example_endpoint" }.compact.each do |ann| ... to: Annotation.find(:all, :joins => :attribute, :conditions => { :annotatable_type => 'RestMethod', :annotation_attributes => { :name => "example_endpoints" } }).each do |ann| ... At the moment you are loading up ALL annotations on ALL RestMethod objects, regardless of attribute, and then filtering them in memory. Jits noreply at rubyforge.org wrote: > > Revision > 2051 > Author > ebontane > Date > 2010-05-25 14:08:44 -0400 (Tue, 25 May 2010) > > > Log Message > > only add example endpoints from submitters and admins to monitoring > > > Modified Paths > > * trunk/lib/bio_catalogue/monitoring.rb > <#trunklibbio_cataloguemonitoringrb> > > > Diff > > > Modified: trunk/lib/bio_catalogue/monitoring.rb (2050 => 2051) > > > --- trunk/lib/bio_catalogue/monitoring.rb 2010-05-25 16:05:01 UTC (rev 2050) > +++ trunk/lib/bio_catalogue/monitoring.rb 2010-05-25 18:08:44 UTC (rev 2051) > @@ -89,17 +89,20 @@ > > Annotation.find(:all, > :conditions => {:annotatable_type => "RestMethod"}).collect{|a| a if a.attribute.name=="example_endpoint" }.compact.each do |ann| > - monitor = UrlMonitor.find(:first , :conditions => ["parent_id= ? AND parent_type= ?", ann.id, ann.class.name ]) > - if monitor.nil? > - mon = build_url_monitor(ann, 'value', ann.annotatable.rest_resource.rest_service.service) > - if mon > - begin > - if mon.save! > - Rails.logger.debug("Created a new monitor for #{ann.send('value')}") > + > + if from_trusted_source?(ann) > + monitor = UrlMonitor.find(:first , :conditions => ["parent_id= ? AND parent_type= ?", ann.id, ann.class.name ]) > + if monitor.nil? > + mon = build_url_monitor(ann, 'value', ann.annotatable.rest_resource.rest_service.service) > + if mon > + begin > + if mon.save! > + Rails.logger.debug("Created a new monitor for #{ann.send('value')}") > + end > + rescue Exception => ex > + Rails.logger.warn("Could not create url monitor") > + Rails.logger.warn(ex) > end > - rescue Exception => ex > - Rails.logger.warn("Could not create url monitor") > - Rails.logger.warn(ex) > end > end > end > @@ -123,6 +126,21 @@ > end > > end > + > + # Is the "example_endpoint" annotation from a trusted source? > + # Only submitters of the services && admins are considered > + # trusted sources. > + # Maybe in the future this should include anyone with full > + # permission on the service. > + def self.from_trusted_source?(ann) > + if ann.attribute.name.downcase =="example_endpoint" && ann.annotatable.class.name == "RestMethod" > + if ann.source.class.name == "User" > + return true if ann.source.is_admin? > + return true if ann.source == ann.annotatable.rest_resource.rest_service.service.submitter > + end > + end > + return false > + end > > end # MonitorUpdate > > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From jits at cs.man.ac.uk Wed May 26 05:15:59 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 26 May 2010 10:15:59 +0100 Subject: [BioCatalogue-developers] Steps needed for the codebase update In-Reply-To: <4BFCDCB6.2090305@ebi.ac.uk> References: <4BFCDCB6.2090305@ebi.ac.uk> Message-ID: <4BFCE6CF.5060705@cs.man.ac.uk> Another thing,.. These two tasks: * Run the service update checker for all services * rake biocatalogue:submit:run_service_updater_for_all production * Fix activity logs for status change * ruby script/biocatalogue/fix_activity_logs_for_status_change_may10.rb production ... should happen *after* the new app is deployed. I.e: after the memcache / app / workers restart, not before, to ensure they are running on the latest code / db schema. Jits Eric Nzuobontane wrote: > Hi Guys, > Could you please have another look at what needs to be done to update > the codebase? Please let me know if I have missed anything or included > anything which is not necessary > http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes > > > cheers. From ericnzuo at ebi.ac.uk Wed May 26 05:19:27 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 26 May 2010 10:19:27 +0100 Subject: [BioCatalogue-developers] Release notes wiki page In-Reply-To: <4BFCDF93.3060300@cs.man.ac.uk> References: <4BFCDF93.3060300@cs.man.ac.uk> Message-ID: <4BFCE79F.3070004@ebi.ac.uk> Jiten Bhagat wrote: > Regarding this page... > > http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes > > - "service-provider.xml file" should be "service-provider.csv file" > corrected now. Thanks! > - Restart the memcache servers *before* restarting the app and any > workers I have taken note of that... > The last time you did an update we had many errors to do with > memcache, because if you restart the the memcache servers during the > app/workers running it will cause the connections within the app/workers > to be broken. > > Jits > > > 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 Wed May 26 05:27:37 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 26 May 2010 10:27:37 +0100 Subject: [BioCatalogue-developers] Steps needed for the codebase update In-Reply-To: <4BFCE6CF.5060705@cs.man.ac.uk> References: <4BFCDCB6.2090305@ebi.ac.uk> <4BFCE6CF.5060705@cs.man.ac.uk> Message-ID: <4BFCE989.6060801@ebi.ac.uk> Actually running all the scripts should happen after the new app is deployed. Eric Jiten Bhagat wrote: > Another thing,.. > > These two tasks: > > * Run the service update checker for all services > * rake biocatalogue:submit:run_service_updater_for_all production > > * Fix activity logs for status change > * ruby > script/biocatalogue/fix_activity_logs_for_status_change_may10.rb production > > ... should happen *after* the new app is deployed. I.e: after the > memcache / app / workers restart, not before, to ensure they are running > on the latest code / db schema. > > Jits > > > > Eric Nzuobontane wrote: > >> Hi Guys, >> Could you please have another look at what needs to be done to update >> the codebase? Please let me know if I have missed anything or included >> anything which is not necessary >> http://www.biocatalogue.org/wiki/doku.php?id=development:pre_release_notes >> >> >> cheers. >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Wed May 26 05:52:24 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 26 May 2010 10:52:24 +0100 Subject: [BioCatalogue-developers] [2051] trunk/lib/bio_catalogue/monitoring.rb: only add example endpoints from submitters and admins to monitoring In-Reply-To: <4BFCE557.5020803@cs.man.ac.uk> References: <20100525180844.BFB90177993C@rubyforge.org> <4BFCE557.5020803@cs.man.ac.uk> Message-ID: <4BFCEF58.7040005@ebi.ac.uk> Jiten Bhagat wrote: > 2 things: > > 1. For the method 'self.from_trusted_source?', why don't you use > Service#all_responsibles like we do in the Auth, to keep things > consistent? Right now your current code doesn't take into account > example endpoints from curators (ie: role_id = 2) and other people > responsible for a service (through your new responsibility mechanism). > It does not and the reason I decided against that was to keep the potential sources small and hence the note. But if people feel that that is not a problem, that I do not mind changing it. > 2. Change this: > > Annotation.find(:all, > :conditions => {:annotatable_type => > "RestMethod"}).collect{|a| a if a.attribute.name=="example_endpoint" > }.compact.each do |ann| ... > > to: > > Annotation.find(:all, > :joins => :attribute, > :conditions => { :annotatable_type => 