From ytanoh at cs.man.ac.uk Tue Jun 1 06:09:53 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 1 Jun 2010 11:09:53 +0100 Subject: [BioCatalogue-developers] latest data Message-ID: Hi Eric, Hope you had a good break Can you send the latest (from today) data dump to Jits so that he can produce the annotations stats, pls? Cheers, Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue Jun 1 06:22:43 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 01 Jun 2010 11:22:43 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: References: Message-ID: <4C04DF73.2090100@ebi.ac.uk> I will put that in drop box. When are you going out to Denmark? Eric Franck Tanoh wrote: > Hi Eric, > > Hope you had a good break > > Can you send the latest (from today) data dump to Jits so that he can > produce the annotations stats, pls? > > Cheers, > Franck > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From utopia at cs.man.ac.uk Tue Jun 1 07:04:52 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 01 Jun 2010 12:04:52 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'GOR III protein secondary structure prediction (CNRS IBCP)' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'GOR III protein secondary structure prediction (CNRS IBCP)' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/269 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From jits at cs.man.ac.uk Tue Jun 1 07:06:13 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 01 Jun 2010 12:06:13 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: <4C04DF73.2090100@ebi.ac.uk> References: <4C04DF73.2090100@ebi.ac.uk> Message-ID: <4C04E9A5.8050704@cs.man.ac.uk> Franck, Here is the report: Total SOAP Services: 1636 A. How many SOAP Services have a description? 1449 B. How many SOAP Services have a description AND a documentation URL? 898 C. How many SOAP Services have a description AND all operations have a description? 839 D. How many SOAP Services have a description AND all operations have a description and ALL inputs/outputs have a description? 34 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 Does that look right to you? Jits Eric Nzuobontane wrote: > I will put that in drop box. When are you going out to Denmark? > > Eric > > > Franck Tanoh wrote: >> Hi Eric, >> >> Hope you had a good break >> >> Can you send the latest (from today) data dump to Jits so that he can >> produce the annotations stats, pls? >> >> Cheers, >> Franck >> >> -- >> "Science knows no country, because knowledge belongs to humanity, and >> is the torch which illuminates the world." - Louis Pasteur >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > > From ytanoh at cs.man.ac.uk Tue Jun 1 09:07:49 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 1 Jun 2010 14:07:49 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: <4C04E9A5.8050704@cs.man.ac.uk> References: <4C04DF73.2090100@ebi.ac.uk> <4C04E9A5.8050704@cs.man.ac.uk> Message-ID: Hi Jits, Thanks for the report. It doesn't really look right when I compare it to the previous one: <> In the previous report we had 1095 services with description and with all operation annotated. I don't understand why we have now 839. Also there are 34 instead of 38 services with descriptions at the service, operation and parameter level. Cheers, Franck On 1 June 2010 12:06, Jiten Bhagat wrote: > Franck, > > Here is the report: > > Total SOAP Services: 1636 > A. How many SOAP Services have a description? 1449 > B. How many SOAP Services have a description AND a documentation URL? 898 > C. How many SOAP Services have a description AND all operations have a > description? 839 > D. How many SOAP Services have a description AND all operations have a > description and ALL inputs/outputs have a description? 34 > 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 > > Does that look right to you? > > Jits > > > Eric Nzuobontane wrote: > > I will put that in drop box. When are you going out to Denmark? > > > > Eric > > > > > > Franck Tanoh wrote: > >> Hi Eric, > >> > >> Hope you had a good break > >> > >> Can you send the latest (from today) data dump to Jits so that he can > >> produce the annotations stats, pls? > >> > >> Cheers, > >> Franck > >> > >> -- > >> "Science knows no country, because knowledge belongs to humanity, and > >> is the torch which illuminates the world." - Louis Pasteur > >> ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> BioCatalogue-developers mailing list > >> BioCatalogue-developers at rubyforge.org > >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > >> > > > > > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Tue Jun 1 09:11:01 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 1 Jun 2010 14:11:01 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: <4C04DF73.2090100@ebi.ac.uk> References: <4C04DF73.2090100@ebi.ac.uk> Message-ID: >I will put that in drop box Thanks >When are you going out to Denmark? I'm not going... Have not got my new passport yet (1week late) . Hamish will cover but I'm trying to join via Skype or other media. Cheers, Franck On 1 June 2010 11:22, Eric Nzuobontane wrote: > I will put that in drop box. When are you going out to Denmark? > > Eric > > > Franck Tanoh wrote: > >> Hi Eric, >> >> Hope you had a good break >> >> Can you send the latest (from today) data dump to Jits so that he can >> produce the annotations stats, pls? >> >> Cheers, >> Franck >> >> -- >> "Science knows no country, because knowledge belongs to humanity, and is >> the torch which illuminates the world." - Louis Pasteur >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> > > > -- > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue Jun 1 09:12:33 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 01 Jun 2010 14:12:33 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: References: <4C04DF73.2090100@ebi.ac.uk> <4C04E9A5.8050704@cs.man.ac.uk> Message-ID: <4C050741.4060601@cs.man.ac.uk> > In the previous report we had 1095 services with description and with > all operation annotated. I don't understand why we have now 839. > Also there are 34 instead of 38 services with descriptions at the > service, operation and parameter level. Could this be because now all the services have been updated (from the WSDL)? So, many new operations etc may have been added that are yet to be annotated. In any case I will check through and make sure again that the script is doing the right thing against the right data. Cheers, Jits Franck Tanoh wrote: > Hi Jits, > > Thanks for the report. > > It doesn't really look right when I compare it to the previous one: > > < 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>> > > In the previous report we had 1095 services with description and with > all operation annotated. I don't understand why we have now 839. > Also there are 34 instead of 38 services with descriptions at the > service, operation and parameter level. > > Cheers, > Franck > > On 1 June 2010 12:06, Jiten Bhagat > wrote: > > Franck, > > Here is the report: > > Total SOAP Services: 1636 > A. How many SOAP Services have a description? 1449 > B. How many SOAP Services have a description AND a documentation > URL? 898 > C. How many SOAP Services have a description AND all operations have a > description? 839 > D. How many SOAP Services have a description AND all operations have a > description and ALL inputs/outputs have a description? 34 > 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 > > Does that look right to you? > > Jits > > > Eric Nzuobontane wrote: > > I will put that in drop box. When are you going out to Denmark? > > > > Eric > > > > > > Franck Tanoh wrote: > >> Hi Eric, > >> > >> Hope you had a good break > >> > >> Can you send the latest (from today) data dump to Jits so that > he can > >> produce the annotations stats, pls? > >> > >> Cheers, > >> Franck > >> > >> -- > >> "Science knows no country, because knowledge belongs to > humanity, and > >> is the torch which illuminates the world." - Louis Pasteur > >> > ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> BioCatalogue-developers mailing list > >> BioCatalogue-developers at rubyforge.org > > >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > >> > > > > > > > > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur From ericnzuo at ebi.ac.uk Tue Jun 1 09:13:39 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 01 Jun 2010 14:13:39 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: References: <4C04DF73.2090100@ebi.ac.uk> <4C04E9A5.8050704@cs.man.ac.uk> Message-ID: <4C050783.90702@ebi.ac.uk> What I can think of is that the data has considerably changed since the last report mostly due to the update checker. It is entirely possible that new operations have been found that are not necessary annotated at the same level as the previously existing ones. Eric Franck Tanoh wrote: > Hi Jits, > > Thanks for the report. > > It doesn't really look right when I compare it to the previous one: > > < 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>> > > In the previous report we had 1095 services with description and with > all operation annotated. I don't understand why we have now 839. > Also there are 34 instead of 38 services with descriptions at the > service, operation and parameter level. > > Cheers, > Franck > > On 1 June 2010 12:06, Jiten Bhagat > wrote: > > Franck, > > Here is the report: > > Total SOAP Services: 1636 > A. How many SOAP Services have a description? 1449 > B. How many SOAP Services have a description AND a documentation > URL? 898 > C. How many SOAP Services have a description AND all operations have a > description? 839 > D. How many SOAP Services have a description AND all operations have a > description and ALL inputs/outputs have a description? 34 > 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 > > Does that look right to you? > > Jits > > > Eric Nzuobontane wrote: > > I will put that in drop box. When are you going out to Denmark? > > > > Eric > > > > > > Franck Tanoh wrote: > >> Hi Eric, > >> > >> Hope you had a good break > >> > >> Can you send the latest (from today) data dump to Jits so that > he can > >> produce the annotations stats, pls? > >> > >> Cheers, > >> Franck > >> > >> -- > >> "Science knows no country, because knowledge belongs to > humanity, and > >> is the torch which illuminates the world." - Louis Pasteur > >> > ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> BioCatalogue-developers mailing list > >> BioCatalogue-developers at rubyforge.org > > >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > >> > > > > > > > > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur -- 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 Jun 1 09:16:01 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 01 Jun 2010 14:16:01 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: <4C050741.4060601@cs.man.ac.uk> References: <4C04DF73.2090100@ebi.ac.uk> <4C04E9A5.8050704@cs.man.ac.uk> <4C050741.4060601@cs.man.ac.uk> Message-ID: <4C050811.30801@ebi.ac.uk> Jiten Bhagat wrote: >> In the previous report we had 1095 services with description and with >> all operation annotated. I don't understand why we have now 839. >> Also there are 34 instead of 38 services with descriptions at the >> service, operation and parameter level. >> > > Could this be because now all the services have been updated (from the > WSDL)? So, many new operations etc may have been added that are yet to > be annotated. > OK, I had not seen this mail but that was my first thought as well as noted in an earlier mail. :) > In any case I will check through and make sure again that the script is > doing the right thing against the right data. > > Cheers, > Jits > > > Franck Tanoh wrote: > >> Hi Jits, >> >> Thanks for the report. >> >> It doesn't really look right when I compare it to the previous one: >> >> <> 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>> >> >> In the previous report we had 1095 services with description and with >> all operation annotated. I don't understand why we have now 839. >> Also there are 34 instead of 38 services with descriptions at the >> service, operation and parameter level. >> >> Cheers, >> Franck >> >> On 1 June 2010 12:06, Jiten Bhagat > > wrote: >> >> Franck, >> >> Here is the report: >> >> Total SOAP Services: 1636 >> A. How many SOAP Services have a description? 1449 >> B. How many SOAP Services have a description AND a documentation >> URL? 898 >> C. How many SOAP Services have a description AND all operations have a >> description? 839 >> D. How many SOAP Services have a description AND all operations have a >> description and ALL inputs/outputs have a description? 34 >> 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 >> >> Does that look right to you? >> >> Jits >> >> >> Eric Nzuobontane wrote: >> > I will put that in drop box. When are you going out to Denmark? >> > >> > Eric >> > >> > >> > Franck Tanoh wrote: >> >> Hi Eric, >> >> >> >> Hope you had a good break >> >> >> >> Can you send the latest (from today) data dump to Jits so that >> he can >> >> produce the annotations stats, pls? >> >> >> >> Cheers, >> >> Franck >> >> >> >> -- >> >> "Science knows no country, because knowledge belongs to >> humanity, and >> >> is the torch which illuminates the world." - Louis Pasteur >> >> >> ------------------------------------------------------------------------ >> >> >> >> _______________________________________________ >> >> BioCatalogue-developers mailing list >> >> BioCatalogue-developers at rubyforge.org >> >> >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> >> > >> > >> >> >> >> >> -- >> "Science knows no country, because knowledge belongs to humanity, and >> is the torch which illuminates the world." - Louis Pasteur >> -- 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 Jun 1 09:19:59 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 01 Jun 2010 14:19:59 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: <4C050811.30801@ebi.ac.uk> References: <4C04DF73.2090100@ebi.ac.uk> <4C04E9A5.8050704@cs.man.ac.uk> <4C050741.4060601@cs.man.ac.uk> <4C050811.30801@ebi.ac.uk> Message-ID: <4C0508FF.5020803@cs.man.ac.uk> Eric Nzuobontane wrote: > Jiten Bhagat wrote: >>> In the previous report we had 1095 services with description and with >>> all operation annotated. I don't understand why we have now 839. >>> Also there are 34 instead of 38 services with descriptions at the >>> service, operation and parameter level. >> >> Could this be because now all the services have been updated (from the >> WSDL)? So, many new operations etc may have been added that are yet to >> be annotated. >> > OK, I had not seen this mail but that was my first thought as well as > noted in an earlier mail. :) Only 1 minute difference between the two emails :-) > >> In any case I will check through and make sure again that the script is >> doing the right thing against the right data. >> >> Cheers, >> Jits >> >> >> Franck Tanoh wrote: >> >>> Hi Jits, >>> >>> Thanks for the report. >>> >>> It doesn't really look right when I compare it to the previous one: >>> >>> <>> 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>> >>> >>> In the previous report we had 1095 services with description and with >>> all operation annotated. I don't understand why we have now 839. >>> Also there are 34 instead of 38 services with descriptions at the >>> service, operation and parameter level. >>> >>> Cheers, >>> Franck >>> >>> On 1 June 2010 12:06, Jiten Bhagat >> > wrote: >>> >>> Franck, >>> >>> Here is the report: >>> >>> Total SOAP Services: 1636 >>> A. How many SOAP Services have a description? 1449 >>> B. How many SOAP Services have a description AND a documentation >>> URL? 898 >>> C. How many SOAP Services have a description AND all operations >>> have a >>> description? 839 >>> D. How many SOAP Services have a description AND all operations >>> have a >>> description and ALL inputs/outputs have a description? 34 >>> 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 >>> >>> Does that look right to you? >>> >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>> > I will put that in drop box. When are you going out to Denmark? >>> > >>> > Eric >>> > >>> > >>> > Franck Tanoh wrote: >>> >> Hi Eric, >>> >> >>> >> Hope you had a good break >>> >> >>> >> Can you send the latest (from today) data dump to Jits so that >>> he can >>> >> produce the annotations stats, pls? >>> >> >>> >> Cheers, >>> >> Franck >>> >> >>> >> -- >>> >> "Science knows no country, because knowledge belongs to >>> humanity, and >>> >> is the torch which illuminates the world." - Louis Pasteur >>> >> >>> >>> ------------------------------------------------------------------------ >>> >>> >> >>> >> _______________________________________________ >>> >> BioCatalogue-developers mailing list >>> >> BioCatalogue-developers at rubyforge.org >>> >>> >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >> >>> > >>> > >>> >>> >>> >>> >>> -- >>> "Science knows no country, because knowledge belongs to humanity, and >>> is the torch which illuminates the world." - Louis Pasteur >>> > > From ytanoh at cs.man.ac.uk Tue Jun 1 09:25:57 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 1 Jun 2010 14:25:57 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: <4C050783.90702@ebi.ac.uk> References: <4C04DF73.2090100@ebi.ac.uk> <4C04E9A5.8050704@cs.man.ac.uk> <4C050783.90702@ebi.ac.uk> Message-ID: >What I can think of is that the data has considerably changed since the last report mostly due to the update checker. It is entirely possible that new operations >have been found that are not necessary annotated at the same level as the previously existing ones. Is it possible to do a diff between those 2 results ( 1095 vs 839) so that I can double check if that's the case. It will also help me to transfer some of the old descriptions to new operations, inputs etc. Cheers, Franck On 1 June 2010 14:13, Eric Nzuobontane wrote: > What I can think of is that the data has considerably changed since the > last report mostly due to the update checker. It is entirely possible that > new operations have been found that are not necessary annotated at the same > level as the previously existing ones. > > Eric > > > Franck Tanoh wrote: > >> Hi Jits, >> >> Thanks for the report. >> >> It doesn't really look right when I compare it to the previous one: >> >> <> 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>> >> >> In the previous report we had 1095 services with description and with all >> operation annotated. I don't understand why we have now 839. >> Also there are 34 instead of 38 services with descriptions at the service, >> operation and parameter level. >> >> Cheers, >> Franck >> >> On 1 June 2010 12:06, Jiten Bhagat > jits at cs.man.ac.uk>> wrote: >> >> Franck, >> >> Here is the report: >> >> Total SOAP Services: 1636 >> A. How many SOAP Services have a description? 1449 >> B. How many SOAP Services have a description AND a documentation >> URL? 898 >> C. How many SOAP Services have a description AND all operations have a >> description? 839 >> D. How many SOAP Services have a description AND all operations have a >> description and ALL inputs/outputs have a description? 34 >> 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 >> >> Does that look right to you? >> >> Jits >> >> >> Eric Nzuobontane wrote: >> > I will put that in drop box. When are you going out to Denmark? >> > >> > Eric >> > >> > >> > Franck Tanoh wrote: >> >> Hi Eric, >> >> >> >> Hope you had a good break >> >> >> >> Can you send the latest (from today) data dump to Jits so that >> he can >> >> produce the annotations stats, pls? >> >> >> >> Cheers, >> >> Franck >> >> >> >> -- >> >> "Science knows no country, because knowledge belongs to >> humanity, and >> >> is the torch which illuminates the world." - Louis Pasteur >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> _______________________________________________ >> >> BioCatalogue-developers mailing list >> >> BioCatalogue-developers at rubyforge.org >> >> >> >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> >> > >> > >> >> >> >> >> -- >> "Science knows no country, because knowledge belongs to humanity, and is >> the torch which illuminates the world." - Louis Pasteur >> > > > -- > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Jun 1 09:31:45 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 01 Jun 2010 14:31:45 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMatScanGFFCollection' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMatScanGFFCollection' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/777 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue Jun 1 10:15:39 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 1 Jun 2010 10:15:39 -0400 (EDT) Subject: [BioCatalogue-developers] [2071] trunk: Added checks (some redundant) to the service annotation report script for archived services, operations, inputs and outputs. Message-ID: <20100601141539.6A6BB1858356@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue Jun 1 10:43:02 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 01 Jun 2010 15:43:02 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: References: <4C04DF73.2090100@ebi.ac.uk> <4C04E9A5.8050704@cs.man.ac.uk> <4C050783.90702@ebi.ac.uk> Message-ID: <4C051C76.2000702@cs.man.ac.uk> Hi Franck, The best I can do is the attached list of URLs (also in Dropbox) for the SOAP operations that have been created in the last week. There are 1892 in total (!). I've added a star (*) after each one that DOES NOT have any description (of which there are 664). Jits Franck Tanoh wrote: > >What I can think of is that the data has considerably changed since > the last report mostly due to the update checker. It is entirely > possible that new operations >have been found that are not necessary > annotated at the same level as the previously existing ones. > Is it possible to do a diff between those 2 results ( 1095 vs 839) so > that I can double check if that's the case. It will also help me to > transfer some of the old descriptions to new operations, inputs etc. > > Cheers, > Franck > > On 1 June 2010 14:13, Eric Nzuobontane > wrote: > > What I can think of is that the data has considerably changed > since the last report mostly due to the update checker. It is > entirely possible that new operations have been found that are not > necessary annotated at the same level as the previously existing ones. > > Eric > > > Franck Tanoh wrote: > > Hi Jits, > > Thanks for the report. > > It doesn't really look right when I compare it to the previous > one: > > < 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>> > > In the previous report we had 1095 services with description > and with all operation annotated. I don't understand why we > have now 839. > Also there are 34 instead of 38 services with descriptions at > the service, operation and parameter level. > > Cheers, > Franck > > On 1 June 2010 12:06, Jiten Bhagat >> wrote: > > Franck, > > Here is the report: > > Total SOAP Services: 1636 > A. How many SOAP Services have a description? 1449 > B. How many SOAP Services have a description AND a > documentation > URL? 898 > C. How many SOAP Services have a description AND all > operations have a > description? 839 > D. How many SOAP Services have a description AND all > operations have a > description and ALL inputs/outputs have a description? 34 > 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 > > Does that look right to you? > > Jits > > > Eric Nzuobontane wrote: > > I will put that in drop box. When are you going out to > Denmark? > > > > Eric > > > > > > Franck Tanoh wrote: > >> Hi Eric, > >> > >> Hope you had a good break > >> > >> Can you send the latest (from today) data dump to Jits > so that > he can > >> produce the annotations stats, pls? > >> > >> Cheers, > >> Franck > >> > >> -- > >> "Science knows no country, because knowledge belongs to > humanity, and > >> is the torch which illuminates the world." - Louis Pasteur > >> > > ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> BioCatalogue-developers mailing list > >> BioCatalogue-developers at rubyforge.org > > > > > >> > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > >> > > > > > > > > > -- > "Science knows no country, because knowledge belongs to > humanity, and is the torch which illuminates the world." - > Louis Pasteur > > > > -- > 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 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: New SOAP operations - 2010-05-26 to 2010-06-01.txt URL: From jits at cs.man.ac.uk Tue Jun 1 10:50:13 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 01 Jun 2010 15:50:13 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: <4C051C76.2000702@cs.man.ac.uk> References: <4C04DF73.2090100@ebi.ac.uk> <4C04E9A5.8050704@cs.man.ac.uk> <4C050783.90702@ebi.ac.uk> <4C051C76.2000702@cs.man.ac.uk> Message-ID: <4C051E25.3010403@cs.man.ac.uk> Revised report... (taking into account archived services etc)... SUMMARY: ======== NOTE: all archived services, operations, inputs and outputs are ignored. Total SOAP Services: 1633 Total SOAP Operations: 11742 Total SOAP Inputs: 13926 Total SOAP Outputs 9969 A. How many SOAP Services have a description? 1446 B. How many SOAP Services have a description AND a documentation URL? 898 C. How many SOAP Services have a description AND all operations have a description? 836 D. How many SOAP Services have a description AND all operations have a description and ALL inputs/outputs have a description? 31 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: > Hi Franck, > > The best I can do is the attached list of URLs (also in Dropbox) for the > SOAP operations that have been created in the last week. There are 1892 > in total (!). I've added a star (*) after each one that DOES NOT have > any description (of which there are 664). > > Jits > > > Franck Tanoh wrote: > >>> What I can think of is that the data has considerably changed since >>> >> the last report mostly due to the update checker. It is entirely >> possible that new operations >have been found that are not necessary >> annotated at the same level as the previously existing ones. >> Is it possible to do a diff between those 2 results ( 1095 vs 839) so >> that I can double check if that's the case. It will also help me to >> transfer some of the old descriptions to new operations, inputs etc. >> >> Cheers, >> Franck >> >> On 1 June 2010 14:13, Eric Nzuobontane > > wrote: >> >> What I can think of is that the data has considerably changed >> since the last report mostly due to the update checker. It is >> entirely possible that new operations have been found that are not >> necessary annotated at the same level as the previously existing ones. >> >> Eric >> >> >> Franck Tanoh wrote: >> >> Hi Jits, >> >> Thanks for the report. >> >> It doesn't really look right when I compare it to the previous >> one: >> >> <> 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>> >> >> In the previous report we had 1095 services with description >> and with all operation annotated. I don't understand why we >> have now 839. >> Also there are 34 instead of 38 services with descriptions at >> the service, operation and parameter level. >> >> Cheers, >> Franck >> >> On 1 June 2010 12:06, Jiten Bhagat > > >> wrote: >> >> Franck, >> >> Here is the report: >> >> Total SOAP Services: 1636 >> A. How many SOAP Services have a description? 1449 >> B. How many SOAP Services have a description AND a >> documentation >> URL? 898 >> C. How many SOAP Services have a description AND all >> operations have a >> description? 839 >> D. How many SOAP Services have a description AND all >> operations have a >> description and ALL inputs/outputs have a description? 34 >> 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 >> >> Does that look right to you? >> >> Jits >> >> >> Eric Nzuobontane wrote: >> > I will put that in drop box. When are you going out to >> Denmark? >> > >> > Eric >> > >> > >> > Franck Tanoh wrote: >> >> Hi Eric, >> >> >> >> Hope you had a good break >> >> >> >> Can you send the latest (from today) data dump to Jits >> so that >> he can >> >> produce the annotations stats, pls? >> >> >> >> Cheers, >> >> Franck >> >> >> >> -- >> >> "Science knows no country, because knowledge belongs to >> humanity, and >> >> is the torch which illuminates the world." - Louis Pasteur >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> _______________________________________________ >> >> BioCatalogue-developers mailing list >> >> BioCatalogue-developers at rubyforge.org >> >> > > >> >> >> >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> >> > >> > >> >> >> >> >> -- >> "Science knows no country, because knowledge belongs to >> humanity, and is the torch which illuminates the world." - >> Louis Pasteur >> >> >> >> -- >> 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 >> > > > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From jits at cs.man.ac.uk Tue Jun 1 11:19:15 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 01 Jun 2010 16:19:15 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: References: <4C04DF73.2090100@ebi.ac.uk> <4C04E9A5.8050704@cs.man.ac.uk> <4C050783.90702@ebi.ac.uk> <4C051C76.2000702@cs.man.ac.uk> Message-ID: <4C0524F3.1020700@cs.man.ac.uk> Franck Tanoh wrote: > >The best I can do is the attached list of URLs (also in Dropbox) for the > >SOAP operations that have been created in the last week. There are 1892 > >in total (!). > that's a lot for a week! looks like the service update checker is the > guilty one :-) > A first glance reveals loads of archived operations. Yeah. There are 107 archived operations. Do you want a curation page for "Copy annotations from operation X to operation Y"? Jits > > Thanks > Franck > > an.ac.uk > wrote: > > Hi Franck, > > The best I can do is the attached list of URLs (also in Dropbox) > for the > SOAP operations that have been created in the last week. There are > 1892 > in total (!). I've added a star (*) after each one that DOES NOT have > any description (of which there are 664). > > Jits > > > Franck Tanoh wrote: > > >What I can think of is that the data has considerably changed since > > the last report mostly due to the update checker. It is entirely > > possible that new operations >have been found that are not necessary > > annotated at the same level as the previously existing ones. > > Is it possible to do a diff between those 2 results ( 1095 vs > 839) so > > that I can double check if that's the case. It will also help me to > > transfer some of the old descriptions to new operations, inputs etc. > > > > Cheers, > > Franck > > > > On 1 June 2010 14:13, Eric Nzuobontane > > >> wrote: > > > > What I can think of is that the data has considerably changed > > since the last report mostly due to the update checker. It is > > entirely possible that new operations have been found that > are not > > necessary annotated at the same level as the previously > existing ones. > > > > Eric > > > > > > Franck Tanoh wrote: > > > > Hi Jits, > > > > Thanks for the report. > > > > It doesn't really look right when I compare it to the > previous > > one: > > > > < > 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>> > > > > In the previous report we had 1095 services with description > > and with all operation annotated. I don't understand why we > > have now 839. > > Also there are 34 instead of 38 services with > descriptions at > > the service, operation and parameter level. > > > > Cheers, > > Franck > > > > On 1 June 2010 12:06, Jiten Bhagat > > > > > > >>> > wrote: > > > > Franck, > > > > Here is the report: > > > > Total SOAP Services: 1636 > > A. How many SOAP Services have a description? 