'RestMethod', > :annotation_attributes => { :name => "example_endpoints" } }).each do > |ann| ... > > At the moment you are loading up ALL annotations on ALL RestMethod > objects, regardless of attribute, and then filtering them in memory. > OK will change that. Eric > Jits > > > > noreply at rubyforge.org wrote: > >> Revision >> 2051 >> Author >> ebontane >> Date >> 2010-05-25 14:08:44 -0400 (Tue, 25 May 2010) >> >> >> Log Message >> >> only add example endpoints from submitters and admins to monitoring >> >> >> Modified Paths >> >> * trunk/lib/bio_catalogue/monitoring.rb >> <#trunklibbio_cataloguemonitoringrb> >> >> >> Diff >> >> >> Modified: trunk/lib/bio_catalogue/monitoring.rb (2050 => 2051) >> >> >> --- trunk/lib/bio_catalogue/monitoring.rb 2010-05-25 16:05:01 UTC (rev 2050) >> +++ trunk/lib/bio_catalogue/monitoring.rb 2010-05-25 18:08:44 UTC (rev 2051) >> @@ -89,17 +89,20 @@ >> >> Annotation.find(:all, >> :conditions => {:annotatable_type => "RestMethod"}).collect{|a| a if a.attribute.name=="example_endpoint" }.compact.each do |ann| >> - monitor = UrlMonitor.find(:first , :conditions => ["parent_id= ? AND parent_type= ?", ann.id, ann.class.name ]) >> - if monitor.nil? >> - mon = build_url_monitor(ann, 'value', ann.annotatable.rest_resource.rest_service.service) >> - if mon >> - begin >> - if mon.save! >> - Rails.logger.debug("Created a new monitor for #{ann.send('value')}") >> + >> + if from_trusted_source?(ann) >> + monitor = UrlMonitor.find(:first , :conditions => ["parent_id= ? AND parent_type= ?", ann.id, ann.class.name ]) >> + if monitor.nil? >> + mon = build_url_monitor(ann, 'value', ann.annotatable.rest_resource.rest_service.service) >> + if mon >> + begin >> + if mon.save! >> + Rails.logger.debug("Created a new monitor for #{ann.send('value')}") >> + end >> + rescue Exception => ex >> + Rails.logger.warn("Could not create url monitor") >> + Rails.logger.warn(ex) >> end >> - rescue Exception => ex >> - Rails.logger.warn("Could not create url monitor") >> - Rails.logger.warn(ex) >> end >> end >> end >> @@ -123,6 +126,21 @@ >> end >> >> end >> + >> + # Is the "example_endpoint" annotation from a trusted source? >> + # Only submitters of the services && admins are considered >> + # trusted sources. >> + # Maybe in the future this should include anyone with full >> + # permission on the service. >> + def self.from_trusted_source?(ann) >> + if ann.attribute.name.downcase =="example_endpoint" && ann.annotatable.class.name == "RestMethod" >> + if ann.source.class.name == "User" >> + return true if ann.source.is_admin? >> + return true if ann.source == ann.annotatable.rest_resource.rest_service.service.submitter >> + end >> + end >> + return false >> + end >> >> end # MonitorUpdate >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Wed May 26 06:19:03 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 26 May 2010 06:19:03 -0400 (EDT) Subject: [BioCatalogue-developers] [2052] trunk/lib/bio_catalogue/monitoring.rb: Extend trust to all responsible for a service & and improve performance in creation of example endpoint monitors Message-ID: <20100526101903.CC34A185834F@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed May 26 07:23:17 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 26 May 2010 12:23:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-353) Remove/Implement endpoints: /soap_operation/{id}/inputs AND /soap_operation/{id}/outputs Message-ID: <31076462.1623.1274872997018.JavaMail.jira@rosalind.cs.man.ac.uk> Remove/Implement endpoints: /soap_operation/{id}/inputs AND /soap_operation/{id}/outputs ---------------------------------------------------------------------------------------- Key: BIOCAT-353 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-353 Project: BioCatalogue Issue Type: Bug Components: REST API, SOAP Services Support Reporter: Mannie Tagarira Assignee: Jiten Bhagat When making calls via the REST API those 2 endpoints are shown in the related section; they do not work. Example: Calling: http://www.biocatalogue.org/soap_operations/15369.xml returns some XML but the key lookout points are: ... ... ... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Wed May 26 10:05:49 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 26 May 2010 15:05:49 +0100 Subject: [BioCatalogue-developers] starting the update now Message-ID: <4BFD2ABD.1010702@ebi.ac.uk> I am going to start the update now. I will send a mail when all is done. 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 Wed May 26 12:51:03 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 26 May 2010 17:51:03 +0100 Subject: [BioCatalogue-developers] starting the update now In-Reply-To: <4BFD2ABD.1010702@ebi.ac.uk> References: <4BFD2ABD.1010702@ebi.ac.uk> Message-ID: <4BFD5177.4070703@ebi.ac.uk> The code update has been done. The service checker is currently running. I will lunch the reindexing when I get home. I will send another status update then. Eric Eric Nzuobontane wrote: > I am going to start the update now. I will send a mail when all is done. > > 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 Wed May 26 13:07:27 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 26 May 2010 18:07:27 +0100 Subject: [BioCatalogue-developers] starting the update now In-Reply-To: <4BFD5177.4070703@ebi.ac.uk> References: <4BFD2ABD.1010702@ebi.ac.uk> <4BFD5177.4070703@ebi.ac.uk> Message-ID: <4BFD554F.9090503@cs.man.ac.uk> Steve and I are getting *many* monitoring status change emails... seems like the test script execution harness thing is not working properly... Jits Eric Nzuobontane wrote: > The code update has been done. The service checker is currently > running. I will lunch the reindexing when I get home. I will send > another status update then. > > Eric > > > Eric Nzuobontane wrote: >> I am going to start the update now. I will send a mail when all is done. >> >> Eric >> > > From ericnzuo at ebi.ac.uk Wed May 26 15:06:20 2010 From: ericnzuo at ebi.ac.uk (ericnzuo at ebi.ac.uk) Date: Wed, 26 May 2010 20:06:20 +0100 (BST) Subject: [BioCatalogue-developers] starting the update now In-Reply-To: <4BFD554F.9090503@cs.man.ac.uk> References: <4BFD2ABD.1010702@ebi.ac.uk> <4BFD5177.4070703@ebi.ac.uk> <4BFD554F.9090503@cs.man.ac.uk> Message-ID: <48973.86.1.40.156.1274900780.squirrel@webmail.ebi.ac.uk> > Steve and I are getting *many* monitoring status change emails... seems > like the test script execution harness thing is not working properly... I have not see any problem with the harness. But if you find a problem please let me know. As you will note the mails are all about URL checks. I received the mails too and they are mostly due to some INB servers. I made a change to the soap endpoint check whereby I now parse the response to see if it is a soap response. Calling the end points of these services does not return a soap response and you will note as well that those are the same services for which the test scripts have been consistently failing. Another thing, hovering over the test script status icon now says since when a test script has been failing. Eric > > > Jits > > > Eric Nzuobontane wrote: >> The code update has been done. The service checker is currently >> running. I will lunch the reindexing when I get home. I will send >> another status update then. >> >> Eric >> >> >> Eric Nzuobontane wrote: >>> I am going