1449 > > B. How many SOAP Services have a description AND a > > documentation > > URL? 898 > > C. How many SOAP Services have a description AND all > > operations have a > > description? 839 > > D. How many SOAP Services have a description AND all > > operations have a > > description and ALL inputs/outputs have a description? 34 > > 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 > > > > Does that look right to you? > > > > Jits > > > > > > Eric Nzuobontane wrote: > > > I will put that in drop box. When are you going out to > > Denmark? > > > > > > Eric > > > > > > > > > Franck Tanoh wrote: > > >> Hi Eric, > > >> > > >> Hope you had a good break > > >> > > >> Can you send the latest (from today) data dump to Jits > > so that > > he can > > >> produce the annotations stats, pls? > > >> > > >> Cheers, > > >> Franck > > >> > > >> -- > > >> "Science knows no country, because knowledge > belongs to > > humanity, and > > >> is the torch which illuminates the world." - Louis > Pasteur > > >> > > > > > ------------------------------------------------------------------------ > > >> > > >> _______________________________________________ > > >> BioCatalogue-developers mailing list > > >> BioCatalogue-developers at rubyforge.org > > > > > > > > >> > > > > >> > > > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > >> > > > > > > > > > > > > > > > > -- > > "Science knows no country, because knowledge belongs to > > humanity, and is the torch which illuminates the world." - > > Louis Pasteur > > > > > > > > -- > > 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 > > > > -- > "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 Jun 1 11:13:39 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 1 Jun 2010 16:13:39 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: <4C051C76.2000702@cs.man.ac.uk> References: <4C04DF73.2090100@ebi.ac.uk> <4C04E9A5.8050704@cs.man.ac.uk> <4C050783.90702@ebi.ac.uk> <4C051C76.2000702@cs.man.ac.uk> Message-ID: >The best I can do is the attached list of URLs (also in Dropbox) for the >SOAP operations that have been created in the last week. There are 1892 >in total (!). that's a lot for a week! looks like the service update checker is the guilty one :-) A first glance reveals loads of archived operations. Thanks Franck an.ac.uk> wrote: > Hi Franck, > > The best I can do is the attached list of URLs (also in Dropbox) for the > SOAP operations that have been created in the last week. There are 1892 > in total (!). I've added a star (*) after each one that DOES NOT have > any description (of which there are 664). > > Jits > > > Franck Tanoh wrote: > > >What I can think of is that the data has considerably changed since > > the last report mostly due to the update checker. It is entirely > > possible that new operations >have been found that are not necessary > > annotated at the same level as the previously existing ones. > > Is it possible to do a diff between those 2 results ( 1095 vs 839) so > > that I can double check if that's the case. It will also help me to > > transfer some of the old descriptions to new operations, inputs etc. > > > > Cheers, > > Franck > > > > On 1 June 2010 14:13, Eric Nzuobontane > > wrote: > > > > What I can think of is that the data has considerably changed > > since the last report mostly due to the update checker. It is > > entirely possible that new operations have been found that are not > > necessary annotated at the same level as the previously existing > ones. > > > > Eric > > > > > > Franck Tanoh wrote: > > > > Hi Jits, > > > > Thanks for the report. > > > > It doesn't really look right when I compare it to the previous > > one: > > > > < > 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>> > > > > In the previous report we had 1095 services with description > > and with all operation annotated. I don't understand why we > > have now 839. > > Also there are 34 instead of 38 services with descriptions at > > the service, operation and parameter level. > > > > Cheers, > > Franck > > > > On 1 June 2010 12:06, Jiten Bhagat > > >> wrote: > > > > Franck, > > > > Here is the report: > > > > Total SOAP Services: 1636 > > A. How many SOAP Services have a description? 1449 > > B. How many SOAP Services have a description AND a > > documentation > > URL? 898 > > C. How many SOAP Services have a description AND all > > operations have a > > description? 839 > > D. How many SOAP Services have a description AND all > > operations have a > > description and ALL inputs/outputs have a description? 34 > > 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 > > > > Does that look right to you? > > > > Jits > > > > > > Eric Nzuobontane wrote: > > > I will put that in drop box. When are you going out to > > Denmark? > > > > > > Eric > > > > > > > > > Franck Tanoh wrote: > > >> Hi Eric, > > >> > > >> Hope you had a good break > > >> > > >> Can you send the latest (from today) data dump to Jits > > so that > > he can > > >> produce the annotations stats, pls? > > >> > > >> Cheers, > > >> Franck > > >> > > >> -- > > >> "Science knows no country, because knowledge belongs to > > humanity, and > > >> is the torch which illuminates the world." - Louis Pasteur > > >> > > > > > ------------------------------------------------------------------------ > > >> > > >> _______________________________________________ > > >> BioCatalogue-developers mailing list > > >> BioCatalogue-developers at rubyforge.org > > > > > > > > > > >> > > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > >> > > > > > > > > > > > > > > > > -- > > "Science knows no country, because knowledge belongs to > > humanity, and is the torch which illuminates the world." - > > Louis Pasteur > > > > > > > > -- > > 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 > > > Total = 1892 > Total without any descriptions = 664 > > URLs: (a star [*] indicates that it does not have any description) > > http://www.biocatalogue.org/soap_operations/19684 > http://www.biocatalogue.org/soap_operations/19683 > http://www.biocatalogue.org/soap_operations/19682 > http://www.biocatalogue.org/soap_operations/19678 > http://www.biocatalogue.org/soap_operations/19679 > http://www.biocatalogue.org/soap_operations/19680 > http://www.biocatalogue.org/soap_operations/19681 > http://www.biocatalogue.org/soap_operations/19675 > http://www.biocatalogue.org/soap_operations/19676 > http://www.biocatalogue.org/soap_operations/19677 > http://www.biocatalogue.org/soap_operations/19674 > http://www.biocatalogue.org/soap_operations/19670 > http://www.biocatalogue.org/soap_operations/19671 > http://www.biocatalogue.org/soap_operations/19672 > http://www.biocatalogue.org/soap_operations/19673 > http://www.biocatalogue.org/soap_operations/19667 > http://www.biocatalogue.org/soap_operations/19668 > http://www.biocatalogue.org/soap_operations/19669 > http://www.biocatalogue.org/soap_operations/19664 > http://www.biocatalogue.org/soap_operations/19665 > http://www.biocatalogue.org/soap_operations/19666 > http://www.biocatalogue.org/soap_operations/19661 > http://www.biocatalogue.org/soap_operations/19662 > http://www.biocatalogue.org/soap_operations/19663 > http://www.biocatalogue.org/soap_operations/19657 > http://www.biocatalogue.org/soap_operations/19658 > http://www.biocatalogue.org/soap_operations/19659 > http://www.biocatalogue.org/soap_operations/19660 > http://www.biocatalogue.org/soap_operations/19654 > http://www.biocatalogue.org/soap_operations/19655 > http://www.biocatalogue.org/soap_operations/19656 > http://www.biocatalogue.org/soap_operations/19651 * > http://www.biocatalogue.org/soap_operations/19652 * > http://www.biocatalogue.org/soap_operations/19653 * > http://www.biocatalogue.org/soap_operations/19650 * > http://www.biocatalogue.org/soap_operations/19649 * > http://www.biocatalogue.org/soap_operations/19647 * > http://www.biocatalogue.org/soap_operations/19648 * > http://www.biocatalogue.org/soap_operations/19645 * > http://www.biocatalogue.org/soap_operations/19646 * > http://www.biocatalogue.org/soap_operations/19643 * > http://www.biocatalogue.org/soap_operations/19644 * > http://www.biocatalogue.org/soap_operations/19642 * > http://www.biocatalogue.org/soap_operations/19641 * > http://www.biocatalogue.org/soap_operations/19640 * > http://www.biocatalogue.org/soap_operations/19639 * > http://www.biocatalogue.org/soap_operations/19638 > http://www.biocatalogue.org/soap_operations/19635 > http://www.biocatalogue.org/soap_operations/19636 > http://www.biocatalogue.org/soap_operations/19637 > http://www.biocatalogue.org/soap_operations/19633 > http://www.biocatalogue.org/soap_operations/19634 > http://www.biocatalogue.org/soap_operations/19631 > http://www.biocatalogue.org/soap_operations/19632 > http://www.biocatalogue.org/soap_operations/19629 > http://www.biocatalogue.org/soap_operations/19630 > http://www.biocatalogue.org/soap_operations/19626 > http://www.biocatalogue.org/soap_operations/19627 > http://www.biocatalogue.org/soap_operations/19628 > http://www.biocatalogue.org/soap_operations/19625 * > http://www.biocatalogue.org/soap_operations/19624 * > http://www.biocatalogue.org/soap_operations/19621 > http://www.biocatalogue.org/soap_operations/19622 > http://www.biocatalogue.org/soap_operations/19623 > http://www.biocatalogue.org/soap_operations/19616 > http://www.biocatalogue.org/soap_operations/19617 > http://www.biocatalogue.org/soap_operations/19618 > http://www.biocatalogue.org/soap_operations/19619 > http://www.biocatalogue.org/soap_operations/19620 > http://www.biocatalogue.org/soap_operations/19612 > http://www.biocatalogue.org/soap_operations/19613 > http://www.biocatalogue.org/soap_operations/19614 > http://www.biocatalogue.org/soap_operations/19615 > http://www.biocatalogue.org/soap_operations/19611 * > http://www.biocatalogue.org/soap_operations/19609 * > http://www.biocatalogue.org/soap_operations/19610 * > http://www.biocatalogue.org/soap_operations/19608 > http://www.biocatalogue.org/soap_operations/19605 > http://www.biocatalogue.org/soap_operations/19606 > http://www.biocatalogue.org/soap_operations/19607 > http://www.biocatalogue.org/soap_operations/19604 * > http://www.biocatalogue.org/soap_operations/19603 * > http://www.biocatalogue.org/soap_operations/19602 > http://www.biocatalogue.org/soap_operations/19601 > http://www.biocatalogue.org/soap_operations/19597 > http://www.biocatalogue.org/soap_operations/19598 > http://www.biocatalogue.org/soap_operations/19599 > http://www.biocatalogue.org/soap_operations/19600 > http://www.biocatalogue.org/soap_operations/19593 > http://www.biocatalogue.org/soap_operations/19594 > http://www.biocatalogue.org/soap_operations/19595 > http://www.biocatalogue.org/soap_operations/19596 > http://www.biocatalogue.org/soap_operations/19589 > http://www.biocatalogue.org/soap_operations/19590 > http://www.biocatalogue.org/soap_operations/19591 > http://www.biocatalogue.org/soap_operations/19592 > http://www.biocatalogue.org/soap_operations/19588 > http://www.biocatalogue.org/soap_operations/19587 * > http://www.biocatalogue.org/soap_operations/19578 * > http://www.biocatalogue.org/soap_operations/19579 * > http://www.biocatalogue.org/soap_operations/19580 * > http://www.biocatalogue.org/soap_operations/19581 * > http://www.biocatalogue.org/soap_operations/19582 * > http://www.biocatalogue.org/soap_operations/19583 * > http://www.biocatalogue.org/soap_operations/19584 * > http://www.biocatalogue.org/soap_operations/19585 * > http://www.biocatalogue.org/soap_operations/19586 * > http://www.biocatalogue.org/soap_operations/19576 * > http://www.biocatalogue.org/soap_operations/19577 * > http://www.biocatalogue.org/soap_operations/19575 * > http://www.biocatalogue.org/soap_operations/19571 * > http://www.biocatalogue.org/soap_operations/19572 * > http://www.biocatalogue.org/soap_operations/19573 * > http://www.biocatalogue.org/soap_operations/19574 * > http://www.biocatalogue.org/soap_operations/19566 * > http://www.biocatalogue.org/soap_operations/19567 * > http://www.biocatalogue.org/soap_operations/19568 * > http://www.biocatalogue.org/soap_operations/19569 * > http://www.biocatalogue.org/soap_operations/19570 * > http://www.biocatalogue.org/soap_operations/19563 * > http://www.biocatalogue.org/soap_operations/19564 * > http://www.biocatalogue.org/soap_operations/19565 * > http://www.biocatalogue.org/soap_operations/19562 * > http://www.biocatalogue.org/soap_operations/19561 * > http://www.biocatalogue.org/soap_operations/19559 * > http://www.biocatalogue.org/soap_operations/19560 * > http://www.biocatalogue.org/soap_operations/19556 * > http://www.biocatalogue.org/soap_operations/19557 * > http://www.biocatalogue.org/soap_operations/19558 * > http://www.biocatalogue.org/soap_operations/19553 * > http://www.biocatalogue.org/soap_operations/19554 * > http://www.biocatalogue.org/soap_operations/19555 * > http://www.biocatalogue.org/soap_operations/19552 > http://www.biocatalogue.org/soap_operations/19549 > http://www.biocatalogue.org/soap_operations/19550 > http://www.biocatalogue.org/soap_operations/19551 > http://www.biocatalogue.org/soap_operations/19548 * > http://www.biocatalogue.org/soap_operations/19546 > http://www.biocatalogue.org/soap_operations/19547 > http://www.biocatalogue.org/soap_operations/19544 * > http://www.biocatalogue.org/soap_operations/19545 * > http://www.biocatalogue.org/soap_operations/19543 * > http://www.biocatalogue.org/soap_operations/19541 * > http://www.biocatalogue.org/soap_operations/19542 * > http://www.biocatalogue.org/soap_operations/19540 * > http://www.biocatalogue.org/soap_operations/19535 > http://www.biocatalogue.org/soap_operations/19536 > http://www.biocatalogue.org/soap_operations/19537 > http://www.biocatalogue.org/soap_operations/19538 > http://www.biocatalogue.org/soap_operations/19539 * > http://www.biocatalogue.org/soap_operations/19534 * > http://www.biocatalogue.org/soap_operations/19529 > http://www.biocatalogue.org/soap_operations/19530 > http://www.biocatalogue.org/soap_operations/19531 > http://www.biocatalogue.org/soap_operations/19532 > http://www.biocatalogue.org/soap_operations/19533 * > http://www.biocatalogue.org/soap_operations/19526 > http://www.biocatalogue.org/soap_operations/19527 * > http://www.biocatalogue.org/soap_operations/19528 * > http://www.biocatalogue.org/soap_operations/19523 > http://www.biocatalogue.org/soap_operations/19524 > http://www.biocatalogue.org/soap_operations/19525 > http://www.biocatalogue.org/soap_operations/19520 > http://www.biocatalogue.org/soap_operations/19521 * > http://www.biocatalogue.org/soap_operations/19522 * > http://www.biocatalogue.org/soap_operations/19517 > http://www.biocatalogue.org/soap_operations/19518 > http://www.biocatalogue.org/soap_operations/19519 > http://www.biocatalogue.org/soap_operations/19515 * > http://www.biocatalogue.org/soap_operations/19516 * > http://www.biocatalogue.org/soap_operations/19511 > http://www.biocatalogue.org/soap_operations/19512 > http://www.biocatalogue.org/soap_operations/19513 > http://www.biocatalogue.org/soap_operations/19514 > http://www.biocatalogue.org/soap_operations/19507 > http://www.biocatalogue.org/soap_operations/19508 > http://www.biocatalogue.org/soap_operations/19509 * > http://www.biocatalogue.org/soap_operations/19510 * > http://www.biocatalogue.org/soap_operations/19505 > http://www.biocatalogue.org/soap_operations/19506 > http://www.biocatalogue.org/soap_operations/19502 > http://www.biocatalogue.org/soap_operations/19503 * > http://www.biocatalogue.org/soap_operations/19504 * > http://www.biocatalogue.org/soap_operations/19499 > http://www.biocatalogue.org/soap_operations/19500 > http://www.biocatalogue.org/soap_operations/19501 > http://www.biocatalogue.org/soap_operations/19495 > http://www.biocatalogue.org/soap_operations/19496 > http://www.biocatalogue.org/soap_operations/19497 * > http://www.biocatalogue.org/soap_operations/19498 * > http://www.biocatalogue.org/soap_operations/19493 > http://www.biocatalogue.org/soap_operations/19494 > http://www.biocatalogue.org/soap_operations/19488 > http://www.biocatalogue.org/soap_operations/19489 > http://www.biocatalogue.org/soap_operations/19490 > http://www.biocatalogue.org/soap_operations/19491 * > http://www.biocatalogue.org/soap_operations/19492 * > http://www.biocatalogue.org/soap_operations/19487 > http://www.biocatalogue.org/soap_operations/19486 * > http://www.biocatalogue.org/soap_operations/19481 > http://www.biocatalogue.org/soap_operations/19482 > http://www.biocatalogue.org/soap_operations/19483 > http://www.biocatalogue.org/soap_operations/19484 > http://www.biocatalogue.org/soap_operations/19485 * > http://www.biocatalogue.org/soap_operations/19476 > http://www.biocatalogue.org/soap_operations/19477 > http://www.biocatalogue.org/soap_operations/19478 > http://www.biocatalogue.org/soap_operations/19479 * > http://www.biocatalogue.org/soap_operations/19480 * > http://www.biocatalogue.org/soap_operations/19475 > http://www.biocatalogue.org/soap_operations/19474 * > http://www.biocatalogue.org/soap_operations/19469 > http://www.biocatalogue.org/soap_operations/19470 > http://www.biocatalogue.org/soap_operations/19471 > http://www.biocatalogue.org/soap_operations/19472 > http://www.biocatalogue.org/soap_operations/19473 * > http://www.biocatalogue.org/soap_operations/19468 * > http://www.biocatalogue.org/soap_operations/19463 > http://www.biocatalogue.org/soap_operations/19464 > http://www.biocatalogue.org/soap_operations/19465 > http://www.biocatalogue.org/soap_operations/19466 > http://www.biocatalogue.org/soap_operations/19467 * > http://www.biocatalogue.org/soap_operations/19460 > http://www.biocatalogue.org/soap_operations/19461 * > http://www.biocatalogue.org/soap_operations/19462 * > http://www.biocatalogue.org/soap_operations/19457 > http://www.biocatalogue.org/soap_operations/19458 > http://www.biocatalogue.org/soap_operations/19459 > http://www.biocatalogue.org/soap_operations/19454 > http://www.biocatalogue.org/soap_operations/19455 * > http://www.biocatalogue.org/soap_operations/19456 * > http://www.biocatalogue.org/soap_operations/19451 > http://www.biocatalogue.org/soap_operations/19452 > http://www.biocatalogue.org/soap_operations/19453 > http://www.biocatalogue.org/soap_operations/19448 > http://www.biocatalogue.org/soap_operations/19449 * > http://www.biocatalogue.org/soap_operations/19450 * > http://www.biocatalogue.org/soap_operations/19445 > http://www.biocatalogue.org/soap_operations/19446 > http://www.biocatalogue.org/soap_operations/19447 > http://www.biocatalogue.org/soap_operations/19441 > http://www.biocatalogue.org/soap_operations/19442 > http://www.biocatalogue.org/soap_operations/19443 * > http://www.biocatalogue.org/soap_operations/19444 * > http://www.biocatalogue.org/soap_operations/19439 > http://www.biocatalogue.org/soap_operations/19440 > http://www.biocatalogue.org/soap_operations/19433 > http://www.biocatalogue.org/soap_operations/19434 > http://www.biocatalogue.org/soap_operations/19435 > http://www.biocatalogue.org/soap_operations/19436 > http://www.biocatalogue.org/soap_operations/19437 * > http://www.biocatalogue.org/soap_operations/19438 * > http://www.biocatalogue.org/soap_operations/19429 > http://www.biocatalogue.org/soap_operations/19430 > http://www.biocatalogue.org/soap_operations/19431 * > http://www.biocatalogue.org/soap_operations/19432 * > http://www.biocatalogue.org/soap_operations/19427 > http://www.biocatalogue.org/soap_operations/19428 > http://www.biocatalogue.org/soap_operations/19421 > http://www.biocatalogue.org/soap_operations/19422 > http://www.biocatalogue.org/soap_operations/19423 > http://www.biocatalogue.org/soap_operations/19424 > http://www.biocatalogue.org/soap_operations/19425 * > http://www.biocatalogue.org/soap_operations/19426 * > http://www.biocatalogue.org/soap_operations/19420 * > http://www.biocatalogue.org/soap_operations/19415 > http://www.biocatalogue.org/soap_operations/19416 > http://www.biocatalogue.org/soap_operations/19417 > http://www.biocatalogue.org/soap_operations/19418 > http://www.biocatalogue.org/soap_operations/19419 * > http://www.biocatalogue.org/soap_operations/19413 * > http://www.biocatalogue.org/soap_operations/19414 * > http://www.biocatalogue.org/soap_operations/19409 > http://www.biocatalogue.org/soap_operations/19410 > http://www.biocatalogue.org/soap_operations/19411 > http://www.biocatalogue.org/soap_operations/19412 > http://www.biocatalogue.org/soap_operations/19407 * > http://www.biocatalogue.org/soap_operations/19408 * > http://www.biocatalogue.org/soap_operations/19405 > http://www.biocatalogue.org/soap_operations/19406 > http://www.biocatalogue.org/soap_operations/19403 > http://www.biocatalogue.org/soap_operations/19404 > http://www.biocatalogue.org/soap_operations/19400 > http://www.biocatalogue.org/soap_operations/19401 * > http://www.biocatalogue.org/soap_operations/19402 * > http://www.biocatalogue.org/soap_operations/19397 > http://www.biocatalogue.org/soap_operations/19398 > http://www.biocatalogue.org/soap_operations/19399 > http://www.biocatalogue.org/soap_operations/19393 > http://www.biocatalogue.org/soap_operations/19394 > http://www.biocatalogue.org/soap_operations/19395 * > http://www.biocatalogue.org/soap_operations/19396 * > http://www.biocatalogue.org/soap_operations/19391 > http://www.biocatalogue.org/soap_operations/19392 > http://www.biocatalogue.org/soap_operations/19385 > http://www.biocatalogue.org/soap_operations/19386 > http://www.biocatalogue.org/soap_operations/19387 > http://www.biocatalogue.org/soap_operations/19388 > http://www.biocatalogue.org/soap_operations/19389 * > http://www.biocatalogue.org/soap_operations/19390 * > http://www.biocatalogue.org/soap_operations/19379 > http://www.biocatalogue.org/soap_operations/19380 > http://www.biocatalogue.org/soap_operations/19381 > http://www.biocatalogue.org/soap_operations/19382 > http://www.biocatalogue.org/soap_operations/19383 * > http://www.biocatalogue.org/soap_operations/19384 * > http://www.biocatalogue.org/soap_operations/19377 * > http://www.biocatalogue.org/soap_operations/19378 * > http://www.biocatalogue.org/soap_operations/19373 > http://www.biocatalogue.org/soap_operations/19374 > http://www.biocatalogue.org/soap_operations/19375 > http://www.biocatalogue.org/soap_operations/19376 > http://www.biocatalogue.org/soap_operations/19372 * > http://www.biocatalogue.org/soap_operations/19367 > http://www.biocatalogue.org/soap_operations/19368 > http://www.biocatalogue.org/soap_operations/19369 > http://www.biocatalogue.org/soap_operations/19370 > http://www.biocatalogue.org/soap_operations/19371 * > http://www.biocatalogue.org/soap_operations/19364 > http://www.biocatalogue.org/soap_operations/19365 * > http://www.biocatalogue.org/soap_operations/19366 * > http://www.biocatalogue.org/soap_operations/19361 > http://www.biocatalogue.org/soap_operations/19362 > http://www.biocatalogue.org/soap_operations/19363 > http://www.biocatalogue.org/soap_operations/19358 > http://www.biocatalogue.org/soap_operations/19359 * > http://www.biocatalogue.org/soap_operations/19360 * > http://www.biocatalogue.org/soap_operations/19355 > http://www.biocatalogue.org/soap_operations/19356 > http://www.biocatalogue.org/soap_operations/19357 > http://www.biocatalogue.org/soap_operations/19352 > http://www.biocatalogue.org/soap_operations/19353 * > http://www.biocatalogue.org/soap_operations/19354 * > http://www.biocatalogue.org/soap_operations/19349 > http://www.biocatalogue.org/soap_operations/19350 > http://www.biocatalogue.org/soap_operations/19351 > http://www.biocatalogue.org/soap_operations/19346 > http://www.biocatalogue.org/soap_operations/19347 * > http://www.biocatalogue.org/soap_operations/19348 * > http://www.biocatalogue.org/soap_operations/19343 > http://www.biocatalogue.org/soap_operations/19344 > http://www.biocatalogue.org/soap_operations/19345 > http://www.biocatalogue.org/soap_operations/19340 > http://www.biocatalogue.org/soap_operations/19341 * > http://www.biocatalogue.org/soap_operations/19342 * > http://www.biocatalogue.org/soap_operations/19337 > http://www.biocatalogue.org/soap_operations/19338 > http://www.biocatalogue.org/soap_operations/19339 > http://www.biocatalogue.org/soap_operations/19334 > http://www.biocatalogue.org/soap_operations/19335 * > http://www.biocatalogue.org/soap_operations/19336 * > http://www.biocatalogue.org/soap_operations/19331 > http://www.biocatalogue.org/soap_operations/19332 > http://www.biocatalogue.org/soap_operations/19333 > http://www.biocatalogue.org/soap_operations/19328 > http://www.biocatalogue.org/soap_operations/19329 * > http://www.biocatalogue.org/soap_operations/19330 * > http://www.biocatalogue.org/soap_operations/19325 > http://www.biocatalogue.org/soap_operations/19326 > http://www.biocatalogue.org/soap_operations/19327 > http://www.biocatalogue.org/soap_operations/19320 > http://www.biocatalogue.org/soap_operations/19321 > http://www.biocatalogue.org/soap_operations/19322 > http://www.biocatalogue.org/soap_operations/19323 * > http://www.biocatalogue.org/soap_operations/19324 * > http://www.biocatalogue.org/soap_operations/19319 > http://www.biocatalogue.org/soap_operations/19316 > http://www.biocatalogue.org/soap_operations/19317 * > http://www.biocatalogue.org/soap_operations/19318 * > http://www.biocatalogue.org/soap_operations/19313 > http://www.biocatalogue.org/soap_operations/19314 > http://www.biocatalogue.org/soap_operations/19315 > http://www.biocatalogue.org/soap_operations/19309 > http://www.biocatalogue.org/soap_operations/19310 > http://www.biocatalogue.org/soap_operations/19311 * > http://www.biocatalogue.org/soap_operations/19312 * > http://www.biocatalogue.org/soap_operations/19307 > http://www.biocatalogue.org/soap_operations/19308 > http://www.biocatalogue.org/soap_operations/19301 > http://www.biocatalogue.org/soap_operations/19302 > http://www.biocatalogue.org/soap_operations/19303 > http://www.biocatalogue.org/soap_operations/19304 > http://www.biocatalogue.org/soap_operations/19305 * > http://www.biocatalogue.org/soap_operations/19306 * > http://www.biocatalogue.org/soap_operations/19298 > http://www.biocatalogue.org/soap_operations/19299 * > http://www.biocatalogue.org/soap_operations/19300 * > http://www.biocatalogue.org/soap_operations/19295 > http://www.biocatalogue.org/soap_operations/19296 > http://www.biocatalogue.org/soap_operations/19297 > http://www.biocatalogue.org/soap_operations/19290 > http://www.biocatalogue.org/soap_operations/19291 > http://www.biocatalogue.org/soap_operations/19292 > http://www.biocatalogue.org/soap_operations/19293 * > http://www.biocatalogue.org/soap_operations/19294 * > http://www.biocatalogue.org/soap_operations/19289 > http://www.biocatalogue.org/soap_operations/19286 > http://www.biocatalogue.org/soap_operations/19287 * > http://www.biocatalogue.org/soap_operations/19288 * > http://www.biocatalogue.org/soap_operations/19285 > http://www.biocatalogue.org/soap_operations/19283 > http://www.biocatalogue.org/soap_operations/19284 > http://www.biocatalogue.org/soap_operations/19278 > http://www.biocatalogue.org/soap_operations/19279 > http://www.biocatalogue.org/soap_operations/19280 > http://www.biocatalogue.org/soap_operations/19281 * > http://www.biocatalogue.org/soap_operations/19282 * > http://www.biocatalogue.org/soap_operations/19277 > http://www.biocatalogue.org/soap_operations/19274 > http://www.biocatalogue.org/soap_operations/19275 * > http://www.biocatalogue.org/soap_operations/19276 * > http://www.biocatalogue.org/soap_operations/19271 > http://www.biocatalogue.org/soap_operations/19272 > http://www.biocatalogue.org/soap_operations/19273 > http://www.biocatalogue.org/soap_operations/19265 > http://www.biocatalogue.org/soap_operations/19266 > http://www.biocatalogue.org/soap_operations/19267 > http://www.biocatalogue.org/soap_operations/19268 > http://www.biocatalogue.org/soap_operations/19269 * > http://www.biocatalogue.org/soap_operations/19270 * > http://www.biocatalogue.org/soap_operations/19264 * > http://www.biocatalogue.org/soap_operations/19259 > http://www.biocatalogue.org/soap_operations/19260 > http://www.biocatalogue.org/soap_operations/19261 > http://www.biocatalogue.org/soap_operations/19262 > http://www.biocatalogue.org/soap_operations/19263 * > http://www.biocatalogue.org/soap_operations/19257 * > http://www.biocatalogue.org/soap_operations/19258 * > http://www.biocatalogue.org/soap_operations/19253 > http://www.biocatalogue.org/soap_operations/19254 > http://www.biocatalogue.org/soap_operations/19255 > http://www.biocatalogue.org/soap_operations/19256 > http://www.biocatalogue.org/soap_operations/19251 * > http://www.biocatalogue.org/soap_operations/19252 * > http://www.biocatalogue.org/soap_operations/19247 > http://www.biocatalogue.org/soap_operations/19248 > http://www.biocatalogue.org/soap_operations/19249 > http://www.biocatalogue.org/soap_operations/19250 > http://www.biocatalogue.org/soap_operations/19244 > http://www.biocatalogue.org/soap_operations/19245 * > http://www.biocatalogue.org/soap_operations/19246 * > http://www.biocatalogue.org/soap_operations/19241 > http://www.biocatalogue.org/soap_operations/19242 > http://www.biocatalogue.org/soap_operations/19243 > http://www.biocatalogue.org/soap_operations/19237 > http://www.biocatalogue.org/soap_operations/19238 > http://www.biocatalogue.org/soap_operations/19239 * > http://www.biocatalogue.org/soap_operations/19240 * > http://www.biocatalogue.org/soap_operations/19235 > http://www.biocatalogue.org/soap_operations/19236 > http://www.biocatalogue.org/soap_operations/19232 > http://www.biocatalogue.org/soap_operations/19233 * > http://www.biocatalogue.org/soap_operations/19234 * > http://www.biocatalogue.org/soap_operations/19229 > http://www.biocatalogue.org/soap_operations/19230 > http://www.biocatalogue.org/soap_operations/19231 > http://www.biocatalogue.org/soap_operations/19225 > http://www.biocatalogue.org/soap_operations/19226 > http://www.biocatalogue.org/soap_operations/19227 * > http://www.biocatalogue.org/soap_operations/19228 * > http://www.biocatalogue.org/soap_operations/19223 > http://www.biocatalogue.org/soap_operations/19224 > http://www.biocatalogue.org/soap_operations/19217 > http://www.biocatalogue.org/soap_operations/19218 > http://www.biocatalogue.org/soap_operations/19219 > http://www.biocatalogue.org/soap_operations/19220 > http://www.biocatalogue.org/soap_operations/19221 * > http://www.biocatalogue.org/soap_operations/19222 * > http://www.biocatalogue.org/soap_operations/19212 > http://www.biocatalogue.org/soap_operations/19213 > http://www.biocatalogue.org/soap_operations/19214 > http://www.biocatalogue.org/soap_operations/19215 * > http://www.biocatalogue.org/soap_operations/19216 * > http://www.biocatalogue.org/soap_operations/19211 > http://www.biocatalogue.org/soap_operations/19205 > http://www.biocatalogue.org/soap_operations/19206 > http://www.biocatalogue.org/soap_operations/19207 > http://www.biocatalogue.org/soap_operations/19208 > http://www.biocatalogue.org/soap_operations/19209 * > http://www.biocatalogue.org/soap_operations/19210 * > http://www.biocatalogue.org/soap_operations/19204 * > http://www.biocatalogue.org/soap_operations/19199 > http://www.biocatalogue.org/soap_operations/19200 > http://www.biocatalogue.org/soap_operations/19201 > http://www.biocatalogue.org/soap_operations/19202 > http://www.biocatalogue.org/soap_operations/19203 * > http://www.biocatalogue.org/soap_operations/19198 * > http://www.biocatalogue.org/soap_operations/19193 > http://www.biocatalogue.org/soap_operations/19194 > http://www.biocatalogue.org/soap_operations/19195 > http://www.biocatalogue.org/soap_operations/19196 > http://www.biocatalogue.org/soap_operations/19197 * > http://www.biocatalogue.org/soap_operations/19192 * > http://www.biocatalogue.org/soap_operations/19187 > http://www.biocatalogue.org/soap_operations/19188 > http://www.biocatalogue.org/soap_operations/19189 > http://www.biocatalogue.org/soap_operations/19190 > http://www.biocatalogue.org/soap_operations/19191 * > http://www.biocatalogue.org/soap_operations/19181 > http://www.biocatalogue.org/soap_operations/19182 > http://www.biocatalogue.org/soap_operations/19183 > http://www.biocatalogue.org/soap_operations/19184 > http://www.biocatalogue.org/soap_operations/19185 * > http://www.biocatalogue.org/soap_operations/19186 * > http://www.biocatalogue.org/soap_operations/19178 > http://www.biocatalogue.org/soap_operations/19179 * > http://www.biocatalogue.org/soap_operations/19180 * > http://www.biocatalogue.org/soap_operations/19175 > http://www.biocatalogue.org/soap_operations/19176 > http://www.biocatalogue.org/soap_operations/19177 > http://www.biocatalogue.org/soap_operations/19172 > http://www.biocatalogue.org/soap_operations/19173 * > http://www.biocatalogue.org/soap_operations/19174 * > http://www.biocatalogue.org/soap_operations/19169 > http://www.biocatalogue.org/soap_operations/19170 > http://www.biocatalogue.org/soap_operations/19171 > http://www.biocatalogue.org/soap_operations/19167 * > http://www.biocatalogue.org/soap_operations/19168 * > http://www.biocatalogue.org/soap_operations/19163 > http://www.biocatalogue.org/soap_operations/19164 > http://www.biocatalogue.org/soap_operations/19165 > http://www.biocatalogue.org/soap_operations/19166 > http://www.biocatalogue.org/soap_operations/19160 > http://www.biocatalogue.org/soap_operations/19161 * > http://www.biocatalogue.org/soap_operations/19162 * > http://www.biocatalogue.org/soap_operations/19157 > http://www.biocatalogue.org/soap_operations/19158 > http://www.biocatalogue.org/soap_operations/19159 > http://www.biocatalogue.org/soap_operations/19154 > http://www.biocatalogue.org/soap_operations/19155 * > http://www.biocatalogue.org/soap_operations/19156 * > http://www.biocatalogue.org/soap_operations/19151 > http://www.biocatalogue.org/soap_operations/19152 > http://www.biocatalogue.org/soap_operations/19153 > http://www.biocatalogue.org/soap_operations/19148 > http://www.biocatalogue.org/soap_operations/19149 * > http://www.biocatalogue.org/soap_operations/19150 * > http://www.biocatalogue.org/soap_operations/19145 > http://www.biocatalogue.org/soap_operations/19146 > http://www.biocatalogue.org/soap_operations/19147 > http://www.biocatalogue.org/soap_operations/19140 > http://www.biocatalogue.org/soap_operations/19141 > http://www.biocatalogue.org/soap_operations/19142 > http://www.biocatalogue.org/soap_operations/19143 * > http://www.biocatalogue.org/soap_operations/19144 * > http://www.biocatalogue.org/soap_operations/19139 > http://www.biocatalogue.org/soap_operations/19133 > http://www.biocatalogue.org/soap_operations/19134 > http://www.biocatalogue.org/soap_operations/19135 > http://www.biocatalogue.org/soap_operations/19136 > http://www.biocatalogue.org/soap_operations/19137 * > http://www.biocatalogue.org/soap_operations/19138 * > http://www.biocatalogue.org/soap_operations/19132 * > http://www.biocatalogue.org/soap_operations/19129 > http://www.biocatalogue.org/soap_operations/19130 > http://www.biocatalogue.org/soap_operations/19131 * > http://www.biocatalogue.org/soap_operations/19127 > http://www.biocatalogue.org/soap_operations/19128 > http://www.biocatalogue.org/soap_operations/19121 > http://www.biocatalogue.org/soap_operations/19122 > http://www.biocatalogue.org/soap_operations/19123 > http://www.biocatalogue.org/soap_operations/19124 > http://www.biocatalogue.org/soap_operations/19125 * > http://www.biocatalogue.org/soap_operations/19126 * > http://www.biocatalogue.org/soap_operations/19119 * > http://www.biocatalogue.org/soap_operations/19120 * > http://www.biocatalogue.org/soap_operations/19115 > http://www.biocatalogue.org/soap_operations/19116 > http://www.biocatalogue.org/soap_operations/19117 > http://www.biocatalogue.org/soap_operations/19118 > http://www.biocatalogue.org/soap_operations/19112 > http://www.biocatalogue.org/soap_operations/19113 * > http://www.biocatalogue.org/soap_operations/19114 * > http://www.biocatalogue.org/soap_operations/19109 > http://www.biocatalogue.org/soap_operations/19110 > http://www.biocatalogue.org/soap_operations/19111 > http://www.biocatalogue.org/soap_operations/19107 * > http://www.biocatalogue.org/soap_operations/19108 * > http://www.biocatalogue.org/soap_operations/19103 > http://www.biocatalogue.org/soap_operations/19104 > http://www.biocatalogue.org/soap_operations/19105 > http://www.biocatalogue.org/soap_operations/19106 > http://www.biocatalogue.org/soap_operations/19100 > http://www.biocatalogue.org/soap_operations/19101 * > http://www.biocatalogue.org/soap_operations/19102 * > http://www.biocatalogue.org/soap_operations/19097 > http://www.biocatalogue.org/soap_operations/19098 > http://www.biocatalogue.org/soap_operations/19099 > http://www.biocatalogue.org/soap_operations/19094 > http://www.biocatalogue.org/soap_operations/19095 * > http://www.biocatalogue.org/soap_operations/19096 * > http://www.biocatalogue.org/soap_operations/19091 > http://www.biocatalogue.org/soap_operations/19092 > http://www.biocatalogue.org/soap_operations/19093 > http://www.biocatalogue.org/soap_operations/19086 > http://www.biocatalogue.org/soap_operations/19087 > http://www.biocatalogue.org/soap_operations/19088 > http://www.biocatalogue.org/soap_operations/19089 * > http://www.biocatalogue.org/soap_operations/19090 * > http://www.biocatalogue.org/soap_operations/19085 > http://www.biocatalogue.org/soap_operations/19083 * > http://www.biocatalogue.org/soap_operations/19084 * > http://www.biocatalogue.org/soap_operations/19079 > http://www.biocatalogue.org/soap_operations/19080 > http://www.biocatalogue.org/soap_operations/19081 > http://www.biocatalogue.org/soap_operations/19082 > http://www.biocatalogue.org/soap_operations/19076 > http://www.biocatalogue.org/soap_operations/19077 * > http://www.biocatalogue.org/soap_operations/19078 * > http://www.biocatalogue.org/soap_operations/19073 > http://www.biocatalogue.org/soap_operations/19074 > http://www.biocatalogue.org/soap_operations/19075 > http://www.biocatalogue.org/soap_operations/19072 * > http://www.biocatalogue.org/soap_operations/19067 > http://www.biocatalogue.org/soap_operations/19068 > http://www.biocatalogue.org/soap_operations/19069 > http://www.biocatalogue.org/soap_operations/19070 > http://www.biocatalogue.org/soap_operations/19071 * > http://www.biocatalogue.org/soap_operations/19064 > http://www.biocatalogue.org/soap_operations/19065 * > http://www.biocatalogue.org/soap_operations/19066 * > http://www.biocatalogue.org/soap_operations/19061 > http://www.biocatalogue.org/soap_operations/19062 > http://www.biocatalogue.org/soap_operations/19063 > http://www.biocatalogue.org/soap_operations/19058 > http://www.biocatalogue.org/soap_operations/19059 * > http://www.biocatalogue.org/soap_operations/19060 * > http://www.biocatalogue.org/soap_operations/19055 > http://www.biocatalogue.org/soap_operations/19056 > http://www.biocatalogue.org/soap_operations/19057 > http://www.biocatalogue.org/soap_operations/19049 > http://www.biocatalogue.org/soap_operations/19050 > http://www.biocatalogue.org/soap_operations/19051 > http://www.biocatalogue.org/soap_operations/19052 > http://www.biocatalogue.org/soap_operations/19053 * > http://www.biocatalogue.org/soap_operations/19054 * > http://www.biocatalogue.org/soap_operations/19043 > http://www.biocatalogue.org/soap_operations/19044 > http://www.biocatalogue.org/soap_operations/19045 > http://www.biocatalogue.org/soap_operations/19046 > http://www.biocatalogue.org/soap_operations/19047 * > http://www.biocatalogue.org/soap_operations/19048 * > http://www.biocatalogue.org/soap_operations/19042 * > http://www.biocatalogue.org/soap_operations/19037 > http://www.biocatalogue.org/soap_operations/19038 > http://www.biocatalogue.org/soap_operations/19039 > http://www.biocatalogue.org/soap_operations/19040 > http://www.biocatalogue.org/soap_operations/19041 * > http://www.biocatalogue.org/soap_operations/19035 * > http://www.biocatalogue.org/soap_operations/19036 * > http://www.biocatalogue.org/soap_operations/19031 > http://www.biocatalogue.org/soap_operations/19032 > http://www.biocatalogue.org/soap_operations/19033 > http://www.biocatalogue.org/soap_operations/19034 > http://www.biocatalogue.org/soap_operations/19027 > http://www.biocatalogue.org/soap_operations/19028 > http://www.biocatalogue.org/soap_operations/19029 * > http://www.biocatalogue.org/soap_operations/19030 * > http://www.biocatalogue.org/soap_operations/19025 > http://www.biocatalogue.org/soap_operations/19026 > http://www.biocatalogue.org/soap_operations/19022 > http://www.biocatalogue.org/soap_operations/19023 * > http://www.biocatalogue.org/soap_operations/19024 * > http://www.biocatalogue.org/soap_operations/19019 > http://www.biocatalogue.org/soap_operations/19020 > http://www.biocatalogue.org/soap_operations/19021 > http://www.biocatalogue.org/soap_operations/19015 > http://www.biocatalogue.org/soap_operations/19016 > http://www.biocatalogue.org/soap_operations/19017 * > http://www.biocatalogue.org/soap_operations/19018 * > http://www.biocatalogue.org/soap_operations/19013 > http://www.biocatalogue.org/soap_operations/19014 > http://www.biocatalogue.org/soap_operations/19007 > http://www.biocatalogue.org/soap_operations/19008 > http://www.biocatalogue.org/soap_operations/19009 > http://www.biocatalogue.org/soap_operations/19010 > http://www.biocatalogue.org/soap_operations/19011 * > http://www.biocatalogue.org/soap_operations/19012 * > http://www.biocatalogue.org/soap_operations/19002 > http://www.biocatalogue.org/soap_operations/19003 > http://www.biocatalogue.org/soap_operations/19004 > http://www.biocatalogue.org/soap_operations/19005 * > http://www.biocatalogue.org/soap_operations/19006 * > http://www.biocatalogue.org/soap_operations/19001 > http://www.biocatalogue.org/soap_operations/18997 > http://www.biocatalogue.org/soap_operations/18998 > http://www.biocatalogue.org/soap_operations/18999 * > http://www.biocatalogue.org/soap_operations/19000 * > http://www.biocatalogue.org/soap_operations/18995 > http://www.biocatalogue.org/soap_operations/18996 > http://www.biocatalogue.org/soap_operations/18991 > http://www.biocatalogue.org/soap_operations/18992 > http://www.biocatalogue.org/soap_operations/18993 * > http://www.biocatalogue.org/soap_operations/18994 * > http://www.biocatalogue.org/soap_operations/18989 > http://www.biocatalogue.org/soap_operations/18990 > http://www.biocatalogue.org/soap_operations/18983 > http://www.biocatalogue.org/soap_operations/18984 > http://www.biocatalogue.org/soap_operations/18985 > http://www.biocatalogue.org/soap_operations/18986 > http://www.biocatalogue.org/soap_operations/18987 * > http://www.biocatalogue.org/soap_operations/18988 * > http://www.biocatalogue.org/soap_operations/18977 > http://www.biocatalogue.org/soap_operations/18978 > http://www.biocatalogue.org/soap_operations/18979 > http://www.biocatalogue.org/soap_operations/18980 > http://www.biocatalogue.org/soap_operations/18981 * > http://www.biocatalogue.org/soap_operations/18982 * > http://www.biocatalogue.org/soap_operations/18975 * > http://www.biocatalogue.org/soap_operations/18976 * > http://www.biocatalogue.org/soap_operations/18971 > http://www.biocatalogue.org/soap_operations/18972 > http://www.biocatalogue.org/soap_operations/18973 > http://www.biocatalogue.org/soap_operations/18974 > http://www.biocatalogue.org/soap_operations/18970 * > http://www.biocatalogue.org/soap_operations/18965 > http://www.biocatalogue.org/soap_operations/18966 > http://www.biocatalogue.org/soap_operations/18967 > http://www.biocatalogue.org/soap_operations/18968 > http://www.biocatalogue.org/soap_operations/18969 * > http://www.biocatalogue.org/soap_operations/18964 * > http://www.biocatalogue.org/soap_operations/18959 > http://www.biocatalogue.org/soap_operations/18960 > http://www.biocatalogue.org/soap_operations/18961 > http://www.biocatalogue.org/soap_operations/18962 > http://www.biocatalogue.org/soap_operations/18963 * > http://www.biocatalogue.org/soap_operations/18956 > http://www.biocatalogue.org/soap_operations/18957 * > http://www.biocatalogue.org/soap_operations/18958 * > http://www.biocatalogue.org/soap_operations/18953 > http://www.biocatalogue.org/soap_operations/18954 > http://www.biocatalogue.org/soap_operations/18955 > http://www.biocatalogue.org/soap_operations/18950 > http://www.biocatalogue.org/soap_operations/18951 * > http://www.biocatalogue.org/soap_operations/18952 * > http://www.biocatalogue.org/soap_operations/18947 > http://www.biocatalogue.org/soap_operations/18948 > http://www.biocatalogue.org/soap_operations/18949 > http://www.biocatalogue.org/soap_operations/18944 > http://www.biocatalogue.org/soap_operations/18945 * > http://www.biocatalogue.org/soap_operations/18946 * > http://www.biocatalogue.org/soap_operations/18941 > http://www.biocatalogue.org/soap_operations/18942 > http://www.biocatalogue.org/soap_operations/18943 > http://www.biocatalogue.org/soap_operations/18938 > http://www.biocatalogue.org/soap_operations/18939 * > http://www.biocatalogue.org/soap_operations/18940 * > http://www.biocatalogue.org/soap_operations/18935 > http://www.biocatalogue.org/soap_operations/18936 > http://www.biocatalogue.org/soap_operations/18937 > http://www.biocatalogue.org/soap_operations/18929 > http://www.biocatalogue.org/soap_operations/18930 > http://www.biocatalogue.org/soap_operations/18931 > http://www.biocatalogue.org/soap_operations/18932 > http://www.biocatalogue.org/soap_operations/18933 * > http://www.biocatalogue.org/soap_operations/18934 * > http://www.biocatalogue.org/soap_operations/18928 * > http://www.biocatalogue.org/soap_operations/18923 > http://www.biocatalogue.org/soap_operations/18924 > http://www.biocatalogue.org/soap_operations/18925 > http://www.biocatalogue.org/soap_operations/18926 > http://www.biocatalogue.org/soap_operations/18927 * > http://www.biocatalogue.org/soap_operations/18920 > http://www.biocatalogue.org/soap_operations/18921 * > http://www.biocatalogue.org/soap_operations/18922 * > http://www.biocatalogue.org/soap_operations/18917 > http://www.biocatalogue.org/soap_operations/18918 > http://www.biocatalogue.org/soap_operations/18919 > http://www.biocatalogue.org/soap_operations/18913 > http://www.biocatalogue.org/soap_operations/18914 > http://www.biocatalogue.org/soap_operations/18915 * > http://www.biocatalogue.org/soap_operations/18916 * > http://www.biocatalogue.org/soap_operations/18911 > http://www.biocatalogue.org/soap_operations/18912 > http://www.biocatalogue.org/soap_operations/18907 > http://www.biocatalogue.org/soap_operations/18908 > http://www.biocatalogue.org/soap_operations/18909 * > http://www.biocatalogue.org/soap_operations/18910 * > http://www.biocatalogue.org/soap_operations/18905 > http://www.biocatalogue.org/soap_operations/18906 > http://www.biocatalogue.org/soap_operations/18899 > http://www.biocatalogue.org/soap_operations/18900 > http://www.biocatalogue.org/soap_operations/18901 > http://www.biocatalogue.org/soap_operations/18902 > http://www.biocatalogue.org/soap_operations/18903 * > http://www.biocatalogue.org/soap_operations/18904 * > http://www.biocatalogue.org/soap_operations/18898 * > http://www.biocatalogue.org/soap_operations/18893 > http://www.biocatalogue.org/soap_operations/18894 > http://www.biocatalogue.org/soap_operations/18895 > http://www.biocatalogue.org/soap_operations/18896 > http://www.biocatalogue.org/soap_operations/18897 * > http://www.biocatalogue.org/soap_operations/18892 * > http://www.biocatalogue.org/soap_operations/18887 > http://www.biocatalogue.org/soap_operations/18888 > http://www.biocatalogue.org/soap_operations/18889 > http://www.biocatalogue.org/soap_operations/18890 > http://www.biocatalogue.org/soap_operations/18891 * > http://www.biocatalogue.org/soap_operations/18884 > http://www.biocatalogue.org/soap_operations/18885 * > http://www.biocatalogue.org/soap_operations/18886 * > http://www.biocatalogue.org/soap_operations/18881 > http://www.biocatalogue.org/soap_operations/18882 > http://www.biocatalogue.org/soap_operations/18883 > http://www.biocatalogue.org/soap_operations/18878 > http://www.biocatalogue.org/soap_operations/18879 * > http://www.biocatalogue.org/soap_operations/18880 * > http://www.biocatalogue.org/soap_operations/18875 > http://www.biocatalogue.org/soap_operations/18876 > http://www.biocatalogue.org/soap_operations/18877 > http://www.biocatalogue.org/soap_operations/18872 > http://www.biocatalogue.org/soap_operations/18873 * > http://www.biocatalogue.org/soap_operations/18874 * > http://www.biocatalogue.org/soap_operations/18869 > http://www.biocatalogue.org/soap_operations/18870 > http://www.biocatalogue.org/soap_operations/18871 > http://www.biocatalogue.org/soap_operations/18866 > http://www.biocatalogue.org/soap_operations/18867 * > http://www.biocatalogue.org/soap_operations/18868 * > http://www.biocatalogue.org/soap_operations/18863 > http://www.biocatalogue.org/soap_operations/18864 > http://www.biocatalogue.org/soap_operations/18865 > http://www.biocatalogue.org/soap_operations/18859 > http://www.biocatalogue.org/soap_operations/18860 > http://www.biocatalogue.org/soap_operations/18861 * > http://www.biocatalogue.org/soap_operations/18862 * > http://www.biocatalogue.org/soap_operations/18857 > http://www.biocatalogue.org/soap_operations/18858 > http://www.biocatalogue.org/soap_operations/18853 > http://www.biocatalogue.org/soap_operations/18854 > http://www.biocatalogue.org/soap_operations/18855 * > http://www.biocatalogue.org/soap_operations/18856 * > http://www.biocatalogue.org/soap_operations/18851 > http://www.biocatalogue.org/soap_operations/18852 > http://www.biocatalogue.org/soap_operations/18845 > http://www.biocatalogue.org/soap_operations/18846 > http://www.biocatalogue.org/soap_operations/18847 > http://www.biocatalogue.org/soap_operations/18848 > http://www.biocatalogue.org/soap_operations/18849 * > http://www.biocatalogue.org/soap_operations/18850 * > http://www.biocatalogue.org/soap_operations/18839 > http://www.biocatalogue.org/soap_operations/18840 > http://www.biocatalogue.org/soap_operations/18841 > http://www.biocatalogue.org/soap_operations/18842 > http://www.biocatalogue.org/soap_operations/18843 * > http://www.biocatalogue.org/soap_operations/18844 * > http://www.biocatalogue.org/soap_operations/18838 * > http://www.biocatalogue.org/soap_operations/18833 > http://www.biocatalogue.org/soap_operations/18834 > http://www.biocatalogue.org/soap_operations/18835 > http://www.biocatalogue.org/soap_operations/18836 > http://www.biocatalogue.org/soap_operations/18837 * > http://www.biocatalogue.org/soap_operations/18827 > http://www.biocatalogue.org/soap_operations/18828 > http://www.biocatalogue.org/soap_operations/18829 > http://www.biocatalogue.org/soap_operations/18830 > http://www.biocatalogue.org/soap_operations/18831 * > http://www.biocatalogue.org/soap_operations/18832 * > http://www.biocatalogue.org/soap_operations/18825 * > http://www.biocatalogue.org/soap_operations/18826 * > http://www.biocatalogue.org/soap_operations/18821 > http://www.biocatalogue.org/soap_operations/18822 > http://www.biocatalogue.org/soap_operations/18823 > http://www.biocatalogue.org/soap_operations/18824 > http://www.biocatalogue.org/soap_operations/18819 * > http://www.biocatalogue.org/soap_operations/18820 * > http://www.biocatalogue.org/soap_operations/18815 > http://www.biocatalogue.org/soap_operations/18816 > http://www.biocatalogue.org/soap_operations/18817 > http://www.biocatalogue.org/soap_operations/18818 > http://www.biocatalogue.org/soap_operations/18812 > http://www.biocatalogue.org/soap_operations/18813 * > http://www.biocatalogue.org/soap_operations/18814 * > http://www.biocatalogue.org/soap_operations/18809 > http://www.biocatalogue.org/soap_operations/18810 > http://www.biocatalogue.org/soap_operations/18811 > http://www.biocatalogue.org/soap_operations/18806 > http://www.biocatalogue.org/soap_operations/18807 * > http://www.biocatalogue.org/soap_operations/18808 * > http://www.biocatalogue.org/soap_operations/18803 > http://www.biocatalogue.org/soap_operations/18804 > http://www.biocatalogue.org/soap_operations/18805 > http://www.biocatalogue.org/soap_operations/18800 > http://www.biocatalogue.org/soap_operations/18801 * > http://www.biocatalogue.org/soap_operations/18802 * > http://www.biocatalogue.org/soap_operations/18797 > http://www.biocatalogue.org/soap_operations/18798 > http://www.biocatalogue.org/soap_operations/18799 > http://www.biocatalogue.org/soap_operations/18793 > http://www.biocatalogue.org/soap_operations/18794 > http://www.biocatalogue.org/soap_operations/18795 * > http://www.biocatalogue.org/soap_operations/18796 * > http://www.biocatalogue.org/soap_operations/18791 > http://www.biocatalogue.org/soap_operations/18792 > http://www.biocatalogue.org/soap_operations/18785 > http://www.biocatalogue.org/soap_operations/18786 > http://www.biocatalogue.org/soap_operations/18787 > http://www.biocatalogue.org/soap_operations/18788 > http://www.biocatalogue.org/soap_operations/18789 * > http://www.biocatalogue.org/soap_operations/18790 * > http://www.biocatalogue.org/soap_operations/18783 * > http://www.biocatalogue.org/soap_operations/18784 * > http://www.biocatalogue.org/soap_operations/18779 > http://www.biocatalogue.org/soap_operations/18780 > http://www.biocatalogue.org/soap_operations/18781 > http://www.biocatalogue.org/soap_operations/18782 > http://www.biocatalogue.org/soap_operations/18778 * > http://www.biocatalogue.org/soap_operations/18773 > http://www.biocatalogue.org/soap_operations/18774 > http://www.biocatalogue.org/soap_operations/18775 > http://www.biocatalogue.org/soap_operations/18776 > http://www.biocatalogue.org/soap_operations/18777 * > http://www.biocatalogue.org/soap_operations/18770 > http://www.biocatalogue.org/soap_operations/18771 * > http://www.biocatalogue.org/soap_operations/18772 * > http://www.biocatalogue.org/soap_operations/18767 > http://www.biocatalogue.org/soap_operations/18768 > http://www.biocatalogue.org/soap_operations/18769 > http://www.biocatalogue.org/soap_operations/18764 > http://www.biocatalogue.org/soap_operations/18765 * > http://www.biocatalogue.org/soap_operations/18766 * > http://www.biocatalogue.org/soap_operations/18761 > http://www.biocatalogue.org/soap_operations/18762 > http://www.biocatalogue.org/soap_operations/18763 > http://www.biocatalogue.org/soap_operations/18760 * > http://www.biocatalogue.org/soap_operations/18755 > http://www.biocatalogue.org/soap_operations/18756 > http://www.biocatalogue.org/soap_operations/18757 > http://www.biocatalogue.org/soap_operations/18758 > http://www.biocatalogue.org/soap_operations/18759 * > http://www.biocatalogue.org/soap_operations/18752 > http://www.biocatalogue.org/soap_operations/18753 * > http://www.biocatalogue.org/soap_operations/18754 * > http://www.biocatalogue.org/soap_operations/18749 > http://www.biocatalogue.org/soap_operations/18750 > http://www.biocatalogue.org/soap_operations/18751 > http://www.biocatalogue.org/soap_operations/18746 > http://www.biocatalogue.org/soap_operations/18747 * > http://www.biocatalogue.org/soap_operations/18748 * > http://www.biocatalogue.org/soap_operations/18743 > http://www.biocatalogue.org/soap_operations/18744 > http://www.biocatalogue.org/soap_operations/18745 > http://www.biocatalogue.org/soap_operations/18738 > http://www.biocatalogue.org/soap_operations/18739 > http://www.biocatalogue.org/soap_operations/18740 > http://www.biocatalogue.org/soap_operations/18741 * > http://www.biocatalogue.org/soap_operations/18742 * > http://www.biocatalogue.org/soap_operations/18737 > http://www.biocatalogue.org/soap_operations/18736 * > http://www.biocatalogue.org/soap_operations/18731 > http://www.biocatalogue.org/soap_operations/18732 > http://www.biocatalogue.org/soap_operations/18733 > http://www.biocatalogue.org/soap_operations/18734 > http://www.biocatalogue.org/soap_operations/18735 * > http://www.biocatalogue.org/soap_operations/18728 > http://www.biocatalogue.org/soap_operations/18729 * > http://www.biocatalogue.org/soap_operations/18730 * > http://www.biocatalogue.org/soap_operations/18725 > http://www.biocatalogue.org/soap_operations/18726 > http://www.biocatalogue.org/soap_operations/18727 > http://www.biocatalogue.org/soap_operations/18722 > http://www.biocatalogue.org/soap_operations/18723 * > http://www.biocatalogue.org/soap_operations/18724 * > http://www.biocatalogue.org/soap_operations/18719 > http://www.biocatalogue.org/soap_operations/18720 > http://www.biocatalogue.org/soap_operations/18721 > http://www.biocatalogue.org/soap_operations/18717 * > http://www.biocatalogue.org/soap_operations/18718 * > http://www.biocatalogue.org/soap_operations/18713 > http://www.biocatalogue.org/soap_operations/18714 > http://www.biocatalogue.org/soap_operations/18715 > http://www.biocatalogue.org/soap_operations/18716 > http://www.biocatalogue.org/soap_operations/18709 > http://www.biocatalogue.org/soap_operations/18710 > http://www.biocatalogue.org/soap_operations/18711 * > http://www.biocatalogue.org/soap_operations/18712 * > http://www.biocatalogue.org/soap_operations/18707 > http://www.biocatalogue.org/soap_operations/18708 > http://www.biocatalogue.org/soap_operations/18701 > http://www.biocatalogue.org/soap_operations/18702 > http://www.biocatalogue.org/soap_operations/18703 > http://www.biocatalogue.org/soap_operations/18704 > http://www.biocatalogue.org/soap_operations/18705 * > http://www.biocatalogue.org/soap_operations/18706 * > http://www.biocatalogue.org/soap_operations/18699 * > http://www.biocatalogue.org/soap_operations/18700 * > http://www.biocatalogue.org/soap_operations/18695 > http://www.biocatalogue.org/soap_operations/18696 > http://www.biocatalogue.org/soap_operations/18697 > http://www.biocatalogue.org/soap_operations/18698 > http://www.biocatalogue.org/soap_operations/18694 * > http://www.biocatalogue.org/soap_operations/18689 > http://www.biocatalogue.org/soap_operations/18690 > http://www.biocatalogue.org/soap_operations/18691 > http://www.biocatalogue.org/soap_operations/18692 > http://www.biocatalogue.org/soap_operations/18693 * > http://www.biocatalogue.org/soap_operations/18686 > http://www.biocatalogue.org/soap_operations/18687 * > http://www.biocatalogue.org/soap_operations/18688 * > http://www.biocatalogue.org/soap_operations/18683 > http://www.biocatalogue.org/soap_operations/18684 > http://www.biocatalogue.org/soap_operations/18685 > http://www.biocatalogue.org/soap_operations/18678 > http://www.biocatalogue.org/soap_operations/18679 > http://www.biocatalogue.org/soap_operations/18680 > http://www.biocatalogue.org/soap_operations/18681 * > http://www.biocatalogue.org/soap_operations/18682 * > http://www.biocatalogue.org/soap_operations/18677 > http://www.biocatalogue.org/soap_operations/18673 > http://www.biocatalogue.org/soap_operations/18674 > http://www.biocatalogue.org/soap_operations/18675 * > http://www.biocatalogue.org/soap_operations/18676 * > http://www.biocatalogue.org/soap_operations/18671 > http://www.biocatalogue.org/soap_operations/18672 > http://www.biocatalogue.org/soap_operations/18670 * > http://www.biocatalogue.org/soap_operations/18666 > http://www.biocatalogue.org/soap_operations/18667 > http://www.biocatalogue.org/soap_operations/18668 > http://www.biocatalogue.org/soap_operations/18669 * > http://www.biocatalogue.org/soap_operations/18665 > http://www.biocatalogue.org/soap_operations/18659 > http://www.biocatalogue.org/soap_operations/18660 > http://www.biocatalogue.org/soap_operations/18661 > http://www.biocatalogue.org/soap_operations/18662 > http://www.biocatalogue.org/soap_operations/18663 * > http://www.biocatalogue.org/soap_operations/18664 * > http://www.biocatalogue.org/soap_operations/18657 * > http://www.biocatalogue.org/soap_operations/18658 * > http://www.biocatalogue.org/soap_operations/18653 > http://www.biocatalogue.org/soap_operations/18654 > http://www.biocatalogue.org/soap_operations/18655 > http://www.biocatalogue.org/soap_operations/18656 > http://www.biocatalogue.org/soap_operations/18652 * > http://www.biocatalogue.org/soap_operations/18650 > http://www.biocatalogue.org/soap_operations/18651 * > http://www.biocatalogue.org/soap_operations/18647 > http://www.biocatalogue.org/soap_operations/18648 > http://www.biocatalogue.org/soap_operations/18649 > http://www.biocatalogue.org/soap_operations/18645 * > http://www.biocatalogue.org/soap_operations/18646 * > http://www.biocatalogue.org/soap_operations/18641 > http://www.biocatalogue.org/soap_operations/18642 > http://www.biocatalogue.org/soap_operations/18643 > http://www.biocatalogue.org/soap_operations/18644 > http://www.biocatalogue.org/soap_operations/18640 * > http://www.biocatalogue.org/soap_operations/18635 > http://www.biocatalogue.org/soap_operations/18636 > http://www.biocatalogue.org/soap_operations/18637 > http://www.biocatalogue.org/soap_operations/18638 > http://www.biocatalogue.org/soap_operations/18639 * > http://www.biocatalogue.org/soap_operations/18633 * > http://www.biocatalogue.org/soap_operations/18634 * > http://www.biocatalogue.org/soap_operations/18629 > http://www.biocatalogue.org/soap_operations/18630 > http://www.biocatalogue.org/soap_operations/18631 > http://www.biocatalogue.org/soap_operations/18632 > http://www.biocatalogue.org/soap_operations/18626 > http://www.biocatalogue.org/soap_operations/18627 * > http://www.biocatalogue.org/soap_operations/18628 * > http://www.biocatalogue.org/soap_operations/18623 > http://www.biocatalogue.org/soap_operations/18624 > http://www.biocatalogue.org/soap_operations/18625 > http://www.biocatalogue.org/soap_operations/18621 * > http://www.biocatalogue.org/soap_operations/18622 * > http://www.biocatalogue.org/soap_operations/18617 > http://www.biocatalogue.org/soap_operations/18618 > http://www.biocatalogue.org/soap_operations/18619 > http://www.biocatalogue.org/soap_operations/18620 > http://www.biocatalogue.org/soap_operations/18616 * > http://www.biocatalogue.org/soap_operations/18611 > http://www.biocatalogue.org/soap_operations/18612 > http://www.biocatalogue.org/soap_operations/18613 > http://www.biocatalogue.org/soap_operations/18614 > http://www.biocatalogue.org/soap_operations/18615 * > http://www.biocatalogue.org/soap_operations/18609 * > http://www.biocatalogue.org/soap_operations/18610 * > http://www.biocatalogue.org/soap_operations/18605 > http://www.biocatalogue.org/soap_operations/18606 > http://www.biocatalogue.org/soap_operations/18607 > http://www.biocatalogue.org/soap_operations/18608 > http://www.biocatalogue.org/soap_operations/18603 * > http://www.biocatalogue.org/soap_operations/18604 * > http://www.biocatalogue.org/soap_operations/18599 > http://www.biocatalogue.org/soap_operations/18600 > http://www.biocatalogue.org/soap_operations/18601 > http://www.biocatalogue.org/soap_operations/18602 > http://www.biocatalogue.org/soap_operations/18597 * > http://www.biocatalogue.org/soap_operations/18598 * > http://www.biocatalogue.org/soap_operations/18593 > http://www.biocatalogue.org/soap_operations/18594 > http://www.biocatalogue.org/soap_operations/18595 > http://www.biocatalogue.org/soap_operations/18596 > http://www.biocatalogue.org/soap_operations/18592 * > http://www.biocatalogue.org/soap_operations/18587 > http://www.biocatalogue.org/soap_operations/18588 > http://www.biocatalogue.org/soap_operations/18589 > http://www.biocatalogue.org/soap_operations/18590 > http://www.biocatalogue.org/soap_operations/18591 * > http://www.biocatalogue.org/soap_operations/18585 * > http://www.biocatalogue.org/soap_operations/18586 * > http://www.biocatalogue.org/soap_operations/18581 > http://www.biocatalogue.org/soap_operations/18582 > http://www.biocatalogue.org/soap_operations/18583 > http://www.biocatalogue.org/soap_operations/18584 > http://www.biocatalogue.org/soap_operations/18579 * > http://www.biocatalogue.org/soap_operations/18580 * > http://www.biocatalogue.org/soap_operations/18577 > http://www.biocatalogue.org/soap_operations/18578 > http://www.biocatalogue.org/soap_operations/18575 > http://www.biocatalogue.org/soap_operations/18576 > http://www.biocatalogue.org/soap_operations/18573 * > http://www.biocatalogue.org/soap_operations/18574 * > http://www.biocatalogue.org/soap_operations/18569 > http://www.biocatalogue.org/soap_operations/18570 > http://www.biocatalogue.org/soap_operations/18571 > http://www.biocatalogue.org/soap_operations/18572 > http://www.biocatalogue.org/soap_operations/18566 > http://www.biocatalogue.org/soap_operations/18567 * > http://www.biocatalogue.org/soap_operations/18568 * > http://www.biocatalogue.org/soap_operations/18563 > http://www.biocatalogue.org/soap_operations/18564 > http://www.biocatalogue.org/soap_operations/18565 > http://www.biocatalogue.org/soap_operations/18557 > http://www.biocatalogue.org/soap_operations/18558 > http://www.biocatalogue.org/soap_operations/18559 > http://www.biocatalogue.org/soap_operations/18560 > http://www.biocatalogue.org/soap_operations/18561 * > http://www.biocatalogue.org/soap_operations/18562 * > http://www.biocatalogue.org/soap_operations/18552 > http://www.biocatalogue.org/soap_operations/18553 > http://www.biocatalogue.org/soap_operations/18554 > http://www.biocatalogue.org/soap_operations/18555 * > http://www.biocatalogue.org/soap_operations/18556 * > http://www.biocatalogue.org/soap_operations/18551 > http://www.biocatalogue.org/soap_operations/18546 > http://www.biocatalogue.org/soap_operations/18547 > http://www.biocatalogue.org/soap_operations/18548 > http://www.biocatalogue.org/soap_operations/18549 * > http://www.biocatalogue.org/soap_operations/18550 * > http://www.biocatalogue.org/soap_operations/18545 > http://www.biocatalogue.org/soap_operations/18544 * > http://www.biocatalogue.org/soap_operations/18539 > http://www.biocatalogue.org/soap_operations/18540 > http://www.biocatalogue.org/soap_operations/18541 > http://www.biocatalogue.org/soap_operations/18542 > http://www.biocatalogue.org/soap_operations/18543 * > http://www.biocatalogue.org/soap_operations/18538 * > http://www.biocatalogue.org/soap_operations/18533 > http://www.biocatalogue.org/soap_operations/18534 > http://www.biocatalogue.org/soap_operations/18535 > http://www.biocatalogue.org/soap_operations/18536 > http://www.biocatalogue.org/soap_operations/18537 * > http://www.biocatalogue.org/soap_operations/18531 * > http://www.biocatalogue.org/soap_operations/18532 * > http://www.biocatalogue.org/soap_operations/18527 > http://www.biocatalogue.org/soap_operations/18528 > http://www.biocatalogue.org/soap_operations/18529 > http://www.biocatalogue.org/soap_operations/18530 > http://www.biocatalogue.org/soap_operations/18524 > http://www.biocatalogue.org/soap_operations/18525 * > http://www.biocatalogue.org/soap_operations/18526 * > http://www.biocatalogue.org/soap_operations/18521 > http://www.biocatalogue.org/soap_operations/18522 > http://www.biocatalogue.org/soap_operations/18523 > http://www.biocatalogue.org/soap_operations/18519 * > http://www.biocatalogue.org/soap_operations/18520 * > http://www.biocatalogue.org/soap_operations/18515 > http://www.biocatalogue.org/soap_operations/18516 > http://www.biocatalogue.org/soap_operations/18517 > http://www.biocatalogue.org/soap_operations/18518 > http://www.biocatalogue.org/soap_operations/18512 > http://www.biocatalogue.org/soap_operations/18513 * > http://www.biocatalogue.org/soap_operations/18514 * > http://www.biocatalogue.org/soap_operations/18509 > http://www.biocatalogue.org/soap_operations/18510 > http://www.biocatalogue.org/soap_operations/18511 > http://www.biocatalogue.org/soap_operations/18503 > http://www.biocatalogue.org/soap_operations/18504 > http://www.biocatalogue.org/soap_operations/18505 > http://www.biocatalogue.org/soap_operations/18506 > http://www.biocatalogue.org/soap_operations/18507 * > http://www.biocatalogue.org/soap_operations/18508 * > http://www.biocatalogue.org/soap_operations/18498 > http://www.biocatalogue.org/soap_operations/18499 > http://www.biocatalogue.org/soap_operations/18500 > http://www.biocatalogue.org/soap_operations/18501 * > http://www.biocatalogue.org/soap_operations/18502 * > http://www.biocatalogue.org/soap_operations/18497 > http://www.biocatalogue.org/soap_operations/18495 * > http://www.biocatalogue.org/soap_operations/18496 * > http://www.biocatalogue.org/soap_operations/18491 > http://www.biocatalogue.org/soap_operations/18492 > http://www.biocatalogue.org/soap_operations/18493 > http://www.biocatalogue.org/soap_operations/18494 > http://www.biocatalogue.org/soap_operations/18489 * > http://www.biocatalogue.org/soap_operations/18490 * > http://www.biocatalogue.org/soap_operations/18485 > http://www.biocatalogue.org/soap_operations/18486 > http://www.biocatalogue.org/soap_operations/18487 > http://www.biocatalogue.org/soap_operations/18488 > http://www.biocatalogue.org/soap_operations/18484 * > http://www.biocatalogue.org/soap_operations/18479 > http://www.biocatalogue.org/soap_operations/18480 > http://www.biocatalogue.org/soap_operations/18481 > http://www.biocatalogue.org/soap_operations/18482 > http://www.biocatalogue.org/soap_operations/18483 * > http://www.biocatalogue.org/soap_operations/18477 * > http://www.biocatalogue.org/soap_operations/18478 * > http://www.biocatalogue.org/soap_operations/18473 > http://www.biocatalogue.org/soap_operations/18474 > http://www.biocatalogue.org/soap_operations/18475 > http://www.biocatalogue.org/soap_operations/18476 > http://www.biocatalogue.org/soap_operations/18470 > http://www.biocatalogue.org/soap_operations/18471 * > http://www.biocatalogue.org/soap_operations/18472 * > http://www.biocatalogue.org/soap_operations/18467 > http://www.biocatalogue.org/soap_operations/18468 > http://www.biocatalogue.org/soap_operations/18469 > http://www.biocatalogue.org/soap_operations/18464 > http://www.biocatalogue.org/soap_operations/18465 * > http://www.biocatalogue.org/soap_operations/18466 * > http://www.biocatalogue.org/soap_operations/18461 > http://www.biocatalogue.org/soap_operations/18462 > http://www.biocatalogue.org/soap_operations/18463 > http://www.biocatalogue.org/soap_operations/18458 > http://www.biocatalogue.org/soap_operations/18459 * > http://www.biocatalogue.org/soap_operations/18460 * > http://www.biocatalogue.org/soap_operations/18455 > http://www.biocatalogue.org/soap_operations/18456 > http://www.biocatalogue.org/soap_operations/18457 > http://www.biocatalogue.org/soap_operations/18452 > http://www.biocatalogue.org/soap_operations/18453 * > http://www.biocatalogue.org/soap_operations/18454 * > http://www.biocatalogue.org/soap_operations/18449 > http://www.biocatalogue.org/soap_operations/18450 > http://www.biocatalogue.org/soap_operations/18451 > http://www.biocatalogue.org/soap_operations/18446 > http://www.biocatalogue.org/soap_operations/18447 * > http://www.biocatalogue.org/soap_operations/18448 * > http://www.biocatalogue.org/soap_operations/18443 > http://www.biocatalogue.org/soap_operations/18444 > http://www.biocatalogue.org/soap_operations/18445 > http://www.biocatalogue.org/soap_operations/18440 > http://www.biocatalogue.org/soap_operations/18441 * > http://www.biocatalogue.org/soap_operations/18442 * > http://www.biocatalogue.org/soap_operations/18437 > http://www.biocatalogue.org/soap_operations/18438 > http://www.biocatalogue.org/soap_operations/18439 > http://www.biocatalogue.org/soap_operations/18434 > http://www.biocatalogue.org/soap_operations/18435 * > http://www.biocatalogue.org/soap_operations/18436 * > http://www.biocatalogue.org/soap_operations/18431 > http://www.biocatalogue.org/soap_operations/18432 > http://www.biocatalogue.org/soap_operations/18433 > http://www.biocatalogue.org/soap_operations/18426 > http://www.biocatalogue.org/soap_operations/18427 > http://www.biocatalogue.org/soap_operations/18428 > http://www.biocatalogue.org/soap_operations/18429 * > http://www.biocatalogue.org/soap_operations/18430 * > http://www.biocatalogue.org/soap_operations/18425 > http://www.biocatalogue.org/soap_operations/18419 > http://www.biocatalogue.org/soap_operations/18420 > http://www.biocatalogue.org/soap_operations/18421 > http://www.biocatalogue.org/soap_operations/18422 > http://www.biocatalogue.org/soap_operations/18423 * > http://www.biocatalogue.org/soap_operations/18424 * > http://www.biocatalogue.org/soap_operations/18418 * > http://www.biocatalogue.org/soap_operations/18417 * > http://www.biocatalogue.org/soap_operations/18413 > http://www.biocatalogue.org/soap_operations/18414 > http://www.biocatalogue.org/soap_operations/18415 > http://www.biocatalogue.org/soap_operations/18416 > http://www.biocatalogue.org/soap_operations/18410 > http://www.biocatalogue.org/soap_operations/18411 * > http://www.biocatalogue.org/soap_operations/18412 * > http://www.biocatalogue.org/soap_operations/18407 > http://www.biocatalogue.org/soap_operations/18408 > http://www.biocatalogue.org/soap_operations/18409 > http://www.biocatalogue.org/soap_operations/18403 > http://www.biocatalogue.org/soap_operations/18404 > http://www.biocatalogue.org/soap_operations/18405 * > http://www.biocatalogue.org/soap_operations/18406 * > http://www.biocatalogue.org/soap_operations/18401 > http://www.biocatalogue.org/soap_operations/18402 > http://www.biocatalogue.org/soap_operations/18400 * > http://www.biocatalogue.org/soap_operations/18395 > http://www.biocatalogue.org/soap_operations/18396 > http://www.biocatalogue.org/soap_operations/18397 > http://www.biocatalogue.org/soap_operations/18398 > http://www.biocatalogue.org/soap_operations/18399 * > http://www.biocatalogue.org/soap_operations/18393 * > http://www.biocatalogue.org/soap_operations/18394 * > http://www.biocatalogue.org/soap_operations/18389 > http://www.biocatalogue.org/soap_operations/18390 > http://www.biocatalogue.org/soap_operations/18391 > http://www.biocatalogue.org/soap_operations/18392 > http://www.biocatalogue.org/soap_operations/18387 * > http://www.biocatalogue.org/soap_operations/18388 * > http://www.biocatalogue.org/soap_operations/18383 > http://www.biocatalogue.org/soap_operations/18384 > http://www.biocatalogue.org/soap_operations/18385 > http://www.biocatalogue.org/soap_operations/18386 > http://www.biocatalogue.org/soap_operations/18380 > http://www.biocatalogue.org/soap_operations/18381 * > http://www.biocatalogue.org/soap_operations/18382 * > http://www.biocatalogue.org/soap_operations/18377 > http://www.biocatalogue.org/soap_operations/18378 > http://www.biocatalogue.org/soap_operations/18379 > http://www.biocatalogue.org/soap_operations/18374 > http://www.biocatalogue.org/soap_operations/18375 * > http://www.biocatalogue.org/soap_operations/18376 * > http://www.biocatalogue.org/soap_operations/18371 > http://www.biocatalogue.org/soap_operations/18372 > http://www.biocatalogue.org/soap_operations/18373 > http://www.biocatalogue.org/soap_operations/18365 > http://www.biocatalogue.org/soap_operations/18366 > http://www.biocatalogue.org/soap_operations/18367 > http://www.biocatalogue.org/soap_operations/18368 > http://www.biocatalogue.org/soap_operations/18369 * > http://www.biocatalogue.org/soap_operations/18370 * > http://www.biocatalogue.org/soap_operations/18364 * > http://www.biocatalogue.org/soap_operations/18359 > http://www.biocatalogue.org/soap_operations/18360 > http://www.biocatalogue.org/soap_operations/18361 > http://www.biocatalogue.org/soap_operations/18362 > http://www.biocatalogue.org/soap_operations/18363 * > http://www.biocatalogue.org/soap_operations/18353 > http://www.biocatalogue.org/soap_operations/18354 > http://www.biocatalogue.org/soap_operations/18355 > http://www.biocatalogue.org/soap_operations/18356 > http://www.biocatalogue.org/soap_operations/18357 * > http://www.biocatalogue.org/soap_operations/18358 * > http://www.biocatalogue.org/soap_operations/18350 > http://www.biocatalogue.org/soap_operations/18351 * > http://www.biocatalogue.org/soap_operations/18352 * > http://www.biocatalogue.org/soap_operations/18347 > http://www.biocatalogue.org/soap_operations/18348 > http://www.biocatalogue.org/soap_operations/18349 > http://www.biocatalogue.org/soap_operations/18344 > http://www.biocatalogue.org/soap_operations/18345 * > http://www.biocatalogue.org/soap_operations/18346 * > http://www.biocatalogue.org/soap_operations/18341 > http://www.biocatalogue.org/soap_operations/18342 > http://www.biocatalogue.org/soap_operations/18343 > http://www.biocatalogue.org/soap_operations/18338 > http://www.biocatalogue.org/soap_operations/18339 * > http://www.biocatalogue.org/soap_operations/18340 * > http://www.biocatalogue.org/soap_operations/18335 > http://www.biocatalogue.org/soap_operations/18336 > http://www.biocatalogue.org/soap_operations/18337 > http://www.biocatalogue.org/soap_operations/18332 > http://www.biocatalogue.org/soap_operations/18333 * > http://www.biocatalogue.org/soap_operations/18334 * > http://www.biocatalogue.org/soap_operations/18329 > http://www.biocatalogue.org/soap_operations/18330 > http://www.biocatalogue.org/soap_operations/18331 > http://www.biocatalogue.org/soap_operations/18326 > http://www.biocatalogue.org/soap_operations/18327 * > http://www.biocatalogue.org/soap_operations/18328 * > http://www.biocatalogue.org/soap_operations/18323 > http://www.biocatalogue.org/soap_operations/18324 > http://www.biocatalogue.org/soap_operations/18325 > http://www.biocatalogue.org/soap_operations/18320 > http://www.biocatalogue.org/soap_operations/18321 * > http://www.biocatalogue.org/soap_operations/18322 * > http://www.biocatalogue.org/soap_operations/18317 > http://www.biocatalogue.org/soap_operations/18318 > http://www.biocatalogue.org/soap_operations/18319 > http://www.biocatalogue.org/soap_operations/18314 > http://www.biocatalogue.org/soap_operations/18315 * > http://www.biocatalogue.org/soap_operations/18316 * > http://www.biocatalogue.org/soap_operations/18311 > http://www.biocatalogue.org/soap_operations/18312 > http://www.biocatalogue.org/soap_operations/18313 > http://www.biocatalogue.org/soap_operations/18308 > http://www.biocatalogue.org/soap_operations/18309 * > http://www.biocatalogue.org/soap_operations/18310 * > http://www.biocatalogue.org/soap_operations/18305 > http://www.biocatalogue.org/soap_operations/18306 > http://www.biocatalogue.org/soap_operations/18307 > http://www.biocatalogue.org/soap_operations/18302 > http://www.biocatalogue.org/soap_operations/18303 * > http://www.biocatalogue.org/soap_operations/18304 * > http://www.biocatalogue.org/soap_operations/18299 > http://www.biocatalogue.org/soap_operations/18300 > http://www.biocatalogue.org/soap_operations/18301 > http://www.biocatalogue.org/soap_operations/18296 > http://www.biocatalogue.org/soap_operations/18297 * > http://www.biocatalogue.org/soap_operations/18298 * > http://www.biocatalogue.org/soap_operations/18293 > http://www.biocatalogue.org/soap_operations/18294 > http://www.biocatalogue.org/soap_operations/18295 > http://www.biocatalogue.org/soap_operations/18287 > http://www.biocatalogue.org/soap_operations/18288 > http://www.biocatalogue.org/soap_operations/18289 > http://www.biocatalogue.org/soap_operations/18290 > http://www.biocatalogue.org/soap_operations/18291 * > http://www.biocatalogue.org/soap_operations/18292 * > http://www.biocatalogue.org/soap_operations/18284 > http://www.biocatalogue.org/soap_operations/18285 * > http://www.biocatalogue.org/soap_operations/18286 * > http://www.biocatalogue.org/soap_operations/18281 > http://www.biocatalogue.org/soap_operations/18282 > http://www.biocatalogue.org/soap_operations/18283 > http://www.biocatalogue.org/soap_operations/18280 * > http://www.biocatalogue.org/soap_operations/18275 > http://www.biocatalogue.org/soap_operations/18276 > http://www.biocatalogue.org/soap_operations/18277 > http://www.biocatalogue.org/soap_operations/18278 > http://www.biocatalogue.org/soap_operations/18279 * > http://www.biocatalogue.org/soap_operations/18274 * > http://www.biocatalogue.org/soap_operations/18269 > http://www.biocatalogue.org/soap_operations/18270 > http://www.biocatalogue.org/soap_operations/18271 > http://www.biocatalogue.org/soap_operations/18272 > http://www.biocatalogue.org/soap_operations/18273 * > http://www.biocatalogue.org/soap_operations/18268 * > http://www.biocatalogue.org/soap_operations/18263 > http://www.biocatalogue.org/soap_operations/18264 > http://www.biocatalogue.org/soap_operations/18265 > http://www.biocatalogue.org/soap_operations/18266 > http://www.biocatalogue.org/soap_operations/18267 * > http://www.biocatalogue.org/soap_operations/18260 > http://www.biocatalogue.org/soap_operations/18261 * > http://www.biocatalogue.org/soap_operations/18262 * > http://www.biocatalogue.org/soap_operations/18257 > http://www.biocatalogue.org/soap_operations/18258 > http://www.biocatalogue.org/soap_operations/18259 > http://www.biocatalogue.org/soap_operations/18254 > http://www.biocatalogue.org/soap_operations/18255 * > http://www.biocatalogue.org/soap_operations/18256 * > http://www.biocatalogue.org/soap_operations/18251 > http://www.biocatalogue.org/soap_operations/18252 > http://www.biocatalogue.org/soap_operations/18253 > http://www.biocatalogue.org/soap_operations/18247 > http://www.biocatalogue.org/soap_operations/18248 > http://www.biocatalogue.org/soap_operations/18249 * > http://www.biocatalogue.org/soap_operations/18250 * > http://www.biocatalogue.org/soap_operations/18245 > http://www.biocatalogue.org/soap_operations/18246 > http://www.biocatalogue.org/soap_operations/18239 > http://www.biocatalogue.org/soap_operations/18240 > http://www.biocatalogue.org/soap_operations/18241 > http://www.biocatalogue.org/soap_operations/18242 > http://www.biocatalogue.org/soap_operations/18243 * > http://www.biocatalogue.org/soap_operations/18244 * > http://www.biocatalogue.org/soap_operations/18238 * > http://www.biocatalogue.org/soap_operations/18233 > http://www.biocatalogue.org/soap_operations/18234 > http://www.biocatalogue.org/soap_operations/18235 > http://www.biocatalogue.org/soap_operations/18236 > http://www.biocatalogue.org/soap_operations/18237 * > http://www.biocatalogue.org/soap_operations/18228 > http://www.biocatalogue.org/soap_operations/18229 > http://www.biocatalogue.org/soap_operations/18230 > http://www.biocatalogue.org/soap_operations/18231 * > http://www.biocatalogue.org/soap_operations/18232 * > http://www.biocatalogue.org/soap_operations/18227 > http://www.biocatalogue.org/soap_operations/18226 * > http://www.biocatalogue.org/soap_operations/18221 > http://www.biocatalogue.org/soap_operations/18222 > http://www.biocatalogue.org/soap_operations/18223 > http://www.biocatalogue.org/soap_operations/18224 > http://www.biocatalogue.org/soap_operations/18225 * > http://www.biocatalogue.org/soap_operations/18218 > http://www.biocatalogue.org/soap_operations/18219 * > http://www.biocatalogue.org/soap_operations/18220 * > http://www.biocatalogue.org/soap_operations/18215 > http://www.biocatalogue.org/soap_operations/18216 > http://www.biocatalogue.org/soap_operations/18217 > http://www.biocatalogue.org/soap_operations/18211 > http://www.biocatalogue.org/soap_operations/18212 > http://www.biocatalogue.org/soap_operations/18213 * > http://www.biocatalogue.org/soap_operations/18214 * > http://www.biocatalogue.org/soap_operations/18209 > http://www.biocatalogue.org/soap_operations/18210 > http://www.biocatalogue.org/soap_operations/18203 > http://www.biocatalogue.org/soap_operations/18204 > http://www.biocatalogue.org/soap_operations/18205 > http://www.biocatalogue.org/soap_operations/18206 > http://www.biocatalogue.org/soap_operations/18207 * > http://www.biocatalogue.org/soap_operations/18208 * > http://www.biocatalogue.org/soap_operations/18201 * > http://www.biocatalogue.org/soap_operations/18202 * > http://www.biocatalogue.org/soap_operations/18197 > http://www.biocatalogue.org/soap_operations/18198 > http://www.biocatalogue.org/soap_operations/18199 > http://www.biocatalogue.org/soap_operations/18200 > http://www.biocatalogue.org/soap_operations/18191 > http://www.biocatalogue.org/soap_operations/18192 > http://www.biocatalogue.org/soap_operations/18193 > http://www.biocatalogue.org/soap_operations/18194 > http://www.biocatalogue.org/soap_operations/18195 * > http://www.biocatalogue.org/soap_operations/18196 * > http://www.biocatalogue.org/soap_operations/18185 > http://www.biocatalogue.org/soap_operations/18186 > http://www.biocatalogue.org/soap_operations/18187 > http://www.biocatalogue.org/soap_operations/18188 > http://www.biocatalogue.org/soap_operations/18189 * > http://www.biocatalogue.org/soap_operations/18190 * > http://www.biocatalogue.org/soap_operations/18184 * > http://www.biocatalogue.org/soap_operations/18179 > http://www.biocatalogue.org/soap_operations/18180 > http://www.biocatalogue.org/soap_operations/18181 > http://www.biocatalogue.org/soap_operations/18182 > http://www.biocatalogue.org/soap_operations/18183 * > http://www.biocatalogue.org/soap_operations/18176 > http://www.biocatalogue.org/soap_operations/18177 * > http://www.biocatalogue.org/soap_operations/18178 * > http://www.biocatalogue.org/soap_operations/18173 > http://www.biocatalogue.org/soap_operations/18174 > http://www.biocatalogue.org/soap_operations/18175 > http://www.biocatalogue.org/soap_operations/18170 > http://www.biocatalogue.org/soap_operations/18171 * > http://www.biocatalogue.org/soap_operations/18172 * > http://www.biocatalogue.org/soap_operations/18167 > http://www.biocatalogue.org/soap_operations/18168 > http://www.biocatalogue.org/soap_operations/18169 > http://www.biocatalogue.org/soap_operations/18164 > http://www.biocatalogue.org/soap_operations/18165 * > http://www.biocatalogue.org/soap_operations/18166 * > http://www.biocatalogue.org/soap_operations/18161 > http://www.biocatalogue.org/soap_operations/18162 > http://www.biocatalogue.org/soap_operations/18163 > http://www.biocatalogue.org/soap_operations/18157 > http://www.biocatalogue.org/soap_operations/18158 > http://www.biocatalogue.org/soap_operations/18159 * > http://www.biocatalogue.org/soap_operations/18160 * > http://www.biocatalogue.org/soap_operations/18155 > http://www.biocatalogue.org/soap_operations/18156 > http://www.biocatalogue.org/soap_operations/18150 > http://www.biocatalogue.org/soap_operations/18151 > http://www.biocatalogue.org/soap_operations/18152 > http://www.biocatalogue.org/soap_operations/18153 * > http://www.biocatalogue.org/soap_operations/18154 * > http://www.biocatalogue.org/soap_operations/18149 > http://www.biocatalogue.org/soap_operations/18143 > http://www.biocatalogue.org/soap_operations/18144 > http://www.biocatalogue.org/soap_operations/18145 > http://www.biocatalogue.org/soap_operations/18146 > http://www.biocatalogue.org/soap_operations/18147 * > http://www.biocatalogue.org/soap_operations/18148 * > http://www.biocatalogue.org/soap_operations/18138 > http://www.biocatalogue.org/soap_operations/18139 > http://www.biocatalogue.org/soap_operations/18140 > http://www.biocatalogue.org/soap_operations/18141 * > http://www.biocatalogue.org/soap_operations/18142 * > http://www.biocatalogue.org/soap_operations/18137 > http://www.biocatalogue.org/soap_operations/18131 > http://www.biocatalogue.org/soap_operations/18132 > http://www.biocatalogue.org/soap_operations/18133 > http://www.biocatalogue.org/soap_operations/18134 > http://www.biocatalogue.org/soap_operations/18135 * > http://www.biocatalogue.org/soap_operations/18136 * > http://www.biocatalogue.org/soap_operations/18125 > http://www.biocatalogue.org/soap_operations/18126 > http://www.biocatalogue.org/soap_operations/18127 > http://www.biocatalogue.org/soap_operations/18128 > http://www.biocatalogue.org/soap_operations/18129 * > http://www.biocatalogue.org/soap_operations/18130 * > http://www.biocatalogue.org/soap_operations/18120 > http://www.biocatalogue.org/soap_operations/18121 > http://www.biocatalogue.org/soap_operations/18122 > http://www.biocatalogue.org/soap_operations/18123 * > http://www.biocatalogue.org/soap_operations/18124 * > http://www.biocatalogue.org/soap_operations/18119 > http://www.biocatalogue.org/soap_operations/18114 > http://www.biocatalogue.org/soap_operations/18115 > http://www.biocatalogue.org/soap_operations/18116 > http://www.biocatalogue.org/soap_operations/18117 * > http://www.biocatalogue.org/soap_operations/18118 * > http://www.biocatalogue.org/soap_operations/18113 > http://www.biocatalogue.org/soap_operations/18109 > http://www.biocatalogue.org/soap_operations/18110 > http://www.biocatalogue.org/soap_operations/18111 * > http://www.biocatalogue.org/soap_operations/18112 * > http://www.biocatalogue.org/soap_operations/18107 > http://www.biocatalogue.org/soap_operations/18108 > http://www.biocatalogue.org/soap_operations/18103 * > http://www.biocatalogue.org/soap_operations/18104 * > http://www.biocatalogue.org/soap_operations/18105 * > http://www.biocatalogue.org/soap_operations/18106 * > http://www.biocatalogue.org/soap_operations/18096 * > http://www.biocatalogue.org/soap_operations/18097 * > http://www.biocatalogue.org/soap_operations/18098 * > http://www.biocatalogue.org/soap_operations/18099 * > http://www.biocatalogue.org/soap_operations/18100 * > http://www.biocatalogue.org/soap_operations/18101 * > http://www.biocatalogue.org/soap_operations/18102 * > http://www.biocatalogue.org/soap_operations/18092 * > http://www.biocatalogue.org/soap_operations/18093 * > http://www.biocatalogue.org/soap_operations/18094 * > http://www.biocatalogue.org/soap_operations/18095 * > http://www.biocatalogue.org/soap_operations/18088 * > http://www.biocatalogue.org/soap_operations/18089 * > http://www.biocatalogue.org/soap_operations/18090 * > http://www.biocatalogue.org/soap_operations/18091 * > http://www.biocatalogue.org/soap_operations/18079 * > http://www.biocatalogue.org/soap_operations/18080 * > http://www.biocatalogue.org/soap_operations/18081 * > http://www.biocatalogue.org/soap_operations/18082 * > http://www.biocatalogue.org/soap_operations/18083 * > http://www.biocatalogue.org/soap_operations/18084 * > http://www.biocatalogue.org/soap_operations/18085 * > http://www.biocatalogue.org/soap_operations/18086 * > http://www.biocatalogue.org/soap_operations/18087 * > http://www.biocatalogue.org/soap_operations/18077 * > http://www.biocatalogue.org/soap_operations/18078 * > http://www.biocatalogue.org/soap_operations/18076 > http://www.biocatalogue.org/soap_operations/18072 > http://www.biocatalogue.org/soap_operations/18073 > http://www.biocatalogue.org/soap_operations/18074 > http://www.biocatalogue.org/soap_operations/18075 > http://www.biocatalogue.org/soap_operations/18068 > http://www.biocatalogue.org/soap_operations/18069 > http://www.biocatalogue.org/soap_operations/18070 * > http://www.biocatalogue.org/soap_operations/18071 * > http://www.biocatalogue.org/soap_operations/18066 > http://www.biocatalogue.org/soap_operations/18067 > http://www.biocatalogue.org/soap_operations/18060 > http://www.biocatalogue.org/soap_operations/18061 > http://www.biocatalogue.org/soap_operations/18062 > http://www.biocatalogue.org/soap_operations/18063 > http://www.biocatalogue.org/soap_operations/18064 * > http://www.biocatalogue.org/soap_operations/18065 * > http://www.biocatalogue.org/soap_operations/18058 * > http://www.biocatalogue.org/soap_operations/18059 * > http://www.biocatalogue.org/soap_operations/18054 > http://www.biocatalogue.org/soap_operations/18055 > http://www.biocatalogue.org/soap_operations/18056 > http://www.biocatalogue.org/soap_operations/18057 > http://www.biocatalogue.org/soap_operations/18051 > http://www.biocatalogue.org/soap_operations/18052 * > http://www.biocatalogue.org/soap_operations/18053 * > http://www.biocatalogue.org/soap_operations/18048 > http://www.biocatalogue.org/soap_operations/18049 > http://www.biocatalogue.org/soap_operations/18050 > http://www.biocatalogue.org/soap_operations/18045 > http://www.biocatalogue.org/soap_operations/18046 * > http://www.biocatalogue.org/soap_operations/18047 * > http://www.biocatalogue.org/soap_operations/18042 > http://www.biocatalogue.org/soap_operations/18043 > http://www.biocatalogue.org/soap_operations/18044 > http://www.biocatalogue.org/soap_operations/18036 > http://www.biocatalogue.org/soap_operations/18037 > http://www.biocatalogue.org/soap_operations/18038 > http://www.biocatalogue.org/soap_operations/18039 > http://www.biocatalogue.org/soap_operations/18040 * > http://www.biocatalogue.org/soap_operations/18041 * > http://www.biocatalogue.org/soap_operations/18034 * > http://www.biocatalogue.org/soap_operations/18035 * > http://www.biocatalogue.org/soap_operations/18030 > http://www.biocatalogue.org/soap_operations/18031 > http://www.biocatalogue.org/soap_operations/18032 > http://www.biocatalogue.org/soap_operations/18033 > http://www.biocatalogue.org/soap_operations/18028 * > http://www.biocatalogue.org/soap_operations/18029 * > http://www.biocatalogue.org/soap_operations/18024 > http://www.biocatalogue.org/soap_operations/18025 > http://www.biocatalogue.org/soap_operations/18026 > http://www.biocatalogue.org/soap_operations/18027 > http://www.biocatalogue.org/soap_operations/18023 * > http://www.biocatalogue.org/soap_operations/18018 > http://www.biocatalogue.org/soap_operations/18019 > http://www.biocatalogue.org/soap_operations/18020 > http://www.biocatalogue.org/soap_operations/18021 > http://www.biocatalogue.org/soap_operations/18022 * > http://www.biocatalogue.org/soap_operations/18015 > http://www.biocatalogue.org/soap_operations/18016 * > http://www.biocatalogue.org/soap_operations/18017 * > http://www.biocatalogue.org/soap_operations/18012 > http://www.biocatalogue.org/soap_operations/18013 > http://www.biocatalogue.org/soap_operations/18014 > http://www.biocatalogue.org/soap_operations/18009 > http://www.biocatalogue.org/soap_operations/18010 * > http://www.biocatalogue.org/soap_operations/18011 * > http://www.biocatalogue.org/soap_operations/18006 > http://www.biocatalogue.org/soap_operations/18007 > http://www.biocatalogue.org/soap_operations/18008 > http://www.biocatalogue.org/soap_operations/18000 > http://www.biocatalogue.org/soap_operations/18001 > http://www.biocatalogue.org/soap_operations/18002 > http://www.biocatalogue.org/soap_operations/18003 > http://www.biocatalogue.org/soap_operations/18004 * > http://www.biocatalogue.org/soap_operations/18005 * > http://www.biocatalogue.org/soap_operations/17999 * > http://www.biocatalogue.org/soap_operations/17994 > http://www.biocatalogue.org/soap_operations/17995 > http://www.biocatalogue.org/soap_operations/17996 > http://www.biocatalogue.org/soap_operations/17997 > http://www.biocatalogue.org/soap_operations/17998 * > http://www.biocatalogue.org/soap_operations/17991 > http://www.biocatalogue.org/soap_operations/17992 * > http://www.biocatalogue.org/soap_operations/17993 * > http://www.biocatalogue.org/soap_operations/17988 > http://www.biocatalogue.org/soap_operations/17989 > http://www.biocatalogue.org/soap_operations/17990 > http://www.biocatalogue.org/soap_operations/17986 * > http://www.biocatalogue.org/soap_operations/17987 * > http://www.biocatalogue.org/soap_operations/17982 > http://www.biocatalogue.org/soap_operations/17983 > http://www.biocatalogue.org/soap_operations/17984 > http://www.biocatalogue.org/soap_operations/17985 > http://www.biocatalogue.org/soap_operations/17979 > http://www.biocatalogue.org/soap_operations/17980 * > http://www.biocatalogue.org/soap_operations/17981 * > http://www.biocatalogue.org/soap_operations/17976 > http://www.biocatalogue.org/soap_operations/17977 > http://www.biocatalogue.org/soap_operations/17978 > http://www.biocatalogue.org/soap_operations/17973 > http://www.biocatalogue.org/soap_operations/17974 * > http://www.biocatalogue.org/soap_operations/17975 * > http://www.biocatalogue.org/soap_operations/17970 > http://www.biocatalogue.org/soap_operations/17971 > http://www.biocatalogue.org/soap_operations/17972 > http://www.biocatalogue.org/soap_operations/17968 * > http://www.biocatalogue.org/soap_operations/17969 * > http://www.biocatalogue.org/soap_operations/17964 > http://www.biocatalogue.org/soap_operations/17965 > http://www.biocatalogue.org/soap_operations/17966 > http://www.biocatalogue.org/soap_operations/17967 > http://www.biocatalogue.org/soap_operations/17961 > http://www.biocatalogue.org/soap_operations/17962 * > http://www.biocatalogue.org/soap_operations/17963 * > http://www.biocatalogue.org/soap_operations/17958 > http://www.biocatalogue.org/soap_operations/17959 > http://www.biocatalogue.org/soap_operations/17960 > http://www.biocatalogue.org/soap_operations/17955 > http://www.biocatalogue.org/soap_operations/17956 * > http://www.biocatalogue.org/soap_operations/17957 * > http://www.biocatalogue.org/soap_operations/17952 > http://www.biocatalogue.org/soap_operations/17953 > http://www.biocatalogue.org/soap_operations/17954 > http://www.biocatalogue.org/soap_operations/17946 > http://www.biocatalogue.org/soap_operations/17947 > http://www.biocatalogue.org/soap_operations/17948 > http://www.biocatalogue.org/soap_operations/17949 > http://www.biocatalogue.org/soap_operations/17950 * > http://www.biocatalogue.org/soap_operations/17951 * > http://www.biocatalogue.org/soap_operations/17941 > http://www.biocatalogue.org/soap_operations/17942 > http://www.biocatalogue.org/soap_operations/17943 > http://www.biocatalogue.org/soap_operations/17944 * > http://www.biocatalogue.org/soap_operations/17945 * > http://www.biocatalogue.org/soap_operations/17940 > http://www.biocatalogue.org/soap_operations/17939 * > http://www.biocatalogue.org/soap_operations/17934 > http://www.biocatalogue.org/soap_operations/17935 > http://www.biocatalogue.org/soap_operations/17936 > http://www.biocatalogue.org/soap_operations/17937 > http://www.biocatalogue.org/soap_operations/17938 * > http://www.biocatalogue.org/soap_operations/17931 > http://www.biocatalogue.org/soap_operations/17932 * > http://www.biocatalogue.org/soap_operations/17933 * > http://www.biocatalogue.org/soap_operations/17928 > http://www.biocatalogue.org/soap_operations/17929 > http://www.biocatalogue.org/soap_operations/17930 > http://www.biocatalogue.org/soap_operations/17927 * > http://www.biocatalogue.org/soap_operations/17922 > http://www.biocatalogue.org/soap_operations/17923 > http://www.biocatalogue.org/soap_operations/17924 > http://www.biocatalogue.org/soap_operations/17925 > http://www.biocatalogue.org/soap_operations/17926 * > http://www.biocatalogue.org/soap_operations/17920 * > http://www.biocatalogue.org/soap_operations/17921 * > http://www.biocatalogue.org/soap_operations/17916 > http://www.biocatalogue.org/soap_operations/17917 > http://www.biocatalogue.org/soap_operations/17918 > http://www.biocatalogue.org/soap_operations/17919 > http://www.biocatalogue.org/soap_operations/17910 > http://www.biocatalogue.org/soap_operations/17911 > http://www.biocatalogue.org/soap_operations/17912 > http://www.biocatalogue.org/soap_operations/17913 > http://www.biocatalogue.org/soap_operations/17914 * > http://www.biocatalogue.org/soap_operations/17915 * > http://www.biocatalogue.org/soap_operations/17909 * > http://www.biocatalogue.org/soap_operations/17906 > http://www.biocatalogue.org/soap_operations/17907 > http://www.biocatalogue.org/soap_operations/17908 * > http://www.biocatalogue.org/soap_operations/17904 > http://www.biocatalogue.org/soap_operations/17905 > http://www.biocatalogue.org/soap_operations/17900 > http://www.biocatalogue.org/soap_operations/17901 > http://www.biocatalogue.org/soap_operations/17902 * > http://www.biocatalogue.org/soap_operations/17903 * > http://www.biocatalogue.org/soap_operations/17898 > http://www.biocatalogue.org/soap_operations/17899 > http://www.biocatalogue.org/soap_operations/17892 > http://www.biocatalogue.org/soap_operations/17893 > http://www.biocatalogue.org/soap_operations/17894 > http://www.biocatalogue.org/soap_operations/17895 > http://www.biocatalogue.org/soap_operations/17896 * > http://www.biocatalogue.org/soap_operations/17897 * > http://www.biocatalogue.org/soap_operations/17891 * > http://www.biocatalogue.org/soap_operations/17888 > http://www.biocatalogue.org/soap_operations/17889 > http://www.biocatalogue.org/soap_operations/17890 * > http://www.biocatalogue.org/soap_operations/17886 > http://www.biocatalogue.org/soap_operations/17887 > http://www.biocatalogue.org/soap_operations/17885 * > http://www.biocatalogue.org/soap_operations/17880 > http://www.biocatalogue.org/soap_operations/17881 > http://www.biocatalogue.org/soap_operations/17882 > http://www.biocatalogue.org/soap_operations/17883 > http://www.biocatalogue.org/soap_operations/17884 * > http://www.biocatalogue.org/soap_operations/17877 > http://www.biocatalogue.org/soap_operations/17878 * > http://www.biocatalogue.org/soap_operations/17879 * > http://www.biocatalogue.org/soap_operations/17874 > http://www.biocatalogue.org/soap_operations/17875 > http://www.biocatalogue.org/soap_operations/17876 > http://www.biocatalogue.org/soap_operations/17871 > http://www.biocatalogue.org/soap_operations/17872 * > http://www.biocatalogue.org/soap_operations/17873 * > http://www.biocatalogue.org/soap_operations/17868 > http://www.biocatalogue.org/soap_operations/17869 > http://www.biocatalogue.org/soap_operations/17870 > http://www.biocatalogue.org/soap_operations/17865 > http://www.biocatalogue.org/soap_operations/17866 * > http://www.biocatalogue.org/soap_operations/17867 * > http://www.biocatalogue.org/soap_operations/17862 > http://www.biocatalogue.org/soap_operations/17863 > http://www.biocatalogue.org/soap_operations/17864 > http://www.biocatalogue.org/soap_operations/17857 > http://www.biocatalogue.org/soap_operations/17858 > http://www.biocatalogue.org/soap_operations/17859 > http://www.biocatalogue.org/soap_operations/17860 * > http://www.biocatalogue.org/soap_operations/17861 * > http://www.biocatalogue.org/soap_operations/17856 > http://www.biocatalogue.org/soap_operations/17855 * > http://www.biocatalogue.org/soap_operations/17850 > http://www.biocatalogue.org/soap_operations/17851 > http://www.biocatalogue.org/soap_operations/17852 > http://www.biocatalogue.org/soap_operations/17853 > http://www.biocatalogue.org/soap_operations/17854 * > http://www.biocatalogue.org/soap_operations/17848 * > http://www.biocatalogue.org/soap_operations/17849 * > http://www.biocatalogue.org/soap_operations/17844 > http://www.biocatalogue.org/soap_operations/17845 > http://www.biocatalogue.org/soap_operations/17846 > http://www.biocatalogue.org/soap_operations/17847 > http://www.biocatalogue.org/soap_operations/17842 * > http://www.biocatalogue.org/soap_operations/17843 * > http://www.biocatalogue.org/soap_operations/17838 > http://www.biocatalogue.org/soap_operations/17839 > http://www.biocatalogue.org/soap_operations/17840 > http://www.biocatalogue.org/soap_operations/17841 > http://www.biocatalogue.org/soap_operations/17835 > http://www.biocatalogue.org/soap_operations/17836 * > http://www.biocatalogue.org/soap_operations/17837 * > http://www.biocatalogue.org/soap_operations/17832 > http://www.biocatalogue.org/soap_operations/17833 > http://www.biocatalogue.org/soap_operations/17834 > http://www.biocatalogue.org/soap_operations/17829 > http://www.biocatalogue.org/soap_operations/17830 * > http://www.biocatalogue.org/soap_operations/17831 * > http://www.biocatalogue.org/soap_operations/17826 > http://www.biocatalogue.org/soap_operations/17827 > http://www.biocatalogue.org/soap_operations/17828 > http://www.biocatalogue.org/soap_operations/17823 > http://www.biocatalogue.org/soap_operations/17824 * > http://www.biocatalogue.org/soap_operations/17825 * > http://www.biocatalogue.org/soap_operations/17820 > http://www.biocatalogue.org/soap_operations/17821 > http://www.biocatalogue.org/soap_operations/17822 > http://www.biocatalogue.org/soap_operations/17817 > http://www.biocatalogue.org/soap_operations/17818 * > http://www.biocatalogue.org/soap_operations/17819 * > http://www.biocatalogue.org/soap_operations/17814 > http://www.biocatalogue.org/soap_operations/17815 > http://www.biocatalogue.org/soap_operations/17816 > http://www.biocatalogue.org/soap_operations/17811 > http://www.biocatalogue.org/soap_operations/17812 * > http://www.biocatalogue.org/soap_operations/17813 * > http://www.biocatalogue.org/soap_operations/17808 > http://www.biocatalogue.org/soap_operations/17809 > http://www.biocatalogue.org/soap_operations/17810 > http://www.biocatalogue.org/soap_operations/17804 > http://www.biocatalogue.org/soap_operations/17805 > http://www.biocatalogue.org/soap_operations/17806 * > http://www.biocatalogue.org/soap_operations/17807 * > http://www.biocatalogue.org/soap_operatio > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Tue Jun 1 11:52:12 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 1 Jun 2010 16:52:12 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: <4C0524F3.1020700@cs.man.ac.uk> References: <4C04DF73.2090100@ebi.ac.uk> <4C04E9A5.8050704@cs.man.ac.uk> <4C050783.90702@ebi.ac.uk> <4C051C76.2000702@cs.man.ac.uk> <4C0524F3.1020700@cs.man.ac.uk> Message-ID: >Do you want a curation page for "Copy annotations from operation X to operation Y"? Please, if you can...that will help a lot. Cheers, Franck On 1 June 2010 16:19, Jiten Bhagat wrote: > Franck Tanoh wrote: > > >The best I can do is the attached list of URLs (also in Dropbox) for the > > >SOAP operations that have been created in the last week. There are 1892 > > >in total (!). > > that's a lot for a week! looks like the service update checker is the > > guilty one :-) > > A first glance reveals loads of archived operations. > > Yeah. There are 107 archived operations. > > Do you want a curation page for "Copy annotations from operation X to > operation Y"? > > Jits > > > > > Thanks > > Franck > > > > an.ac.uk > wrote: > > > > Hi Franck, > > > > The best I can do is the attached list of URLs (also in Dropbox) > > for the > > SOAP operations that have been created in the last week. There are > > 1892 > > in total (!). I've added a star (*) after each one that DOES NOT have > > any description (of which there are 664). > > > > Jits > > > > > > Franck Tanoh wrote: > > > >What I can think of is that the data has considerably changed > since > > > the last report mostly due to the update checker. It is entirely > > > possible that new operations >have been found that are not > necessary > > > annotated at the same level as the previously existing ones. > > > Is it possible to do a diff between those 2 results ( 1095 vs > > 839) so > > > that I can double check if that's the case. It will also help me to > > > transfer some of the old descriptions to new operations, inputs > etc. > > > > > > Cheers, > > > Franck > > > > > > On 1 June 2010 14:13, Eric Nzuobontane > > > > >> wrote: > > > > > > What I can think of is that the data has considerably changed > > > since the last report mostly due to the update checker. It is > > > entirely possible that new operations have been found that > > are not > > > necessary annotated at the same level as the previously > > existing ones. > > > > > > Eric > > > > > > > > > Franck Tanoh wrote: > > > > > > Hi Jits, > > > > > > Thanks for the report. > > > > > > It doesn't really look right when I compare it to the > > previous > > > one: > > > > > > < > > 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>> > > > > > > In the previous report we had 1095 services with > description > > > and with all operation annotated. I don't understand why > we > > > have now 839. > > > Also there are 34 instead of 38 services with > > descriptions at > > > the service, operation and parameter level. > > > > > > Cheers, > > > Franck > > > > > > On 1 June 2010 12:06, Jiten Bhagat > > > > > > > > > > >>> > > wrote: > > > > > > Franck, > > > > > > Here is the report: > > > > > > Total SOAP Services: 1636 > > > A. How many SOAP Services have a description? 1449 > > > B. How many SOAP Services have a description AND a > > > documentation > > > URL? 898 > > > C. How many SOAP Services have a description AND all > > > operations have a > > > description? 839 > > > D. How many SOAP Services have a description AND all > > > operations have a > > > description and ALL inputs/outputs have a description? > 34 > > > 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 > > > > > > Does that look right to you? > > > > > > Jits > > > > > > > > > Eric Nzuobontane wrote: > > > > I will put that in drop box. When are you going out to > > > Denmark? > > > > > > > > Eric > > > > > > > > > > > > Franck Tanoh wrote: > > > >> Hi Eric, > > > >> > > > >> Hope you had a good break > > > >> > > > >> Can you send the latest (from today) data dump to > Jits > > > so that > > > he can > > > >> produce the annotations stats, pls? > > > >> > > > >> Cheers, > > > >> Franck > > > >> > > > >> -- > > > >> "Science knows no country, because knowledge > > belongs to > > > humanity, and > > > >> is the torch which illuminates the world." - Louis > > Pasteur > > > >> > > > > > > > > > ------------------------------------------------------------------------ > > > >> > > > >> _______________________________________________ > > > >> BioCatalogue-developers mailing list > > > >> BioCatalogue-developers at rubyforge.org > > > > > > > > > > > > > > > >> > > > > > > >> > > > > > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > > >> > > > > > > > > > > > > > > > > > > > > > > > -- > > > "Science knows no country, because knowledge belongs to > > > humanity, and is the torch which illuminates the world." - > > > Louis Pasteur > > > > > > > > > > > > -- > > > 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 > > > > > > > > -- > > "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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue Jun 1 11:59:30 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 01 Jun 2010 16:59:30 +0100 Subject: [BioCatalogue-developers] latest data In-Reply-To: References: <4C04DF73.2090100@ebi.ac.uk> <4C04E9A5.8050704@cs.man.ac.uk> <4C050783.90702@ebi.ac.uk> <4C051C76.2000702@cs.man.ac.uk> <4C0524F3.1020700@cs.man.ac.uk> Message-ID: <4C052E62.6010107@cs.man.ac.uk> OK, I'll add to task list. But please remind me again tomorrow afternoon. Thanks, Jits Franck Tanoh wrote: > >Do you want a curation page for "Copy annotations from operation X > to operation Y"? > Please, if you can...that will help a lot. > > Cheers, > Franck > > > On 1 June 2010 16:19, Jiten Bhagat > wrote: > > Franck Tanoh wrote: > > >The best I can do is the attached list of URLs (also in > Dropbox) for the > > >SOAP operations that have been created in the last week. There > are 1892 > > >in total (!). > > that's a lot for a week! looks like the service update checker > is the > > guilty one :-) > > A first glance reveals loads of archived operations. > > Yeah. There are 107 archived operations. > > Do you want a curation page for "Copy annotations from operation X to > operation Y"? > > Jits > > > > > Thanks > > Franck > > > > an.ac.uk > wrote: > > > > Hi Franck, > > > > The best I can do is the attached list of URLs (also in Dropbox) > > for the > > SOAP operations that have been created in the last week. > There are > > 1892 > > in total (!). I've added a star (*) after each one that DOES > NOT have > > any description (of which there are 664). > > > > Jits > > > > > > Franck Tanoh wrote: > > > >What I can think of is that the data has considerably > changed since > > > the last report mostly due to the update checker. It is > entirely > > > possible that new operations >have been found that are not > necessary > > > annotated at the same level as the previously existing ones. > > > Is it possible to do a diff between those 2 results ( 1095 vs > > 839) so > > > that I can double check if that's the case. It will also > help me to > > > transfer some of the old descriptions to new operations, > inputs etc. > > > > > > Cheers, > > > Franck > > > > > > On 1 June 2010 14:13, Eric Nzuobontane > > > > > > > >>> wrote: > > > > > > What I can think of is that the data has considerably > changed > > > since the last report mostly due to the update > checker. It is > > > entirely possible that new operations have been found that > > are not > > > necessary annotated at the same level as the previously > > existing ones. > > > > > > Eric > > > > > > > > > Franck Tanoh wrote: > > > > > > Hi Jits, > > > > > > Thanks for the report. > > > > > > It doesn't really look right when I compare it to the > > previous > > > one: > > > > > > < > > 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>> > > > > > > In the previous report we had 1095 services with > description > > > and with all operation annotated. I don't > understand why we > > > have now 839. > > > Also there are 34 instead of 38 services with > > descriptions at > > > the service, operation and parameter level. > > > > > > Cheers, > > > Franck > > > > > > On 1 June 2010 12:06, Jiten Bhagat > > > > > > > >> > > > > > > > >>>> > > wrote: > > > > > > Franck, > > > > > > Here is the report: > > > > > > Total SOAP Services: 1636 > > > A. How many SOAP Services have a description? 1449 > > > B. How many SOAP Services have a description AND a > > > documentation > > > URL? 898 > > > C. How many SOAP Services have a description > AND all > > > operations have a > > > description? 839 > > > D. How many SOAP Services have a description > AND all > > > operations have a > > > description and ALL inputs/outputs have a > description? 34 > > > 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 > > > > > > Does that look right to you? > > > > > > Jits > > > > > > > > > Eric Nzuobontane wrote: > > > > I will put that in drop box. When are you > going out to > > > Denmark? > > > > > > > > Eric > > > > > > > > > > > > Franck Tanoh wrote: > > > >> Hi Eric, > > > >> > > > >> Hope you had a good break > > > >> > > > >> Can you send the latest (from today) data > dump to Jits > > > so that > > > he can > > > >> produce the annotations stats, pls? > > > >> > > > >> Cheers, > > > >> Franck > > > >> > > > >> -- > > > >> "Science knows no country, because knowledge > > belongs to > > > humanity, and > > > >> is the torch which illuminates the world." - > Louis > > Pasteur > > > >> > > > > > > > > > ------------------------------------------------------------------------ > > > >> > > > >> _______________________________________________ > > > >> BioCatalogue-developers mailing list > > > >> BioCatalogue-developers at rubyforge.org > > > > > > > > > >> > > > > > > > > > > > >>> > > > > > > >> > > > > > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > > >> > > > > > > > > > > > > > > > > > > > > > > > -- > > > "Science knows no country, because knowledge > belongs to > > > humanity, and is the torch which illuminates the > world." - > > > Louis Pasteur > > > > > > > > > > > > -- > > > 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 > > > > > > > > -- > > "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 issues at mygrid.org.uk Tue Jun 1 12:08:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 1 Jun 2010 17:08:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-365) Implement curation page for "Copy annotations from SOAP operation x to SOAP operation y" Message-ID: <16563352.1766.1275408497109.JavaMail.jira@rosalind.cs.man.ac.uk> Implement curation page for "Copy annotations from SOAP operation x to SOAP operation y" ---------------------------------------------------------------------------------------- Key: BIOCAT-365 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-365 Project: BioCatalogue Issue Type: New Feature Components: Curation Dashboard Environment: RoR Reporter: Jiten Bhagat Assignee: Jiten Bhagat Due to the recent additions of so many new SOAP operations (over 1000) due to the service updater, Franck needs a way to easily copy over annotations. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Tue Jun 1 18:03:11 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 01 Jun 2010 23:03:11 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'ProDomCG_evoscen' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'ProDomCG_evoscen' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1871 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 Jun 2 04:13:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 2 Jun 2010 09:13:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-316) url checker should follow redirects Message-ID: <7990169.1814.1275466397126.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 ] Eric Nzuobontane resolved BIOCAT-316. ------------------------------------- Resolution: Fixed follows up to 3 redirect only if redirect location is provided > 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 noreply at rubyforge.org Wed Jun 2 04:55:57 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 2 Jun 2010 04:55:57 -0400 (EDT) Subject: [BioCatalogue-developers] [2072] trunk: Add responsibility requester name in the notification mails Message-ID: <20100602085558.2A5D318582EE@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jun 2 05:16:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 2 Jun 2010 10:16:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-366) Implement a "Most Popular Services" box Message-ID: <17734181.1836.1275470177015.JavaMail.jira@rosalind.cs.man.ac.uk> Implement a "Most Popular Services" box --------------------------------------- Key: BIOCAT-366 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-366 Project: BioCatalogue Issue Type: New Feature Components: Web Interface Reporter: Jiten Bhagat Assignee: Jiten Bhagat Need some way of seeing what the most popular services are in the catalogue. This will require some work to cache viewings/stats counts etc. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Wed Jun 2 09:04:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 2 Jun 2010 09:04:22 -0400 (EDT) Subject: [BioCatalogue-developers] [2073] trunk/script/biocatalogue/service_annotation_report.rb: Added counts for operations, inputs and outputs. Message-ID: <20100602130422.652A91858300@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Wed Jun 2 09:10:22 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 02 Jun 2010 14:10:22 +0100 Subject: [BioCatalogue-developers] [Fwd: [Production ERROR] rest_methods#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400"] Message-ID: <4C06583E.7000209@cs.man.ac.uk> This database timeout issue is still ongoing.... Jits -------- Original Message -------- Subject: [Production ERROR] rest_methods#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400" Date: Wed, 2 Jun 2010 14:07:03 +0100 From: BioCatalogue Errors To: ericnzuo at ebi.ac.uk, jits at cs.man.ac.uk A ActiveRecord::StatementInvalid occurred in rest_methods#destroy: Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400 [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' ------------------------------- Request: ------------------------------- * URL : http://www.biocatalogue.org/rest_methods/80 * Method : DELETE * IP address: 130.88.195.202 * Parameters: {"action"=>"destroy", "_method"=>"delete", "authenticity_token"=>"0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=", "id"=>"80", "controller"=>"rest_methods"} * Rails root: /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue ------------------------------- Session: ------------------------------- * session id: nil * data: nil ------------------------------- Environment: ------------------------------- * CONTENT_LENGTH : 82 * CONTENT_TYPE : application/x-www-form-urlencoded * 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 : en-us,en;q=0.5 * HTTP_CONNECTION : keep-alive * HTTP_CONTENT_TYPE : application/x-www-form-urlencoded * HTTP_COOKIE : __utma=15951013.396796326.1272273201.1275473442.1275482785.119; __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; search_results_tabber=0; stats-tabs_tabber=1; __utmb=15951013.13.10.1275482785 * HTTP_HOST : www.biocatalogue.org * HTTP_KEEP_ALIVE : 300 * HTTP_REFERER : http://www.biocatalogue.org/rest_methods/80 * HTTP_USER_AGENT : Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 Firefox/3.5.9 * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 * PATH_INFO : /rest_methods/80 * QUERY_STRING : * REMOTE_ADDR : 130.88.195.202 * REMOTE_PORT : 59702 * REQUEST_METHOD : DELETE * REQUEST_URI : /rest_methods/80 * SCRIPT_NAME : * SERVER_ADDR : 172.18.1.109 * SERVER_ADMIN : root at localhost * SERVER_NAME : www.biocatalogue.org * SERVER_PORT : 80 * SERVER_PROTOCOL : HTTP/1.1 * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) * _ : _ * action_controller.request.query_parameters : * action_controller.request.request_parameters: authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=_methoddelete * action_controller.rescue.request : # * action_controller.rescue.response : # * rack.errors : # * rack.input : # * rack.methodoverride.original_method : POST * rack.multiprocess : true * rack.multithread : false * rack.request : # * rack.request.cookie_hash : __utma15951013.396796326.1272273201.1275473442.1275482785.119stats-tabs_tabber1__utmb15951013.13.