to start the update now. I will send a mail when all is >>> done. >>> >>> Eric >>> >> >> > From ericnzuo at ebi.ac.uk Wed May 26 15:19:57 2010 From: ericnzuo at ebi.ac.uk (ericnzuo at ebi.ac.uk) Date: Wed, 26 May 2010 20:19:57 +0100 (BST) Subject: [BioCatalogue-developers] starting the update now In-Reply-To: <4BFD554F.9090503@cs.man.ac.uk> References: <4BFD2ABD.1010702@ebi.ac.uk> <4BFD5177.4070703@ebi.ac.uk> <4BFD554F.9090503@cs.man.ac.uk> Message-ID: <55027.86.1.40.156.1274901597.squirrel@webmail.ebi.ac.uk> On second thought, I have decided not to run the re-indexing now because it has potential to fail and the tomcat server in which it runs is system managed. I would prefer to run the re-indexing in the morning when the system administrators are in place to solve any potential problems. Eric > Steve and I are getting *many* monitoring status change emails... seems > like the test script execution harness thing is not working properly... > > Jits > > > Eric Nzuobontane wrote: >> The code update has been done. The service checker is currently >> running. I will lunch the reindexing when I get home. I will send >> another status update then. >> >> Eric >> >> >> Eric Nzuobontane wrote: >>> I am going to start the update now. I will send a mail when all is >>> done. >>> >>> Eric >>> >> >> > From utopia at cs.man.ac.uk Wed May 26 15:59:25 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 26 May 2010 20:59:25 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runParmbsc0PhysicalProperties' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runParmbsc0PhysicalProperties' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1018 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Wed May 26 17:09:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 26 May 2010 22:09:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-354) Deploy new release on the live server [May 2010 Release] Message-ID: <2498401.1655.1274908157140.JavaMail.jira@rosalind.cs.man.ac.uk> Deploy new release on the live server [May 2010 Release] -------------------------------------------------------- Key: BIOCAT-354 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-354 Project: BioCatalogue Issue Type: Task Components: Server Management Environment: RoR, apache, CentOS Reporter: Eric Nzuobontane Assignee: Jiten Bhagat Codebase update and restart of all the related services(job workers, memcached servers, search server...) -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 26 17:09:20 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 26 May 2010 22:09:20 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-354) Deploy new release on the live server [May 2010 Release] In-Reply-To: <2498401.1655.1274908157140.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5931262.1656.1274908160214.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-354?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-354: --------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > Deploy new release on the live server [May 2010 Release] > -------------------------------------------------------- > > Key: BIOCAT-354 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-354 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Environment: RoR, apache, CentOS > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > Codebase update and restart of all the related services(job workers, memcached servers, search server...) -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 26 17:11:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 26 May 2010 22:11:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-355) recreate the search index(by running solr reindex) Message-ID: <4344127.1657.1274908276998.JavaMail.jira@rosalind.cs.man.ac.uk> recreate the search index(by running solr reindex) -------------------------------------------------- Key: BIOCAT-355 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-355 Project: BioCatalogue Issue Type: Sub-task Components: Server Management Environment: SOLR Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 26 17:16:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 26 May 2010 22:16:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-356) verify the MANY test status emails received at the code update on May 26, 2010 Message-ID: <4167848.1658.1274908577047.JavaMail.jira@rosalind.cs.man.ac.uk> verify the MANY test status emails received at the code update on May 26, 2010 ------------------------------------------------------------------------------ Key: BIOCAT-356 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-356 Project: BioCatalogue Issue Type: Sub-task Components: Service Monitoring Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane app indicates a considerable number of test status changes after the update. These need to be verified further. Preliminary checks suggest the validity of these changes. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed May 26 17:31:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 26 May 2010 22:31:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-356) verify the MANY test status emails received at the code update on May 26, 2010 In-Reply-To: <4167848.1658.1274908577047.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5569567.1659.1274909477239.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-356?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14979#action_14979 ] Jiten Bhagat commented on BIOCAT-356: ------------------------------------- Seems like most of those failing are due to failed test scripts. Is the test scripts harness working correctly? > verify the MANY test status emails received at the code update on May 26, 2010 > ------------------------------------------------------------------------------ > > Key: BIOCAT-356 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-356 > Project: BioCatalogue > Issue Type: Sub-task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > app indicates a considerable number of test status changes after the update. These need to be verified further. Preliminary checks suggest the validity of these changes. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu May 27 04:52:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 27 May 2010 09:52:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-357) Add helper text to test script submission UI Message-ID: <24301496.1660.1274950337144.JavaMail.jira@rosalind.cs.man.ac.uk> Add helper text to test script submission UI -------------------------------------------- Key: BIOCAT-357 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-357 Project: BioCatalogue Issue Type: Refinement Components: Web Interface Environment: RoR Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Priority: Minor Add some helper text to explain what test scripts are and how they are used in BioCatalogue, in the same spirit of 'about soaplab helper text' -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu May 27 05:09:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 27 May 2010 10:09:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-358) Add all appropriate REST model resources to the API Message-ID: <27947548.1661.1274951357055.JavaMail.jira@rosalind.cs.man.ac.uk> Add all appropriate REST model resources to the API --------------------------------------------------- Key: BIOCAT-358 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-358 Project: BioCatalogue Issue Type: New Feature Components: REST API Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Minor -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu May 27 05:09:18 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 27 May 2010 10:09:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-298) Add REST Endpoints to search results web UI and API Message-ID: <11539442.1662.1274951358498.