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations * rack.request.cookie_string : __utma=15951013.396796326.1272273201.1275473442.1275482785.119; __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; search_results_tabber=0; stats-tabs_tabber=1; __utmb=15951013.13.10.1275482785 * rack.request.form_hash : authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=_methoddelete * rack.request.form_input : # * rack.request.form_vars : _method=delete&authenticity_token=0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d%2F0hNZ0%3D * rack.request.query_hash : * rack.request.query_string : * rack.routing_args : actiondestroyid80controllerrest_methods * rack.run_once : false * rack.session : search_show_listing_typesimpleprevious_url/rest_methods/80use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=user_id27flashlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= * rack.session.options : securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath/ * rack.session.record : # * rack.url_scheme : http * rack.version : 10 * Process: 14304 * Server : pweb-4a * request.format: text/html ------------------------------- Backtrace: ------------------------------- [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:320:in `execute' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:265:in `update_sql' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:335:in `update_sql' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:270:in `delete_sql' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:54:in `delete_without_query_dirty' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:18:in `delete' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:2578:in `destroy_without_lock' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/locking/optimistic.rb:113:in `destroy_without_callbacks' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:337:in `destroy_without_transactions' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `send' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `with_transaction_returning_status' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in `with_transaction_returning_status' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in `destroy' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_versions' [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `each' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `send' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_versions' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `send' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `evaluate_method' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in `call' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in `run' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `each' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `send' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `run' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in `run_callbacks' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in `callback' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in `destroy_without_transactions' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `send' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `with_transaction_returning_status' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in `with_transaction_returning_status' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in `destroy_without_trash' [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in `destroy' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in `destroy' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_annotations' [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `each' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `send' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_annotations' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `send' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `evaluate_method' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in `call' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in `run' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `each' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `send' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `run' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in `run_callbacks' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in `callback' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in `destroy_without_transactions' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `send' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `with_transaction_returning_status' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in `with_transaction_returning_status' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in `destroy_without_trash' [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in `destroy' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in `destroy' [RAILS_ROOT]/app/controllers/rest_methods_controller.rb:136:in `destroy' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in `send' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in `perform_action_without_filters' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:617:in `call_filters' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:610:in `perform_action_without_benchmark' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in `ms' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:10:in `realtime' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in `ms' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rescue.rb:160:in `perform_action_without_flash' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb:141:in `perform_action' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in `send' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in `process_without_filters' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:606:in `process' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:391:in `process' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:386:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/route_set.rb:433:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:88:in `dispatch' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:111:in `_call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:82:in `initialize' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/methodoverride.rb:24:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/params_parser.rb:15:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rewindable_input.rb:25:in `call' [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in `call' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in `call' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in `cache' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in `cache' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in `call' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `synchronize' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in `call' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in `safe_fork' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in `start' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in `start' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 From ericnzuo at ebi.ac.uk Wed Jun 2 09:13:23 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 02 Jun 2010 14:13:23 +0100 Subject: [BioCatalogue-developers] [Fwd: [Production ERROR] rest_methods#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400"] In-Reply-To: <4C06583E.7000209@cs.man.ac.uk> References: <4C06583E.7000209@cs.man.ac.uk> Message-ID: <4C0658F3.3080909@ebi.ac.uk> Damn!!! Jiten Bhagat wrote: > This database timeout issue is still ongoing.... > > Jits > > > -------- Original Message -------- > Subject: [Production ERROR] rest_methods#destroy > (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout > exceeded; try restarting transaction: DELETE FROM `annotation_versions` > WHERE `id` = 56400" > Date: Wed, 2 Jun 2010 14:07:03 +0100 > From: BioCatalogue Errors > To: ericnzuo at ebi.ac.uk, jits at cs.man.ac.uk > > > > A ActiveRecord::StatementInvalid occurred in rest_methods#destroy: > > Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400 > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' > > ------------------------------- > Request: > ------------------------------- > > * URL : http://www.biocatalogue.org/rest_methods/80 > * Method : DELETE > * IP address: 130.88.195.202 > * Parameters: {"action"=>"destroy", "_method"=>"delete", "authenticity_token"=>"0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=", "id"=>"80", "controller"=>"rest_methods"} > * Rails root: /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue > > ------------------------------- > Session: > ------------------------------- > > * session id: nil > * data: nil > > ------------------------------- > Environment: > ------------------------------- > > * CONTENT_LENGTH : 82 > * CONTENT_TYPE : application/x-www-form-urlencoded > * 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 : en-us,en;q=0.5 > * HTTP_CONNECTION : keep-alive > * HTTP_CONTENT_TYPE : application/x-www-form-urlencoded > * HTTP_COOKIE : __utma=15951013.396796326.1272273201.1275473442.1275482785.119; __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; search_results_tabber=0; stats-tabs_tabber=1; __utmb=15951013.13.10.1275482785 > * HTTP_HOST : www.biocatalogue.org > * HTTP_KEEP_ALIVE : 300 > * HTTP_REFERER : http://www.biocatalogue.org/rest_methods/80 > * HTTP_USER_AGENT : Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 Firefox/3.5.9 > * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 > * PATH_INFO : /rest_methods/80 > * QUERY_STRING : > * REMOTE_ADDR : 130.88.195.202 > * REMOTE_PORT : 59702 > * REQUEST_METHOD : DELETE > * REQUEST_URI : /rest_methods/80 > * SCRIPT_NAME : > * SERVER_ADDR : 172.18.1.109 > * SERVER_ADMIN : root at localhost > * SERVER_NAME : www.biocatalogue.org > * SERVER_PORT : 80 > * SERVER_PROTOCOL : HTTP/1.1 > * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) > * _ : _ > * action_controller.request.query_parameters : > * action_controller.request.request_parameters: authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=_methoddelete > * action_controller.rescue.request : # > * action_controller.rescue.response : # > * rack.errors : # > * rack.input : # > * rack.methodoverride.original_method : POST > * rack.multiprocess : true > * rack.multithread : false > * rack.request : # > * rack.request.cookie_hash : __utma15951013.396796326.1272273201.1275473442.1275482785.119stats-tabs_tabber1__utmb15951013.13.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations > * rack.request.cookie_string : __utma=15951013.396796326.1272273201.1275473442.1275482785.119; __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; search_results_tabber=0; stats-tabs_tabber=1; __utmb=15951013.13.10.1275482785 > * rack.request.form_hash : authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=_methoddelete > * rack.request.form_input : # > * rack.request.form_vars : _method=delete&authenticity_token=0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d%2F0hNZ0%3D > * rack.request.query_hash : > * rack.request.query_string : > * rack.routing_args : actiondestroyid80controllerrest_methods > * rack.run_once : false > * rack.session : search_show_listing_typesimpleprevious_url/rest_methods/80use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=user_id27flashlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= > * rack.session.options : securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath/ > * rack.session.record : # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 14304 > * Server : pweb-4a > > * request.format: text/html > > ------------------------------- > Backtrace: > ------------------------------- > > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:320:in `execute' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:265:in `update_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:335:in `update_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:270:in `delete_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:54:in `delete_without_query_dirty' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:18:in `delete' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:2578:in `destroy_without_lock' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/locking/optimistic.rb:113:in `destroy_without_callbacks' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:337:in `destroy_without_transactions' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_versions' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `each' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_versions' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `evaluate_method' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in `call' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `each' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in `run_callbacks' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in `callback' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in `destroy_without_transactions' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in `destroy_without_trash' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_annotations' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `each' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_annotations' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `evaluate_method' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in `call' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `each' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in `run_callbacks' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in `callback' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in `destroy_without_transactions' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in `destroy_without_trash' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in `destroy' > [RAILS_ROOT]/app/controllers/rest_methods_controller.rb:136:in `destroy' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in `send' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in `perform_action_without_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:617:in `call_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:610:in `perform_action_without_benchmark' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in `ms' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:10:in `realtime' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in `ms' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rescue.rb:160:in `perform_action_without_flash' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb:141:in `perform_action' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in `send' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in `process_without_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:606:in `process' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:391:in `process' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:386:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/route_set.rb:433:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:88:in `dispatch' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:111:in `_call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:82:in `initialize' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/methodoverride.rb:24:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/params_parser.rb:15:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rewindable_input.rb:25:in `call' > [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in `cache' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in `cache' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `synchronize' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in `call' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in `safe_fork' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in `start' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 > > > > _______________________________________________ > 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 Jun 2 09:17:15 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 2 Jun 2010 14:17:15 +0100 Subject: [BioCatalogue-developers] [Fwd: [Production ERROR] rest_methods#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400"] In-Reply-To: <4C06583E.7000209@cs.man.ac.uk> References: <4C06583E.7000209@cs.man.ac.uk> Message-ID: <1B40155A-4D21-493B-8937-85C62E619356@cs.man.ac.uk> I' was trying to delete an endpoint: http://www.biocatalogue.org/rest_methods/80 . After several attempts not sure if it's deleted or not. Deleting is still a nightmare... :-( Franck On 2 Jun 2010, at 14:10, Jiten Bhagat wrote: > This database timeout issue is still ongoing.... > > Jits > > > -------- Original Message -------- > Subject: [Production ERROR] rest_methods#destroy > (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout > exceeded; try restarting transaction: DELETE FROM > `annotation_versions` > WHERE `id` = 56400" > Date: Wed, 2 Jun 2010 14:07:03 +0100 > From: BioCatalogue Errors > To: ericnzuo at ebi.ac.uk, jits at cs.man.ac.uk > > > > A ActiveRecord::StatementInvalid occurred in rest_methods#destroy: > > Mysql::Error: Lock wait timeout exceeded; try restarting > transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400 > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/abstract_adapter.rb:212:in `log' > > ------------------------------- > Request: > ------------------------------- > > * URL : http://www.biocatalogue.org/rest_methods/80 > * Method : DELETE > * IP address: 130.88.195.202 > * Parameters: {"action"=>"destroy", "_method"=>"delete", > "authenticity_token"=>"0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/ > 0hNZ0=", "id"=>"80", "controller"=>"rest_methods"} > * Rails root: /net/nas11a/vol1/alien-www/html/biocatalogue/rails/ > biocatalogue > > ------------------------------- > Session: > ------------------------------- > > * session id: nil > * data: nil > > ------------------------------- > Environment: > ------------------------------- > > * CONTENT_LENGTH : 82 > * CONTENT_TYPE : application/x-www- > form-urlencoded > * 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 : en-us,en;q=0.5 > * HTTP_CONNECTION : keep-alive > * HTTP_CONTENT_TYPE : application/x-www- > form-urlencoded > * HTTP_COOKIE : > __utma=15951013.396796326.1272273201.1275473442.1275482785.119; > __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)| > utmcmd=organic|utmctr=CYGDAnnotations; __utmc=15951013; > _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; > search_results_tabber=0; stats-tabs_tabber=1; > __utmb=15951013.13.10.1275482785 > * HTTP_HOST : www.biocatalogue.org > * HTTP_KEEP_ALIVE : 300 > * HTTP_REFERER : http://www.biocatalogue.org/rest_methods/80 > * HTTP_USER_AGENT : Mozilla/5.0 > (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/ > 20100315 Firefox/3.5.9 > * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 > * PATH_INFO : /rest_methods/80 > * QUERY_STRING : > * REMOTE_ADDR : 130.88.195.202 > * REMOTE_PORT : 59702 > * REQUEST_METHOD : DELETE > * REQUEST_URI : /rest_methods/80 > * SCRIPT_NAME : > * SERVER_ADDR : 172.18.1.109 > * SERVER_ADMIN : root at localhost > * SERVER_NAME : www.biocatalogue.org > * SERVER_PORT : 80 > * SERVER_PROTOCOL : HTTP/1.1 > * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) > * _ : _ > * action_controller.request.query_parameters : > * action_controller.request.request_parameters: > authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/ > 0hNZ0=_methoddelete > * action_controller.rescue.request : > # > * action_controller.rescue.response : > # > * rack.errors : # > * rack.input : # 0x2aaaafd9c720> > * rack.methodoverride.original_method : POST > * rack.multiprocess : true > * rack.multithread : false > * rack.request : # 0x2aaaafd9d3f0> > * rack.request.cookie_hash : > __utma15951013.396796326.1272273201.1275473442.1275482785.119stats- > tabs_tabber1__utmb15951013.13.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4 > .utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations > * rack.request.cookie_string : > __utma=15951013.396796326.1272273201.1275473442.1275482785.119; > __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)| > utmcmd=organic|utmctr=CYGDAnnotations; __utmc=15951013; > _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; > search_results_tabber=0; stats-tabs_tabber=1; > __utmb=15951013.13.10.1275482785 > * rack.request.form_hash : > authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/ > 0hNZ0=_methoddelete > * rack.request.form_input : # 0x2aaaafd9c720> > * rack.request.form_vars : > _method > =delete&authenticity_token=0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d > %2F0hNZ0%3D > * rack.request.query_hash : > * rack.request.query_string : > * rack.routing_args : > actiondestroyid80controllerrest_methods > * rack.run_once : false > * rack.session : > search_show_listing_typesimpleprevious_url/rest_methods/ > 80use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d > /0hNZ0=user_id27flashlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= > * rack.session.options : > securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath > / > * rack.session.record : > # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 14304 > * Server : pweb-4a > > * request.format: text/html > > ------------------------------- > Backtrace: > ------------------------------- > > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/abstract_adapter.rb:212:in `log' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/mysql_adapter.rb:320:in `execute' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/abstract/database_statements.rb:265:in > `update_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/mysql_adapter.rb:335:in `update_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/abstract/database_statements.rb:270:in > `delete_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/abstract/database_statements.rb:54:in > `delete_without_query_dirty' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/abstract/query_cache.rb:18:in `delete' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb: > 2578:in `destroy_without_lock' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/locking/ > optimistic.rb:113:in `destroy_without_callbacks' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > callbacks.rb:337:in `destroy_without_transactions' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:229:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:229:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/abstract/database_statements.rb:136:in > `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:228:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:192:in `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations.rb:1364:in `has_many_dependent_destroy_for_versions' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/ > finder.rb:168:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations/association_collection.rb:364:in > `method_missing_without_paginate' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations/association_proxy.rb:219:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations/association_proxy.rb:219:in `each' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations/association_proxy.rb:219:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations/association_proxy.rb:219:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations/association_collection.rb:364:in > `method_missing_without_paginate' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/ > finder.rb:168:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations.rb:1364:in `has_many_dependent_destroy_for_versions' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:178:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:178:in `evaluate_method' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:166:in `call' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:93:in `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:92:in `each' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:92:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:92:in `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:276:in `run_callbacks' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > callbacks.rb:344:in `callback' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > callbacks.rb:336:in `destroy_without_transactions' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:229:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:229:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/abstract/database_statements.rb:136:in > `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:228:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:192:in `destroy_without_trash' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/ > acts_as_trashable.rb:41:in `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/abstract/database_statements.rb:136:in > `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/ > acts_as_trashable.rb:38:in `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations.rb:1364:in `has_many_dependent_destroy_for_annotations' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/ > finder.rb:168:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations/association_collection.rb:364:in > `method_missing_without_paginate' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations/association_proxy.rb:219:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations/association_proxy.rb:219:in `each' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations/association_proxy.rb:219:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations/association_proxy.rb:219:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations/association_collection.rb:364:in > `method_missing_without_paginate' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/ > finder.rb:168:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > associations.rb:1364:in `has_many_dependent_destroy_for_annotations' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:178:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:178:in `evaluate_method' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:166:in `call' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:93:in `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:92:in `each' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:92:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:92:in `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ > callbacks.rb:276:in `run_callbacks' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > callbacks.rb:344:in `callback' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > callbacks.rb:336:in `destroy_without_transactions' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:229:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:229:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/abstract/database_statements.rb:136:in > `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:228:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:192:in `destroy_without_trash' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/ > acts_as_trashable.rb:41:in `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/abstract/database_statements.rb:136:in > `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/ > acts_as_trashable.rb:38:in `destroy' > [RAILS_ROOT]/app/controllers/rest_methods_controller.rb:136:in > `destroy' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb: > 1322:in `send' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb: > 1322:in `perform_action_without_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ > filters.rb:617:in `call_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ > filters.rb:610:in `perform_action_without_benchmark' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ > benchmarking.rb:68:in `perform_action_without_rescue' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/ > benchmark.rb:17:in `ms' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/ > benchmark.rb:10:in `realtime' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/ > benchmark.rb:17:in `ms' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ > benchmarking.rb:68:in `perform_action_without_rescue' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ > rescue.rb:160:in `perform_action_without_flash' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb: > 141:in `perform_action' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb: > 523:in `send' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb: > 523:in `process_without_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ > filters.rb:606:in `process' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb: > 391:in `process' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb: > 386:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/ > route_set.rb:433:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ > dispatcher.rb:88:in `dispatch' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ > dispatcher.rb:111:in `_call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ > dispatcher.rb:82:in `initialize' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/ > rack-1.0/rack/head.rb:9:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/ > rack-1.0/rack/head.rb:9:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/ > rack-1.0/rack/methodoverride.rb:24:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ > params_parser.rb:15:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ > rewindable_input.rb:25:in `call' > [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in > `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/ > abstract_store.rb:122:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > query_cache.rb:29:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/abstract/query_cache.rb:34:in `cache' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > query_cache.rb:9:in `cache' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > query_cache.rb:28:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ > connection_adapters/abstract/connection_pool.rb:361:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ > failsafe.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/ > rack-1.0/rack/lock.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/ > rack-1.0/rack/lock.rb:11:in `synchronize' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/ > rack-1.0/rack/lock.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ > dispatcher.rb:106:in `call' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > rack/request_handler.rb:91:in `process_request' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > abstract_request_handler.rb:206:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > railz/application_spawner.rb:376:in `start_request_handler' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > railz/application_spawner.rb:334:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > utils.rb:182:in `safe_fork' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > railz/application_spawner.rb:332:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > abstract_server.rb:351:in `__send__' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > abstract_server.rb:351:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > abstract_server.rb:195:in `start_synchronously' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > abstract_server.rb:162:in `start' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > railz/application_spawner.rb:213:in `start' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > spawn_manager.rb:261:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > abstract_server_collection.rb:126:in `lookup_or_add' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > spawn_manager.rb:255:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > abstract_server_collection.rb:80:in `synchronize' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > abstract_server_collection.rb:79:in `synchronize' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > spawn_manager.rb:254:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > spawn_manager.rb:153:in `spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > spawn_manager.rb:286:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > abstract_server.rb:351:in `__send__' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > abstract_server.rb:351:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/ > abstract_server.rb:195:in `start_synchronously' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn- > server:61 > > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From ericnzuo at ebi.ac.uk Wed Jun 2 09:30:10 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 02 Jun 2010 14:30:10 +0100 Subject: [BioCatalogue-developers] [Fwd: [Production ERROR] rest_methods#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400"] In-Reply-To: <4C06583E.7000209@cs.man.ac.uk> References: <4C06583E.7000209@cs.man.ac.uk> Message-ID: <4C065CE2.2020805@ebi.ac.uk> Can you try to reproduce the error please, I am observing the processes in the data base. The locks especially... Eric Jiten Bhagat wrote: > This database timeout issue is still ongoing.... > > Jits > > > -------- Original Message -------- > Subject: [Production ERROR] rest_methods#destroy > (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout > exceeded; try restarting transaction: DELETE FROM `annotation_versions` > WHERE `id` = 56400" > Date: Wed, 2 Jun 2010 14:07:03 +0100 > From: BioCatalogue Errors > To: ericnzuo at ebi.ac.uk, jits at cs.man.ac.uk > > > > A ActiveRecord::StatementInvalid occurred in rest_methods#destroy: > > Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400 > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' > > ------------------------------- > Request: > ------------------------------- > > * URL : http://www.biocatalogue.org/rest_methods/80 > * Method : DELETE > * IP address: 130.88.195.202 > * Parameters: {"action"=>"destroy", "_method"=>"delete", "authenticity_token"=>"0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=", "id"=>"80", "controller"=>"rest_methods"} > * Rails root: /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue > > ------------------------------- > Session: > ------------------------------- > > * session id: nil > * data: nil > > ------------------------------- > Environment: > ------------------------------- > > * CONTENT_LENGTH : 82 > * CONTENT_TYPE : application/x-www-form-urlencoded > * 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 : en-us,en;q=0.5 > * HTTP_CONNECTION : keep-alive > * HTTP_CONTENT_TYPE : application/x-www-form-urlencoded > * HTTP_COOKIE : __utma=15951013.396796326.1272273201.1275473442.1275482785.119; __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; search_results_tabber=0; stats-tabs_tabber=1; __utmb=15951013.13.10.1275482785 > * HTTP_HOST : www.biocatalogue.org > * HTTP_KEEP_ALIVE : 300 > * HTTP_REFERER : http://www.biocatalogue.org/rest_methods/80 > * HTTP_USER_AGENT : Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 Firefox/3.5.9 > * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 > * PATH_INFO : /rest_methods/80 > * QUERY_STRING : > * REMOTE_ADDR : 130.88.195.202 > * REMOTE_PORT : 59702 > * REQUEST_METHOD : DELETE > * REQUEST_URI : /rest_methods/80 > * SCRIPT_NAME : > * SERVER_ADDR : 172.18.1.109 > * SERVER_ADMIN : root at localhost > * SERVER_NAME : www.biocatalogue.org > * SERVER_PORT : 80 > * SERVER_PROTOCOL : HTTP/1.1 > * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) > * _ : _ > * action_controller.request.query_parameters : > * action_controller.request.request_parameters: authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=_methoddelete > * action_controller.rescue.request : # > * action_controller.rescue.response : # > * rack.errors : # > * rack.input : # > * rack.methodoverride.original_method : POST > * rack.multiprocess : true > * rack.multithread : false > * rack.request : # > * rack.request.cookie_hash : __utma15951013.396796326.1272273201.1275473442.1275482785.119stats-tabs_tabber1__utmb15951013.13.