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-298?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10364 ] Jiten Bhagat logged work on BIOCAT-298: --------------------------------------- Author: Jiten Bhagat Created on: 2010-05-27 10:08 Start Date: 2010-05-13 10:08 Worklog Time Spent: 3 hours Issue Time Tracking ------------------- Remaining Estimate: 0 minutes Time Spent: 3 hours > Add REST Endpoints to search results web UI and API > --------------------------------------------------- > > Key: BIOCAT-298 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-298 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API, Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Time Spent: 3 hours > Remaining Estimate: 0 minutes > > Like for SOAP Operations -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu May 27 05:09:19 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 27 May 2010 10:09:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-298) Add REST Endpoints to search results web UI and API Message-ID: <25654268.1663.1274951359519.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-298?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14980#action_14980 ] Jiten Bhagat commented on BIOCAT-298: ------------------------------------- Added to web UI, now pending to add to search API > Add REST Endpoints to search results web UI and API > --------------------------------------------------- > > Key: BIOCAT-298 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-298 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API, Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Time Spent: 3 hours > Remaining Estimate: 0 minutes > > Like for SOAP Operations -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu May 27 06:20:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 27 May 2010 11:20:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-359) Cleanup pre-release notes and move them to the release notes section Message-ID: <33157500.1664.1274955616998.JavaMail.jira@rosalind.cs.man.ac.uk> Cleanup pre-release notes and move them to the release notes section -------------------------------------------------------------------- Key: BIOCAT-359 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-359 Project: BioCatalogue Issue Type: Sub-task Components: Wiki Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Move pre-release note to the release notes section and update accordingly -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu May 27 06:27:43 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 May 2010 06:27:43 -0400 (EDT) Subject: [BioCatalogue-developers] [2053] trunk: Cleaner way of getting the Time for x days ago. Message-ID: <20100527102743.818471858354@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Thu May 27 06:27:59 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 27 May 2010 11:27:59 +0100 Subject: [BioCatalogue-developers] starting the update now In-Reply-To: <48973.86.1.40.156.1274900780.squirrel@webmail.ebi.ac.uk> References: <4BFD2ABD.1010702@ebi.ac.uk> <4BFD5177.4070703@ebi.ac.uk> <4BFD554F.9090503@cs.man.ac.uk> <48973.86.1.40.156.1274900780.squirrel@webmail.ebi.ac.uk> Message-ID: Hi Eric, Thanks for the updates. >I made a change to the soap endpoint check whereby I now parse the response to see if it is a soap response. That's the problem. I've got through most of these mails and lots of services fails the test because of the endpoint or base URL. The service includes: -all the SOAP ddbj services: http://www.biocatalogue.org/service_providers/4 . I tried couple these services using workflows and they are running fine. - More than 100 INB services have the same endpoints: http://inb.bsc.es/cgi-bin/mobyServices/dispatchers/Dispatcher.cgi which returns an 'Not found' error message. - there are other INB services with the same problem - those well annotated web services by James: http://www.biocatalogue.org/users/238#services , their endpoints look like that: http://gnode1.mib.man.ac.uk:8080/FullTextWebServices/TextCleanerService but monitored as not working. - and many more.... Basically, around half or 1/3 of the service in biocat shows the warning sign. It looks to me that the endpoint (or base URL) accessibility or not does not affect the availability of the service (e.g DDBJ, james services) so I don't really encourage the changes you made. Franck On 26 May 2010 20:06, wrote: > > >> Steve and I are getting *many* monitoring status change emails... seems >> like the test script execution harness thing is not working properly... > I have not see any problem with the harness. But if you find a problem > please let me know. > As you will note the mails are all about URL checks. I received the mails > too and they are mostly due to some INB servers. I made a change to the > soap endpoint check whereby I now parse the response to ?see if it is a > soap response. Calling the end points of these services does not return a > soap response and you will note as well that those are the same services > for which the test scripts have been consistently failing. > > Another thing, hovering over the test script status icon now says since > when a test script has been failing. > > Eric >> > >> >> Jits >> >> >> Eric Nzuobontane wrote: >>> The code update has been done. The service checker is currently >>> running. I will lunch the reindexing when I get home. I will send >>> another status update then. >>> >>> Eric >>> >>> >>> Eric Nzuobontane wrote: >>>> I am going to start the update now. I will send a mail when all is >>>> done. >>>> >>>> Eric >>>> >>> >>> >> > > > _______________________________________________ > 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 Thu May 27 06:30:32 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 May 2010 06:30:32 -0400 (EDT) Subject: [BioCatalogue-developers] [2054] trunk/app/views/search/show.xml.builder: Improved output of search results in the REST API. Message-ID: <20100527103032.526921858354@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 27 06:37:01 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 May 2010 06:37:01 -0400 (EDT) Subject: [BioCatalogue-developers] [2055] trunk/app/controllers/search_controller.rb: Ignore rest_methods search scope in the API, for now. Message-ID: <20100527103701.507AD1858354@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 27 06:44:18 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 May 2010 06:44:18 -0400 (EDT) Subject: [BioCatalogue-developers] [2056] trunk/app/controllers/search_controller.rb: Minor fix Message-ID: <20100527104418.170671858354@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 27 06:47:49 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 May 2010 06:47:49 -0400 (EDT) Subject: [BioCatalogue-developers] [2057] trunk/app/views/search/show.xml.builder: Fixed silly mistakes! Message-ID: <20100527104749.122151858354@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 27 06:51:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 May 2010 06:51:08 -0400 (EDT) Subject: [BioCatalogue-developers] [2058] trunk/app/views/search/show.xml.builder: For Search REST API - don' t generate the related link to the rest_methods scope. Message-ID: <20100527105109.029BD1858356@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu May 27 06:57:11 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 27 May 2010 11:57:11 +0100 Subject: [BioCatalogue-developers] starting the update now In-Reply-To: References: <4BFD2ABD.1010702@ebi.ac.uk> <4BFD5177.4070703@ebi.ac.uk> <4BFD554F.9090503@cs.man.ac.uk> <48973.86.1.40.156.1274900780.squirrel@webmail.ebi.ac.uk> Message-ID: <4BFE5007.3020701@ebi.ac.uk> Hi Franck, OK, I see that the changes I made how an affect which you do not agree with. The question I have is, should endpoints be monitored, if so how? What I implemented to a simple approach. If you send xml to a soap endpoint, you should expect to get back a soap response. Maybe saying it not accessible is the wrong thing. I would chang the accessibility wording to say we did not receive a soap response back. But if someone suggests a better way of monitoring these things, I am happy to go along with it. Eric Franck Tanoh wrote: > Hi Eric, > > Thanks for the updates. > > >> I made a change to the soap endpoint check whereby I now parse the response to see if it is a soap response. >> > That's the problem. I've got through most of these mails and lots of > services fails the test because of the endpoint or base URL. > The service includes: > -all the SOAP ddbj services: > http://www.biocatalogue.org/service_providers/4 . I tried couple these > services using workflows and they are running fine. > - More than 100 INB services have the same endpoints: > http://inb.bsc.es/cgi-bin/mobyServices/dispatchers/Dispatcher.cgi > which returns an 'Not found' error message. > - there are other INB services with the same problem > - those well annotated web services by James: > http://www.biocatalogue.org/users/238#services , their endpoints look > like that: http://gnode1.mib.man.ac.uk:8080/FullTextWebServices/TextCleanerService > but monitored as not working. > - and many more.... > Basically, around half or 1/3 of the service in biocat shows the warning sign. > It looks to me that the endpoint (or base URL) accessibility or not > does not affect the availability of the service (e.g DDBJ, james > services) so I don't really encourage the changes you made. > > Franck > > > > > On 26 May 2010 20:06, wrote: > >> >>> Steve and I are getting *many* monitoring status change emails... seems >>> like the test script execution harness thing is not working properly... >>> >> I have not see any problem with the harness. But if you find a problem >> please let me know. >> As you will note the mails are all about URL checks. I received the mails >> too and they are mostly due to some INB servers. I made a change to the >> soap endpoint check whereby I now parse the response to see if it is a >> soap response. Calling the end points of these services does not return a >> soap response and you will note as well that those are the same services >> for which the test scripts have been consistently failing. >> >> Another thing, hovering over the test script status icon now says since >> when a test script has been failing. >> >> Eric >> >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>> >>>> The code update has been done. The service checker is currently >>>> running. I will lunch the reindexing when I get home. I will send >>>> another status update then. >>>> >>>> Eric >>>> >>>> >>>> Eric Nzuobontane wrote: >>>> >>>>> I am going to start the update now. I will send a mail when all is >>>>> done. >>>>> >>>>> Eric >>>>> >>>>> >>>> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> > > > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Thu May 27 07:00:33 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 May 2010 07:00:33 -0400 (EDT) Subject: [BioCatalogue-developers] [2059] trunk/public/2009/xml/rest/schema-v1.xsd: Updated REST API schema to take into account latest changes to search. Message-ID: <20100527110033.D16A91858354@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu May 27 07:05:34 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 27 May 2010 12:05:34 +0100 Subject: [BioCatalogue-developers] starting the update now In-Reply-To: <4BFE5007.3020701@ebi.ac.uk> References: <4BFD2ABD.1010702@ebi.ac.uk> <4BFD5177.4070703@ebi.ac.uk> <4BFD554F.9090503@cs.man.ac.uk> <48973.86.1.40.156.1274900780.squirrel@webmail.ebi.ac.uk> <4BFE5007.3020701@ebi.ac.uk> Message-ID: <4BFE51FE.6020707@cs.man.ac.uk> What about what we had before? That seemed to work well, and as far as I remember you still had checks for SOAP faults before. So I'm confused as to the latest changes... Jits Eric Nzuobontane wrote: > Hi Franck, > > OK, I see that the changes I made how an affect which you do not agree > with. The question I have is, should endpoints be monitored, if so how? > What I implemented to a simple approach. If you send xml to a soap > endpoint, you should expect to get back a soap response. Maybe saying > it not accessible is the wrong thing. I would chang the accessibility > wording to say we did not receive a soap response back. But if someone > suggests a better way of monitoring these things, I am happy to go > along with it. > > Eric > > > > > Franck Tanoh wrote: >> Hi Eric, >> >> Thanks for the updates. >> >> >>> I made a change to the soap endpoint check whereby I now parse the >>> response to see if it is a soap response. >>> >> That's the problem. I've got through most of these mails and lots of >> services fails the test because of the endpoint or base URL. >> The service includes: >> -all the SOAP ddbj services: >> http://www.biocatalogue.org/service_providers/4 . I tried couple these >> services using workflows and they are running fine. >> - More than 100 INB services have the same endpoints: >> http://inb.bsc.es/cgi-bin/mobyServices/dispatchers/Dispatcher.cgi >> which returns an 'Not found' error message. >> - there are other INB services with the same problem >> - those well annotated web services by James: >> http://www.biocatalogue.org/users/238#services , their endpoints look >> like that: >> http://gnode1.mib.man.ac.uk:8080/FullTextWebServices/TextCleanerService >> but monitored as not working. >> - and many more.... >> Basically, around half or 1/3 of the service in biocat shows the >> warning sign. >> It looks to me that the endpoint (or base URL) accessibility or not >> does not affect the availability of the service (e.g DDBJ, james >> services) so I don't really encourage the changes you made. >> >> Franck >> >> >> >> >> On 26 May 2010 20:06, wrote: >> >>> >>>> Steve and I are getting *many* monitoring status change emails... >>>> seems >>>> like the test script execution harness thing is not working >>>> properly... >>>> >>> I have not see any problem with the harness. But if you find a problem >>> please let me know. >>> As you will note the mails are all about URL checks. I received the >>> mails >>> too and they are mostly due to some INB servers. I made a change to the >>> soap endpoint check whereby I now parse the response to see if it is a >>> soap response. Calling the end points of these services does not >>> return a >>> soap response and you will note as well that those are the same >>> services >>> for which the test scripts have been consistently failing. >>> >>> Another thing, hovering over the test script status icon now says since >>> when a test script has been failing. >>> >>> Eric >>> >>>> Jits >>>> >>>> >>>> Eric Nzuobontane wrote: >>>> >>>>> The code update has been done. The service checker is currently >>>>> running. I will lunch the reindexing when I get home. I will send >>>>> another status update then. >>>>> >>>>> Eric >>>>> >>>>> >>>>> Eric Nzuobontane wrote: >>>>> >>>>>> I am going to start the update now. I will send a mail when all is >>>>>> done. >>>>>> >>>>>> Eric >>>>>> >>>>>> >>>>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >>> >> >> >> >> > > From ericnzuo at ebi.ac.uk Thu May 27 07:23:32 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 27 May 2010 12:23:32 +0100 Subject: [BioCatalogue-developers] starting the update now In-Reply-To: <4BFE51FE.6020707@cs.man.ac.uk> References: <4BFD2ABD.1010702@ebi.ac.uk> <4BFD5177.4070703@ebi.ac.uk> <4BFD554F.9090503@cs.man.ac.uk> <48973.86.1.40.156.1274900780.squirrel@webmail.ebi.ac.uk> <4BFE5007.3020701@ebi.ac.uk> <4BFE51FE.6020707@cs.man.ac.uk> Message-ID: <4BFE5634.8010205@ebi.ac.uk> Jiten Bhagat wrote: > What about what we had before? That seemed to work well, and as far as I > remember you still had checks for SOAP faults before. So I'm confused as > to the latest changes... > Sorry for any confusion. What we hard before was simply checking whether the response had an xml header but not necessarily that the response was soap message. So services like these INB ones which returned an xml header and an html page were ticked OK. Eric > Jits > > > Eric Nzuobontane wrote: > >> Hi Franck, >> >> OK, I see that the changes I made how an affect which you do not agree >> with. The question I have is, should endpoints be monitored, if so how? >> What I implemented to a simple approach. If you send xml to a soap >> endpoint, you should expect to get back a soap response. Maybe saying >> it not accessible is the wrong thing. I would chang the accessibility >> wording to say we did not receive a soap response back. But if someone >> suggests a better way of monitoring these things, I am happy to go >> along with it. >> >> Eric >> >> >> >> >> Franck Tanoh wrote: >> >>> Hi Eric, >>> >>> Thanks for the updates. >>> >>> >>> >>>> I made a change to the soap endpoint check whereby I now parse the >>>> response to see if it is a soap response. >>>> >>>> >>> That's the problem. I've got through most of these mails and lots of >>> services fails the test because of the endpoint or base URL. >>> The service includes: >>> -all the SOAP ddbj services: >>> http://www.biocatalogue.org/service_providers/4 . I tried couple these >>> services using workflows and they are running fine. >>> - More than 100 INB services have the same endpoints: >>> http://inb.bsc.es/cgi-bin/mobyServices/dispatchers/Dispatcher.cgi >>> which returns an 'Not found' error message. >>> - there are other INB services with the same problem >>> - those well annotated web services by James: >>> http://www.biocatalogue.org/users/238#services , their endpoints look >>> like that: >>> http://gnode1.mib.man.ac.uk:8080/FullTextWebServices/TextCleanerService >>> but monitored as not working. >>> - and many more.... >>> Basically, around half or 1/3 of the service in biocat shows the >>> warning sign. >>> It looks to me that the endpoint (or base URL) accessibility or not >>> does not affect the availability of the service (e.g DDBJ, james >>> services) so I don't really encourage the changes you made. >>> >>> Franck >>> >>> >>> >>> >>> On 26 May 2010 20:06, wrote: >>> >>> >>>> >>>> >>>>> Steve and I are getting *many* monitoring status change emails... >>>>> seems >>>>> like the test script execution harness thing is not working >>>>> properly... >>>>> >>>>> >>>> I have not see any problem with the harness. But if you find a problem >>>> please let me know. >>>> As you will note the mails are all about URL checks. I received the >>>> mails >>>> too and they are mostly due to some INB servers. I made a change to the >>>> soap endpoint check whereby I now parse the response to see if it is a >>>> soap response. Calling the end points of these services does not >>>> return a >>>> soap response and you will note as well that those are the same >>>> services >>>> for which the test scripts have been consistently failing. >>>> >>>> Another thing, hovering over the test script status icon now says since >>>> when a test script has been failing. >>>> >>>> Eric >>>> >>>> >>>>> Jits >>>>> >>>>> >>>>> Eric Nzuobontane wrote: >>>>> >>>>> >>>>>> The code update has been done. The service checker is currently >>>>>> running. I will lunch the reindexing when I get home. I will send >>>>>> another status update then. >>>>>> >>>>>> Eric >>>>>> >>>>>> >>>>>> Eric Nzuobontane wrote: >>>>>> >>>>>> >>>>>>> I am going to start the update now. I will send a mail when all is >>>>>>> done. >>>>>>> >>>>>>> Eric >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>> >>>> >>>> >>> >>> >>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Thu May 27 07:27:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 May 2010 07:27:09 -0400 (EDT) Subject: [BioCatalogue-developers] [2060] trunk: More work on ignoring rest_methods search scope in the API. Message-ID: <20100527112709.5BE12185835D@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu May 27 07:29:59 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 27 May 2010 12:29:59 +0100 Subject: [BioCatalogue-developers] starting the update now In-Reply-To: <4BFD2ABD.1010702@ebi.ac.uk> References: <4BFD2ABD.1010702@ebi.ac.uk> Message-ID: <4BFE57B7.5000408@cs.man.ac.uk> Eric, I have committed some fixes to the REST API which slipped in the integration (namely, ignoring REST endpoints, because there is no API for them). I have tested this out locally and on the sandbox, and the schema validation test suite passes. So please could you update the live site. This only requires a code update and restart of apps and workers. Jits Eric Nzuobontane wrote: > I am going to start the update now. I will send a mail when all is done. > > Eric > From ericnzuo at ebi.ac.uk Thu May 27 07:31:01 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 27 May 2010 12:31:01 +0100 Subject: [BioCatalogue-developers] starting the update now In-Reply-To: <4BFE57B7.5000408@cs.man.ac.uk> References: <4BFD2ABD.1010702@ebi.ac.uk> <4BFE57B7.5000408@cs.man.ac.uk> Message-ID: <4BFE57F5.1030409@ebi.ac.uk> I am currently updating the test site but network seems a bit slow. Eric Jiten Bhagat wrote: > Eric, > > I have committed some fixes to the REST API which slipped in the > integration (namely, ignoring REST endpoints, because there is no API > for them). > > I have tested this out locally and on the sandbox, and the schema > validation test suite passes. > > So please could you update the live site. This only requires a code > update and restart of apps and workers. > > Jits > > > Eric Nzuobontane wrote: > >> I am going to start the update now. I will send a mail when all is done. >> >> Eric >> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Thu May 27 09:37:57 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 May 2010 09:37:57 -0400 (EDT) Subject: [BioCatalogue-developers] [2061] trunk/app/views/agents/show.html.erb: Removed redundant tabber code. Message-ID: <20100527133758.0ECE6185835C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 27 11:10:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 May 2010 11:10:22 -0400 (EDT) Subject: [BioCatalogue-developers] [2062] trunk/app/views/users/show.xml.builder: Minor textual change. Message-ID: <20100527151022.90C90185835D@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu May 27 11:20:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 27 May 2010 16:20:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-360) Add the requester (name) and possible role of approver in responsibility request approval mail Message-ID: <24185522.1673.1274973617031.JavaMail.jira@rosalind.cs.man.ac.uk> Add the requester (name) and possible role of approver in responsibility request approval mail ---------------------------------------------------------------------------------------------- Key: BIOCAT-360 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-360 Project: BioCatalogue Issue Type: Refinement Components: User Management Reporter: Eric Nzuobontane Assignee: Jiten Bhagat Add the name of the person that made the request and the to the confirmation mail on approval/turn down -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu May 27 11:20:18 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 27 May 2010 16:20:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-360) Add the requester (name) and possible role of approver in responsibility request approval mail In-Reply-To: <24185522.1673.1274973617031.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10303628.1674.1274973618221.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-360?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-360: --------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > Add the requester (name) and possible role of approver in responsibility request approval mail > ---------------------------------------------------------------------------------------------- > > Key: BIOCAT-360 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-360 > Project: BioCatalogue > Issue Type: Refinement > Components: User Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 2 hours > Remaining Estimate: 2 hours > > Add the name of the person that made the request and the to the confirmation mail on approval/turn down -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu May 27 11:44:46 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 May 2010 11:44:46 -0400 (EDT) Subject: [BioCatalogue-developers] [2063] trunk/app: Added "Other Services Responsible For" tab on user profiles. Message-ID: <20100527154447.06B6C1678217@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 27 12:18:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 May 2010 12:18:47 -0400 (EDT) Subject: [BioCatalogue-developers] [2064] trunk/app/views: Added "Responsbility Requests" link to login links section. Message-ID: <20100527161847.6C605185835E@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 27 12:34:57 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 May 2010 12:34:57 -0400 (EDT) Subject: [BioCatalogue-developers] [2065] trunk/app/views/responsibility_requests/index.html.erb: UI tweaks to the pending responsbility requests index page. Message-ID: <20100527163457.27389185835E@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu May 27 12:35:32 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 27 May 2010 12:35:32 -0400 (EDT) Subject: [BioCatalogue-developers] [2066] trunk/app/views/responsibility_requests/index.html.erb: Wording change. Message-ID: <20100527163532.AC0F5185835F@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu May 27 12:41:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 27 May 2010 17:41:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-361) Add a "User responsible for this service" section on the service's profile page Message-ID: <23419427.1675.1274978476997.JavaMail.jira@rosalind.cs.man.ac.uk> Add a "User responsible for this service" section on the service's profile page ------------------------------------------------------------------------------- Key: BIOCAT-361 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-361 Project: BioCatalogue Issue Type: New Feature Components: Web Interface Reporter: Jiten Bhagat Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Thu May 27 17:42:23 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 27 May 2010 22:42:23 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runFirestar' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runFirestar' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1099 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 May 27 21:21:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 28 May 2010 02:21:06 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:cnio.es:runFASS' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:cnio.es:runFASS' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/980 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 May 28 05:08:41 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 28 May 2010 10:08:41 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runParmbsc0PhysicalProperties' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runParmbsc0PhysicalProperties' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1018 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 May 28 07:31:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 28 May 2010 07:31:08 -0400 (EDT) Subject: [BioCatalogue-developers] [2067] trunk: reverting to the original endpoint check rule of accepting any xml response as indicating availability and adding some help text to test script UI Message-ID: <20100528113109.2C5B5185832B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 28 08:46:25 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 28 May 2010 08:46:25 -0400 (EDT) Subject: [BioCatalogue-developers] [2068] trunk/app/views/test_scripts/_about_testscripts.html.erb: fix typo Message-ID: <20100528124625.4F0AF1678312@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri May 28 09:24:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 28 May 2010 14:24:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-362) Add archive/unarchive events to the ActivityLogs and then the activity feed(s) Message-ID: <27841565.1720.1275053057051.JavaMail.jira@rosalind.cs.man.ac.uk> Add archive/unarchive events to the ActivityLogs and then the activity feed(s) ------------------------------------------------------------------------------ Key: BIOCAT-362 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-362 Project: BioCatalogue Issue Type: New Feature Components: Activity Logging / Feeds / Notifications, Web Interface Environment: RoR Reporter: Jiten Bhagat Assignee: Jiten Bhagat Currently, no ActivityLog events are being made when archive/unarchive services occur. Need to log these events and then show them in the UI. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 28 10:38:16 2010 From: issues at mygrid.org.uk (Franck Tanoh (JIRA)) Date: Fri, 28 May 2010 15:38:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-363) Is it ok to replace the 'Welcome + member name' by something like 'my stuff'. The reason is because It's currently not obvious how to see or access all your services and other stuff in the biocat [ i know search can help but it's not the best option] Message-ID: <20832996.1721.1275057497000.JavaMail.jira@rosalind.cs.man.ac.uk> Is it ok to replace the 'Welcome + member name' by something like 'my stuff'. The reason is because It's currently not obvious how to see or access all your services and other stuff in the biocat [ i know search can help but it's not the best option] ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Key: BIOCAT-363 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-363 Project: BioCatalogue Issue Type: New Feature Components: Web Interface Reporter: Franck Tanoh Assignee: Jiten Bhagat Eric suggested iBioCatalogue Jits suggested myBioCatalogue Franck suggested my stuff -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri May 28 10:40:17 2010 From: issues at mygrid.org.uk (Franck Tanoh (JIRA)) Date: Fri, 28 May 2010 15:40:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-363) Replace the 'Welcome + member name' on the website by something like 'my stuff'. In-Reply-To: <20832996.1721.1275057497000.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23833634.1722.1275057617007.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-363?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Franck Tanoh updated BIOCAT-363: -------------------------------- Summary: Replace the 'Welcome + member name' on the website by something like 'my stuff'. (was: Is it ok to replace the 'Welcome + member name' by something like 'my stuff'. The reason is because It's currently not obvious how to see or access all your services and other stuff in the biocat [ i know search can help but it's not the best option]) Description: Is it ok to replace the 'Welcome + member name' by something like 'my stuff'. The reason is because It's currently not obvious how to see or access all your services and other stuff in the biocat [ i know search can help but it's not the best option] Eric suggested iBioCatalogue Jits suggested myBioCatalogue Franck suggested my stuff was: Eric suggested iBioCatalogue Jits suggested myBioCatalogue Franck suggested my stuff > Replace the 'Welcome + member name' on the website by something like 'my stuff'. > ---------------------------------------------------------------------------------- > > Key: BIOCAT-363 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-363 > Project: BioCatalogue > Issue Type: New Feature > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > > Is it ok to replace the 'Welcome + member name' by something like 'my stuff'. The reason is because It's currently not obvious how to see or access all your services and other stuff in the biocat [ i know search can help but it's not the best option] > Eric suggested iBioCatalogue > Jits suggested myBioCatalogue > Franck suggested my stuff -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri May 28 11:00:10 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 28 May 2010 11:00:10 -0400 (EDT) Subject: [BioCatalogue-developers] [2069] trunk/vendor/plugins/annotations: Pulled latest Annotations plugin changes which fixes the sorting order of annotations that have been updated Message-ID: <20100528150010.E2832185835A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri May 28 11:03:13 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 28 May 2010 11:03:13 -0400 (EDT) Subject: [BioCatalogue-developers] [2070] trunk/vendor/plugins/annotations/.git/objects: Missing files for previous commit Message-ID: <20100528150313.3BC1E185834E@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Sat May 29 02:43:13 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 29 May 2010 07:43:13 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'Genome Atlas' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'Genome Atlas' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1694 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 May 29 08:13:20 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 29 May 2010 13:13:20 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'MultAlin multiple alignment (CNRS IBCP)' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'MultAlin multiple alignment (CNRS IBCP)' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/260 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Sat May 29 08:16:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Sat, 29 May 2010 13:16:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-364) The service update checker should also update ServiceDeployment locations Message-ID: <5338610.1723.1275135377283.JavaMail.jira@rosalind.cs.man.ac.uk> The service update checker should also update ServiceDeployment locations ------------------------------------------------------------------------- Key: BIOCAT-364 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-364 Project: BioCatalogue Issue Type: New Feature Components: Service Container Environment: RoR Reporter: Jiten Bhagat Assignee: Jiten Bhagat Currently, the service update checker process doesn't take into account updating of location info of service deployments. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Sat May 29 15:59:40 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 29 May 2010 20:59:40 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:parseMotifMatricesFromMEME' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:parseMotifMatricesFromMEME' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/775 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 May 31 00:20:51 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 31 May 2010 05:20:51 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runFirestar' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runFirestar' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1099 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon May 31 03:20:21 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 31 May 2010 08:20:21 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'FASTA protein similarity search (CNRS IBCP)' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'FASTA protein similarity search (CNRS IBCP)' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/264 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 May 31 10:36:22 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 31 May 2010 15:36:22 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'PcProf predict physico-chemical profiles of proteins (CNRS IBCP)' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'PcProf predict physico-chemical profiles of proteins (CNRS IBCP)' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/275 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 May 31 21:58:19 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 01 Jun 2010 02:58:19 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'SIMPA protein secondary structure prediction (CNRS IBCP)' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'SIMPA protein secondary structure prediction (CNRS IBCP)' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/272 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