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations > * rack.request.cookie_string : __utma=15951013.396796326.1272273201.1275473442.1275482785.119; __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; search_results_tabber=0; stats-tabs_tabber=1; __utmb=15951013.13.10.1275482785 > * rack.request.form_hash : authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=_methoddelete > * rack.request.form_input : # > * rack.request.form_vars : _method=delete&authenticity_token=0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d%2F0hNZ0%3D > * rack.request.query_hash : > * rack.request.query_string : > * rack.routing_args : actiondestroyid80controllerrest_methods > * rack.run_once : false > * rack.session : search_show_listing_typesimpleprevious_url/rest_methods/80use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=user_id27flashlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= > * rack.session.options : securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath/ > * rack.session.record : # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 14304 > * Server : pweb-4a > > * request.format: text/html > > ------------------------------- > Backtrace: > ------------------------------- > > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:320:in `execute' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:265:in `update_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:335:in `update_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:270:in `delete_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:54:in `delete_without_query_dirty' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:18:in `delete' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:2578:in `destroy_without_lock' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/locking/optimistic.rb:113:in `destroy_without_callbacks' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:337:in `destroy_without_transactions' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_versions' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `each' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_versions' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `evaluate_method' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in `call' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `each' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in `run_callbacks' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in `callback' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in `destroy_without_transactions' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in `destroy_without_trash' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_annotations' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `each' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_annotations' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `evaluate_method' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in `call' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `each' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in `run_callbacks' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in `callback' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in `destroy_without_transactions' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in `destroy_without_trash' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in `destroy' > [RAILS_ROOT]/app/controllers/rest_methods_controller.rb:136:in `destroy' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in `send' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in `perform_action_without_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:617:in `call_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:610:in `perform_action_without_benchmark' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in `ms' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:10:in `realtime' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in `ms' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rescue.rb:160:in `perform_action_without_flash' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb:141:in `perform_action' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in `send' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in `process_without_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:606:in `process' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:391:in `process' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:386:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/route_set.rb:433:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:88:in `dispatch' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:111:in `_call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:82:in `initialize' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/methodoverride.rb:24:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/params_parser.rb:15:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rewindable_input.rb:25:in `call' > [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in `cache' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in `cache' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `synchronize' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in `call' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in `safe_fork' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in `start' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 > > > > _______________________________________________ > 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 Wed Jun 2 09:33:10 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 02 Jun 2010 14:33:10 +0100 Subject: [BioCatalogue-developers] [Fwd: [Production ERROR] rest_methods#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400"] In-Reply-To: <1B40155A-4D21-493B-8937-85C62E619356@cs.man.ac.uk> References: <4C06583E.7000209@cs.man.ac.uk> <1B40155A-4D21-493B-8937-85C62E619356@cs.man.ac.uk> Message-ID: <4C065D96.6040608@ebi.ac.uk> Can you try again please? I am trying to track down the problem... Eric Franck Tanoh wrote: > I' was trying to delete an endpoint: > http://www.biocatalogue.org/rest_methods/80 . After several attempts > not sure if it's deleted or not. > Deleting is still a nightmare... :-( > > Franck > On 2 Jun 2010, at 14:10, Jiten Bhagat wrote: > >> This database timeout issue is still ongoing.... >> >> Jits >> >> >> -------- Original Message -------- >> Subject: [Production ERROR] rest_methods#destroy >> (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout >> exceeded; try restarting transaction: DELETE FROM `annotation_versions` >> WHERE `id` = 56400" >> Date: Wed, 2 Jun 2010 14:07:03 +0100 >> From: BioCatalogue Errors >> To: ericnzuo at ebi.ac.uk, jits at cs.man.ac.uk >> >> >> >> A ActiveRecord::StatementInvalid occurred in rest_methods#destroy: >> >> Mysql::Error: Lock wait timeout exceeded; try restarting >> transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400 >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in >> `log' >> >> ------------------------------- >> Request: >> ------------------------------- >> >> * URL : http://www.biocatalogue.org/rest_methods/80 >> * Method : DELETE >> * IP address: 130.88.195.202 >> * Parameters: {"action"=>"destroy", "_method"=>"delete", >> "authenticity_token"=>"0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=", >> "id"=>"80", "controller"=>"rest_methods"} >> * Rails root: >> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue >> >> ------------------------------- >> Session: >> ------------------------------- >> >> * session id: nil >> * data: nil >> >> ------------------------------- >> Environment: >> ------------------------------- >> >> * CONTENT_LENGTH : 82 >> * CONTENT_TYPE : >> application/x-www-form-urlencoded >> * 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 : en-us,en;q=0.5 >> * HTTP_CONNECTION : keep-alive >> * HTTP_CONTENT_TYPE : >> application/x-www-form-urlencoded >> * HTTP_COOKIE : >> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >> search_results_tabber=0; stats-tabs_tabber=1; >> __utmb=15951013.13.10.1275482785 >> * HTTP_HOST : www.biocatalogue.org >> * HTTP_KEEP_ALIVE : 300 >> * HTTP_REFERER : >> http://www.biocatalogue.org/rest_methods/80 >> * HTTP_USER_AGENT : Mozilla/5.0 >> (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 >> Firefox/3.5.9 >> * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 >> * PATH_INFO : /rest_methods/80 >> * QUERY_STRING : >> * REMOTE_ADDR : 130.88.195.202 >> * REMOTE_PORT : 59702 >> * REQUEST_METHOD : DELETE >> * REQUEST_URI : /rest_methods/80 >> * SCRIPT_NAME : >> * SERVER_ADDR : 172.18.1.109 >> * SERVER_ADMIN : root at localhost >> * SERVER_NAME : www.biocatalogue.org >> * SERVER_PORT : 80 >> * SERVER_PROTOCOL : HTTP/1.1 >> * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) >> * _ : _ >> * action_controller.request.query_parameters : >> * action_controller.request.request_parameters: >> authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=_methoddelete >> >> * action_controller.rescue.request : >> # >> * action_controller.rescue.response : >> # >> * rack.errors : # >> * rack.input : >> # >> * rack.methodoverride.original_method : POST >> * rack.multiprocess : true >> * rack.multithread : false >> * rack.request : >> # >> * rack.request.cookie_hash : >> __utma15951013.396796326.1272273201.1275473442.1275482785.119stats-tabs_tabber1__utmb15951013.13.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations >> >> * rack.request.cookie_string : >> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >> search_results_tabber=0; stats-tabs_tabber=1; >> __utmb=15951013.13.10.1275482785 >> * rack.request.form_hash : >> authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=_methoddelete >> >> * rack.request.form_input : >> # >> * rack.request.form_vars : >> _method=delete&authenticity_token=0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d%2F0hNZ0%3D >> >> * rack.request.query_hash : >> * rack.request.query_string : >> * rack.routing_args : >> actiondestroyid80controllerrest_methods >> * rack.run_once : false >> * rack.session : >> search_show_listing_typesimpleprevious_url/rest_methods/80use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=user_id27flashlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= >> >> * rack.session.options : >> securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath/ >> >> * rack.session.record : >> # >> * rack.url_scheme : http >> * rack.version : 10 >> >> * Process: 14304 >> * Server : pweb-4a >> >> * request.format: text/html >> >> ------------------------------- >> Backtrace: >> ------------------------------- >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in >> `log' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:320:in >> `execute' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:265:in >> `update_sql' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:335:in >> `update_sql' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:270:in >> `delete_sql' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:54:in >> `delete_without_query_dirty' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:18:in >> `delete' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:2578:in >> `destroy_without_lock' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/locking/optimistic.rb:113:in >> `destroy_without_callbacks' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:337:in >> `destroy_without_transactions' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in >> `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in >> `destroy' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >> `has_many_dependent_destroy_for_versions' >> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >> `method_missing_without_paginate' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `each' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >> `method_missing_without_paginate' >> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >> `has_many_dependent_destroy_for_versions' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >> `send' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >> `evaluate_method' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in >> `call' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in >> `run' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `each' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `send' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `run' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in >> `run_callbacks' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in >> `callback' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in >> `destroy_without_transactions' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in >> `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in >> `destroy_without_trash' >> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in >> `destroy' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >> `transaction' >> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in >> `destroy' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >> `has_many_dependent_destroy_for_annotations' >> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >> `method_missing_without_paginate' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `each' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >> `method_missing_without_paginate' >> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >> `has_many_dependent_destroy_for_annotations' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >> `send' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >> `evaluate_method' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in >> `call' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in >> `run' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `each' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `send' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `run' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in >> `run_callbacks' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in >> `callback' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in >> `destroy_without_transactions' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in >> `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in >> `destroy_without_trash' >> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in >> `destroy' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >> `transaction' >> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in >> `destroy' >> [RAILS_ROOT]/app/controllers/rest_methods_controller.rb:136:in >> `destroy' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in >> `send' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in >> `perform_action_without_filters' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:617:in >> `call_filters' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:610:in >> `perform_action_without_benchmark' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in >> `perform_action_without_rescue' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in >> `ms' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:10:in >> `realtime' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in >> `ms' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in >> `perform_action_without_rescue' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rescue.rb:160:in >> `perform_action_without_flash' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb:141:in >> `perform_action' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in >> `send' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in >> `process_without_filters' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:606:in >> `process' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:391:in >> `process' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:386:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/route_set.rb:433:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:88:in >> `dispatch' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:111:in >> `_call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:82:in >> `initialize' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/methodoverride.rb:24:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/params_parser.rb:15:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rewindable_input.rb:25:in >> `call' >> [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in >> `call' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in >> `call' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in >> `cache' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in >> `cache' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in >> `call' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >> `synchronize' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in >> `call' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in >> `process_request' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in >> `main_loop' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in >> `start_request_handler' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in >> `handle_spawn_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in >> `safe_fork' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in >> `handle_spawn_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `__send__' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `main_loop' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in >> `start_synchronously' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in >> `start' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in >> `start' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in >> `spawn_rails_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in >> `lookup_or_add' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in >> `spawn_rails_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in >> `synchronize' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in >> `synchronize' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in >> `spawn_rails_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in >> `spawn_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in >> `handle_spawn_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `__send__' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `main_loop' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in >> `start_synchronously' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 >> >> >> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Wed Jun 2 09:42:39 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 02 Jun 2010 14:42:39 +0100 Subject: [BioCatalogue-developers] [Fwd: [Production ERROR] rest_methods#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400"] In-Reply-To: <1B40155A-4D21-493B-8937-85C62E619356@cs.man.ac.uk> References: <4C06583E.7000209@cs.man.ac.uk> <1B40155A-4D21-493B-8937-85C62E619356@cs.man.ac.uk> Message-ID: <4C065FCF.9060609@ebi.ac.uk> http://bugs.mysql.com/bug.php?id=47180 does not really say of the problem was solved but suggests that people should migrate to a new version. We are not exactly running on the version mentioned in this thread be we are running on 5.0.41 which I suspect shows the same problems. Eric Franck Tanoh wrote: > I' was trying to delete an endpoint: > http://www.biocatalogue.org/rest_methods/80 . After several attempts > not sure if it's deleted or not. > Deleting is still a nightmare... :-( > > Franck > On 2 Jun 2010, at 14:10, Jiten Bhagat wrote: > >> This database timeout issue is still ongoing.... >> >> Jits >> >> >> -------- Original Message -------- >> Subject: [Production ERROR] rest_methods#destroy >> (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout >> exceeded; try restarting transaction: DELETE FROM `annotation_versions` >> WHERE `id` = 56400" >> Date: Wed, 2 Jun 2010 14:07:03 +0100 >> From: BioCatalogue Errors >> To: ericnzuo at ebi.ac.uk, jits at cs.man.ac.uk >> >> >> >> A ActiveRecord::StatementInvalid occurred in rest_methods#destroy: >> >> Mysql::Error: Lock wait timeout exceeded; try restarting >> transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400 >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in >> `log' >> >> ------------------------------- >> Request: >> ------------------------------- >> >> * URL : http://www.biocatalogue.org/rest_methods/80 >> * Method : DELETE >> * IP address: 130.88.195.202 >> * Parameters: {"action"=>"destroy", "_method"=>"delete", >> "authenticity_token"=>"0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=", >> "id"=>"80", "controller"=>"rest_methods"} >> * Rails root: >> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue >> >> ------------------------------- >> Session: >> ------------------------------- >> >> * session id: nil >> * data: nil >> >> ------------------------------- >> Environment: >> ------------------------------- >> >> * CONTENT_LENGTH : 82 >> * CONTENT_TYPE : >> application/x-www-form-urlencoded >> * 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 : en-us,en;q=0.5 >> * HTTP_CONNECTION : keep-alive >> * HTTP_CONTENT_TYPE : >> application/x-www-form-urlencoded >> * HTTP_COOKIE : >> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >> search_results_tabber=0; stats-tabs_tabber=1; >> __utmb=15951013.13.10.1275482785 >> * HTTP_HOST : www.biocatalogue.org >> * HTTP_KEEP_ALIVE : 300 >> * HTTP_REFERER : >> http://www.biocatalogue.org/rest_methods/80 >> * HTTP_USER_AGENT : Mozilla/5.0 >> (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 >> Firefox/3.5.9 >> * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 >> * PATH_INFO : /rest_methods/80 >> * QUERY_STRING : >> * REMOTE_ADDR : 130.88.195.202 >> * REMOTE_PORT : 59702 >> * REQUEST_METHOD : DELETE >> * REQUEST_URI : /rest_methods/80 >> * SCRIPT_NAME : >> * SERVER_ADDR : 172.18.1.109 >> * SERVER_ADMIN : root at localhost >> * SERVER_NAME : www.biocatalogue.org >> * SERVER_PORT : 80 >> * SERVER_PROTOCOL : HTTP/1.1 >> * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) >> * _ : _ >> * action_controller.request.query_parameters : >> * action_controller.request.request_parameters: >> authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=_methoddelete >> >> * action_controller.rescue.request : >> # >> * action_controller.rescue.response : >> # >> * rack.errors : # >> * rack.input : >> # >> * rack.methodoverride.original_method : POST >> * rack.multiprocess : true >> * rack.multithread : false >> * rack.request : >> # >> * rack.request.cookie_hash : >> __utma15951013.396796326.1272273201.1275473442.1275482785.119stats-tabs_tabber1__utmb15951013.13.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations >> >> * rack.request.cookie_string : >> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >> search_results_tabber=0; stats-tabs_tabber=1; >> __utmb=15951013.13.10.1275482785 >> * rack.request.form_hash : >> authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=_methoddelete >> >> * rack.request.form_input : >> # >> * rack.request.form_vars : >> _method=delete&authenticity_token=0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d%2F0hNZ0%3D >> >> * rack.request.query_hash : >> * rack.request.query_string : >> * rack.routing_args : >> actiondestroyid80controllerrest_methods >> * rack.run_once : false >> * rack.session : >> search_show_listing_typesimpleprevious_url/rest_methods/80use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=user_id27flashlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= >> >> * rack.session.options : >> securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath/ >> >> * rack.session.record : >> # >> * rack.url_scheme : http >> * rack.version : 10 >> >> * Process: 14304 >> * Server : pweb-4a >> >> * request.format: text/html >> >> ------------------------------- >> Backtrace: >> ------------------------------- >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in >> `log' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:320:in >> `execute' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:265:in >> `update_sql' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:335:in >> `update_sql' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:270:in >> `delete_sql' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:54:in >> `delete_without_query_dirty' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:18:in >> `delete' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:2578:in >> `destroy_without_lock' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/locking/optimistic.rb:113:in >> `destroy_without_callbacks' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:337:in >> `destroy_without_transactions' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in >> `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in >> `destroy' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >> `has_many_dependent_destroy_for_versions' >> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >> `method_missing_without_paginate' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `each' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >> `method_missing_without_paginate' >> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >> `has_many_dependent_destroy_for_versions' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >> `send' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >> `evaluate_method' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in >> `call' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in >> `run' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `each' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `send' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `run' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in >> `run_callbacks' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in >> `callback' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in >> `destroy_without_transactions' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in >> `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in >> `destroy_without_trash' >> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in >> `destroy' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >> `transaction' >> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in >> `destroy' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >> `has_many_dependent_destroy_for_annotations' >> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >> `method_missing_without_paginate' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `each' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >> `method_missing_without_paginate' >> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >> `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >> `has_many_dependent_destroy_for_annotations' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >> `send' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >> `evaluate_method' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in >> `call' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in >> `run' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `each' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `send' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `run' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in >> `run_callbacks' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in >> `callback' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in >> `destroy_without_transactions' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in >> `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in >> `destroy_without_trash' >> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in >> `destroy' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >> `transaction' >> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in >> `destroy' >> [RAILS_ROOT]/app/controllers/rest_methods_controller.rb:136:in >> `destroy' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in >> `send' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in >> `perform_action_without_filters' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:617:in >> `call_filters' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:610:in >> `perform_action_without_benchmark' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in >> `perform_action_without_rescue' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in >> `ms' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:10:in >> `realtime' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in >> `ms' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in >> `perform_action_without_rescue' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rescue.rb:160:in >> `perform_action_without_flash' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb:141:in >> `perform_action' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in >> `send' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in >> `process_without_filters' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:606:in >> `process' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:391:in >> `process' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:386:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/route_set.rb:433:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:88:in >> `dispatch' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:111:in >> `_call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:82:in >> `initialize' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/methodoverride.rb:24:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/params_parser.rb:15:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rewindable_input.rb:25:in >> `call' >> [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in >> `call' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in >> `call' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in >> `cache' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in >> `cache' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in >> `call' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >> `synchronize' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in >> `call' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in >> `process_request' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in >> `main_loop' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in >> `start_request_handler' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in >> `handle_spawn_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in >> `safe_fork' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in >> `handle_spawn_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `__send__' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `main_loop' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in >> `start_synchronously' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in >> `start' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in >> `start' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in >> `spawn_rails_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in >> `lookup_or_add' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in >> `spawn_rails_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in >> `synchronize' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in >> `synchronize' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in >> `spawn_rails_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in >> `spawn_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in >> `handle_spawn_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `__send__' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `main_loop' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in >> `start_synchronously' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 >> >> >> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Wed Jun 2 09:46:43 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 02 Jun 2010 14:46:43 +0100 Subject: [BioCatalogue-developers] [Production ERROR] application#show (ActionView::TemplateError) "undefined method `service' for nil:NilClass" In-Reply-To: <4c0658be39d6_17ef15b1c078b7d4112@pweb-4a.ebi.ac.uk.tmail> References: <4c0658be39d6_17ef15b1c078b7d4112@pweb-4a.ebi.ac.uk.tmail> Message-ID: <4C0660C3.8030802@ebi.ac.uk> We need to track the process that generates this error. It is crowding the error messages with the possibility of important mails being missed! Eric BioCatalogue Errors wrote: > A ActionView::TemplateError occurred in application#show: > > undefined method `service' for nil:NilClass > On line #16 of app/views/rest_methods/_breadcrumbs.html.erb > > 13: <% if controller.action_name.downcase == "show" -%> > 14:
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    • > 15: > 16:
  • <%= link_to display_name(@rest_service.service), @rest_service.service -%>
    • > 17: > 18:
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    • > 19: > > app/views/rest_methods/_breadcrumbs.html.erb:16 > app/helpers/application_helper.rb:510:in `render_breadcrumbs_after_home' > app/views/widgets/_breadcrumbs_bar.html.erb:18 > app/views/layouts/application_wide.html.erb:52 > passenger (2.2.4) lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' > passenger (2.2.4) lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in `safe_fork' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in `start' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > > ------------------------------- > Request: > ------------------------------- > > * URL : http://www.biocatalogue.org/rest_methods/80 > * Method : GET > * IP address: 130.88.195.202 > * Parameters: {"action"=>"show", "id"=>"80", "controller"=>"rest_methods"} > * 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 : en-us,en;q=0.5 > * HTTP_CONNECTION : keep-alive > * HTTP_COOKIE : __utma=15951013.396796326.1272273201.1275473442.1275482785.119; __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; search_results_tabber=0; stats-tabs_tabber=1; __utmb=15951013.22.10.1275482785 > * HTTP_HOST : www.biocatalogue.org > * HTTP_IF_NONE_MATCH : "611ad19d948de61ee7f406c17aa39604" > * HTTP_KEEP_ALIVE : 300 > * HTTP_REFERER : http://www.biocatalogue.org/services/2699 > * HTTP_USER_AGENT : Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 Firefox/3.5.9 > * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 > * PATH_INFO : /rest_methods/80 > * QUERY_STRING : > * REMOTE_ADDR : 130.88.195.202 > * REMOTE_PORT : 41132 > * REQUEST_METHOD : GET > * REQUEST_URI : /rest_methods/80 > * SCRIPT_NAME : > * SERVER_ADDR : 172.18.1.109 > * SERVER_ADMIN : root at localhost > * SERVER_NAME : www.biocatalogue.org > * SERVER_PORT : 80 > * SERVER_PROTOCOL : HTTP/1.1 > * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) > * _ : _ > * action_controller.request.query_parameters : > * action_controller.request.request_parameters: > * action_controller.rescue.request : # > * action_controller.rescue.response : # > * rack.errors : # > * rack.input : # > * rack.multiprocess : true > * rack.multithread : false > * rack.request : # > * rack.request.cookie_hash : __utma15951013.396796326.1272273201.1275473442.1275482785.119stats-tabs_tabber1__utmb15951013.22.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations > * rack.request.cookie_string : __utma=15951013.396796326.1272273201.1275473442.1275482785.119; __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; search_results_tabber=0; stats-tabs_tabber=1; __utmb=15951013.22.10.1275482785 > * rack.request.query_hash : > * rack.request.query_string : > * rack.routing_args : actionshowid80controllerrest_methods > * rack.run_once : false > * rack.session : search_show_listing_typesimpleprevious_url/rest_methods/80use_tab_cookiefalse_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=services_index_listing_typedetaileduser_id27flashlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= > * rack.session.options : securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath/ > * rack.session.record : # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 6127 > * Server : pweb-4a > > * request.format: text/html > > ------------------------------- > Backtrace: > ------------------------------- > > On line #16 of app/views/rest_methods/_breadcrumbs.html.erb > > 13: <% if controller.action_name.downcase == "show" -%> > 14:
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    • > 15: > 16:
  • <%= link_to display_name(@rest_service.service), @rest_service.service -%>
    • > 17: > 18:
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    • > 19: > > app/views/rest_methods/_breadcrumbs.html.erb:16 > app/helpers/application_helper.rb:510:in `render_breadcrumbs_after_home' > app/views/widgets/_breadcrumbs_bar.html.erb:18 > app/views/layouts/application_wide.html.erb:52 > passenger (2.2.4) lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' > passenger (2.2.4) lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in `safe_fork' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in `start' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > > -- 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 Jun 2 09:52:21 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 2 Jun 2010 09:52:21 -0400 (EDT) Subject: [BioCatalogue-developers] [2074] trunk: - implemented functionality to change reassign a hostname' s provider Message-ID: <20100602135221.608C518582E2@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Wed Jun 2 09:55:20 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 2 Jun 2010 14:55:20 +0100 Subject: [BioCatalogue-developers] [Fwd: [Production ERROR] rest_methods#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400"] In-Reply-To: <4C065CE2.2020805@ebi.ac.uk> References: <4C06583E.7000209@cs.man.ac.uk> <4C065CE2.2020805@ebi.ac.uk> Message-ID: <5D3C5960-F802-4E26-9CA5-FB0933E0A4EC@cs.man.ac.uk> I've tried again... any tracks? Try to delete the following service: http://www.biocatalogue.org/rest_methods/87 if it doesn't work the first time try again and again... Franck On 2 Jun 2010, at 14:30, Eric Nzuobontane wrote: > Can you try to reproduce the error please, I am observing the > processes in the data base. The locks especially... > > Eric > > > Jiten Bhagat wrote: >> This database timeout issue is still ongoing.... >> >> Jits >> >> >> -------- Original Message -------- >> Subject: [Production ERROR] rest_methods#destroy >> (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout >> exceeded; try restarting transaction: DELETE FROM >> `annotation_versions` >> WHERE `id` = 56400" >> Date: Wed, 2 Jun 2010 14:07:03 +0100 >> From: BioCatalogue Errors >> To: ericnzuo at ebi.ac.uk, jits at cs.man.ac.uk >> >> >> >> A ActiveRecord::StatementInvalid occurred in rest_methods#destroy: >> >> Mysql::Error: Lock wait timeout exceeded; try restarting >> transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400 >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/abstract_adapter.rb:212:in `log' >> >> ------------------------------- >> Request: >> ------------------------------- >> >> * URL : http://www.biocatalogue.org/rest_methods/80 >> * Method : DELETE >> * IP address: 130.88.195.202 >> * Parameters: {"action"=>"destroy", "_method"=>"delete", >> "authenticity_token"=>"0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/ >> 0hNZ0=", "id"=>"80", "controller"=>"rest_methods"} >> * Rails root: /net/nas11a/vol1/alien-www/html/biocatalogue/rails/ >> biocatalogue >> >> ------------------------------- >> Session: >> ------------------------------- >> >> * session id: nil >> * data: nil >> >> ------------------------------- >> Environment: >> ------------------------------- >> >> * CONTENT_LENGTH : 82 >> * CONTENT_TYPE : application/x-www- >> form-urlencoded >> * 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 : en-us,en;q=0.5 >> * HTTP_CONNECTION : keep-alive >> * HTTP_CONTENT_TYPE : application/x-www- >> form-urlencoded >> * HTTP_COOKIE : >> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)| >> utmcmd=organic|utmctr=CYGDAnnotations; __utmc=15951013; >> _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >> search_results_tabber=0; stats-tabs_tabber=1; >> __utmb=15951013.13.10.1275482785 >> * HTTP_HOST : www.biocatalogue.org >> * HTTP_KEEP_ALIVE : 300 >> * HTTP_REFERER : http://www.biocatalogue.org/rest_methods/80 >> * HTTP_USER_AGENT : Mozilla/5.0 >> (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/ >> 20100315 Firefox/3.5.9 >> * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 >> * PATH_INFO : /rest_methods/80 >> * QUERY_STRING : * >> REMOTE_ADDR : 130.88.195.202 >> * REMOTE_PORT : 59702 >> * REQUEST_METHOD : DELETE >> * REQUEST_URI : /rest_methods/80 >> * SCRIPT_NAME : * >> SERVER_ADDR : 172.18.1.109 >> * SERVER_ADMIN : root at localhost >> * SERVER_NAME : www.biocatalogue.org >> * SERVER_PORT : 80 >> * SERVER_PROTOCOL : HTTP/1.1 >> * SERVER_SOFTWARE : Apache/2.2.3 >> (CentOS) >> * _ : _ >> * action_controller.request.query_parameters : * >> action_controller.request.request_parameters: >> authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/ >> 0hNZ0=_methoddelete >> * action_controller.rescue.request : >> # >> * action_controller.rescue.response : >> # >> * rack.errors : # >> * rack.input : #> 0x2aaaafd9c720> >> * rack.methodoverride.original_method : POST >> * rack.multiprocess : true >> * rack.multithread : false >> * rack.request : #> 0x2aaaafd9d3f0> >> * rack.request.cookie_hash : >> __utma15951013.396796326.1272273201.1275473442.1275482785.119stats- >> tabs_tabber1__utmb15951013.13.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4 >> .utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations >> * rack.request.cookie_string : >> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)| >> utmcmd=organic|utmctr=CYGDAnnotations; __utmc=15951013; >> _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >> search_results_tabber=0; stats-tabs_tabber=1; >> __utmb=15951013.13.10.1275482785 >> * rack.request.form_hash : >> authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/ >> 0hNZ0=_methoddelete >> * rack.request.form_input : #> 0x2aaaafd9c720> >> * rack.request.form_vars : >> _method >> =delete&authenticity_token=0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d >> %2F0hNZ0%3D >> * rack.request.query_hash : * >> rack.request.query_string : * >> rack.routing_args : >> actiondestroyid80controllerrest_methods >> * rack.run_once : false >> * rack.session : >> search_show_listing_typesimpleprevious_url/rest_methods/ >> 80use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d >> /0hNZ0=user_id27flashlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= >> * rack.session.options : >> securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath >> / >> * rack.session.record : >> # >> * rack.url_scheme : http >> * rack.version : 10 >> * Process: 14304 >> * Server : pweb-4a >> * request.format: text/html >> >> ------------------------------- >> Backtrace: >> ------------------------------- >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/abstract_adapter.rb:212:in `log' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/mysql_adapter.rb:320:in `execute' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/abstract/database_statements.rb:265:in >> `update_sql' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/mysql_adapter.rb:335:in `update_sql' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/abstract/database_statements.rb:270:in >> `delete_sql' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/abstract/database_statements.rb:54:in >> `delete_without_query_dirty' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/abstract/query_cache.rb:18:in `delete' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb: >> 2578:in `destroy_without_lock' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/locking/ >> optimistic.rb:113:in `destroy_without_callbacks' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> callbacks.rb:337:in `destroy_without_transactions' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:229:in `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:229:in `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:182:in `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:228:in `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:192:in `destroy' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations.rb:1364:in `has_many_dependent_destroy_for_versions' >> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/ >> finder.rb:168:in `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations/association_collection.rb:364:in >> `method_missing_without_paginate' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations/association_proxy.rb:219:in `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations/association_proxy.rb:219:in `each' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations/association_proxy.rb:219:in `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations/association_proxy.rb:219:in `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations/association_collection.rb:364:in >> `method_missing_without_paginate' >> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/ >> finder.rb:168:in `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations.rb:1364:in `has_many_dependent_destroy_for_versions' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:178:in `send' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:178:in `evaluate_method' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:166:in `call' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:93:in `run' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:92:in `each' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:92:in `send' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:92:in `run' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:276:in `run_callbacks' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> callbacks.rb:344:in `callback' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> callbacks.rb:336:in `destroy_without_transactions' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:229:in `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:229:in `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:182:in `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:228:in `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:192:in `destroy_without_trash' >> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/ >> acts_as_trashable.rb:41:in `destroy' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:182:in `transaction' >> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/ >> acts_as_trashable.rb:38:in `destroy' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations.rb:1364:in `has_many_dependent_destroy_for_annotations' >> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/ >> finder.rb:168:in `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations/association_collection.rb:364:in >> `method_missing_without_paginate' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations/association_proxy.rb:219:in `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations/association_proxy.rb:219:in `each' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations/association_proxy.rb:219:in `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations/association_proxy.rb:219:in `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations/association_collection.rb:364:in >> `method_missing_without_paginate' >> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/ >> finder.rb:168:in `method_missing' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> associations.rb:1364:in `has_many_dependent_destroy_for_annotations' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:178:in `send' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:178:in `evaluate_method' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:166:in `call' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:93:in `run' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:92:in `each' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:92:in `send' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:92:in `run' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> callbacks.rb:276:in `run_callbacks' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> callbacks.rb:344:in `callback' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> callbacks.rb:336:in `destroy_without_transactions' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:229:in `send' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:229:in `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:182:in `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:228:in `with_transaction_returning_status' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:192:in `destroy_without_trash' >> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/ >> acts_as_trashable.rb:41:in `destroy' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> transactions.rb:182:in `transaction' >> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/ >> acts_as_trashable.rb:38:in `destroy' >> [RAILS_ROOT]/app/controllers/rest_methods_controller.rb:136:in >> `destroy' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb: >> 1322:in `send' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb: >> 1322:in `perform_action_without_filters' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ >> filters.rb:617:in `call_filters' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ >> filters.rb:610:in `perform_action_without_benchmark' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ >> benchmarking.rb:68:in `perform_action_without_rescue' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> core_ext/benchmark.rb:17:in `ms' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> core_ext/benchmark.rb:10:in `realtime' >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/ >> core_ext/benchmark.rb:17:in `ms' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ >> benchmarking.rb:68:in `perform_action_without_rescue' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ >> rescue.rb:160:in `perform_action_without_flash' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ >> flash.rb:141:in `perform_action' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb: >> 523:in `send' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb: >> 523:in `process_without_filters' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ >> filters.rb:606:in `process' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb: >> 391:in `process' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb: >> 386:in `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/ >> route_set.rb:433:in `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ >> dispatcher.rb:88:in `dispatch' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ >> dispatcher.rb:111:in `_call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ >> dispatcher.rb:82:in `initialize' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/ >> rack-1.0/rack/head.rb:9:in `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/ >> rack-1.0/rack/head.rb:9:in `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/ >> rack-1.0/rack/methodoverride.rb:24:in `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ >> params_parser.rb:15:in `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ >> rewindable_input.rb:25:in `call' >> [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in >> `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/ >> abstract_store.rb:122:in `call' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> query_cache.rb:29:in `call' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/abstract/query_cache.rb:34:in `cache' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> query_cache.rb:9:in `cache' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> query_cache.rb:28:in `call' >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/ >> connection_adapters/abstract/connection_pool.rb:361:in `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ >> failsafe.rb:11:in `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/ >> rack-1.0/rack/lock.rb:11:in `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/ >> rack-1.0/rack/lock.rb:11:in `synchronize' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/ >> rack-1.0/rack/lock.rb:11:in `call' >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/ >> dispatcher.rb:106:in `call' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/rack/request_handler.rb:91:in `process_request' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/abstract_request_handler.rb:206:in `main_loop' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/railz/application_spawner.rb:376:in >> `start_request_handler' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/railz/application_spawner.rb:334:in >> `handle_spawn_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/utils.rb:182:in `safe_fork' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/railz/application_spawner.rb:332:in >> `handle_spawn_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/abstract_server.rb:351:in `__send__' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/abstract_server.rb:351:in `main_loop' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/abstract_server.rb:195:in `start_synchronously' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/abstract_server.rb:162:in `start' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/railz/application_spawner.rb:213:in `start' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/abstract_server_collection.rb:126:in >> `lookup_or_add' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/abstract_server_collection.rb:80:in `synchronize' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/abstract_server_collection.rb:79:in `synchronize' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/spawn_manager.rb:153:in `spawn_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/abstract_server.rb:351:in `__send__' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/abstract_server.rb:351:in `main_loop' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/ >> phusion_passenger/abstract_server.rb:195:in `start_synchronously' >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn- >> server:61 >> >> >> >> _______________________________________________ >> 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 > ================================== > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From ericnzuo at ebi.ac.uk Wed Jun 2 10:05:05 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 02 Jun 2010 15:05:05 +0100 Subject: [BioCatalogue-developers] [Production ERROR] application#show (ActionView::TemplateError) "undefined method `service' for nil:NilClass" In-Reply-To: <4c0663df4cb16_66501558cf4fd7c81ba@pweb-3b.ebi.ac.uk.tmail> References: <4c0663df4cb16_66501558cf4fd7c81ba@pweb-3b.ebi.ac.uk.tmail> Message-ID: <4C066511.2070003@ebi.ac.uk> BioCatalogue Errors wrote: > A ActionView::TemplateError occurred in application#show: > > undefined method `service' for nil:NilClass > On line #16 of app/views/rest_methods/_breadcrumbs.html.erb > > 13: <% if controller.action_name.downcase == "show" -%> > 14:
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    • > 15: > 16:
  • <%= link_to display_name(@rest_service.service), @rest_service.service -%>
    • > 17: > 18:
  • »
    • > > 19: > I think this bit of code could check if the @rest_service object is valid before attempting to call the service method on it. Could issue a warning and stop these error messages. Eric > app/views/rest_methods/_breadcrumbs.html.erb:16 > app/helpers/application_helper.rb:510:in `render_breadcrumbs_after_home' > app/views/widgets/_breadcrumbs_bar.html.erb:18 > app/views/layouts/application_wide.html.erb:52 > passenger (2.2.4) lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' > passenger (2.2.4) lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in `safe_fork' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in `start' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > > ------------------------------- > Request: > ------------------------------- > > * URL : http://www.biocatalogue.org/rest_methods/87 > * Method : GET > * IP address: 130.88.195.202 > * Parameters: {"action"=>"show", "id"=>"87", "controller"=>"rest_methods"} > * 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 : en-us,en;q=0.5 > * HTTP_CACHE_CONTROL : max-age=0 > * HTTP_CONNECTION : keep-alive > * HTTP_COOKIE : __utma=15951013.396796326.1272273201.1275473442.1275482785.119; __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; search_results_tabber=0; stats-tabs_tabber=1; __utmb=15951013.47.10.1275482785 > * HTTP_HOST : www.biocatalogue.org > * HTTP_IF_NONE_MATCH : "0180f1b3e6396d6c123bc9e0100888a9" > * HTTP_KEEP_ALIVE : 300 > * HTTP_REFERER : http://www.biocatalogue.org/services/2699 > * HTTP_USER_AGENT : Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 Firefox/3.5.9 > * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 > * PATH_INFO : /rest_methods/87 > * QUERY_STRING : > * REMOTE_ADDR : 130.88.195.202 > * REMOTE_PORT : 47246 > * REQUEST_METHOD : GET > * REQUEST_URI : /rest_methods/87 > * SCRIPT_NAME : > * SERVER_ADDR : 172.18.1.108 > * SERVER_ADMIN : root at localhost > * SERVER_NAME : www.biocatalogue.org > * SERVER_PORT : 80 > * SERVER_PROTOCOL : HTTP/1.1 > * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) > * _ : _ > * action_controller.request.query_parameters : > * action_controller.request.request_parameters: > * action_controller.rescue.request : # > * action_controller.rescue.response : # > * rack.errors : # > * rack.input : # > * rack.multiprocess : true > * rack.multithread : false > * rack.request : # > * rack.request.cookie_hash : __utma15951013.396796326.1272273201.1275473442.1275482785.119stats-tabs_tabber1__utmb15951013.47.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations > * rack.request.cookie_string : __utma=15951013.396796326.1272273201.1275473442.1275482785.119; __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; search_results_tabber=0; stats-tabs_tabber=1; __utmb=15951013.47.10.1275482785 > * rack.request.query_hash : > * rack.request.query_string : > * rack.routing_args : actionshowid87controllerrest_methods > * rack.run_once : false > * rack.session : search_show_listing_typesimpleprevious_url/rest_methods/87use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=user_id27flashnoticeEndpoint GET /goTerms has been deletedlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= > * rack.session.options : securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath/ > * rack.session.record : # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 26192 > * Server : pweb-3b > > * request.format: text/html > > ------------------------------- > Backtrace: > ------------------------------- > > On line #16 of app/views/rest_methods/_breadcrumbs.html.erb > > 13: <% if controller.action_name.downcase == "show" -%> > 14:
  • »
    • > 15: > 16:
  • <%= link_to display_name(@rest_service.service), @rest_service.service -%>
    • > 17: > 18:
  • »
    • > 19: > > app/views/rest_methods/_breadcrumbs.html.erb:16 > app/helpers/application_helper.rb:510:in `render_breadcrumbs_after_home' > app/views/widgets/_breadcrumbs_bar.html.erb:18 > app/views/layouts/application_wide.html.erb:52 > passenger (2.2.4) lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' > passenger (2.2.4) lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in `safe_fork' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in `start' > passenger (2.2.4) lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' > passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `__send__' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > > -- 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 Jun 2 10:11:32 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 02 Jun 2010 15:11:32 +0100 Subject: [BioCatalogue-developers] [Fwd: [Production ERROR] rest_methods#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400"] In-Reply-To: <5D3C5960-F802-4E26-9CA5-FB0933E0A4EC@cs.man.ac.uk> References: <4C06583E.7000209@cs.man.ac.uk> <4C065CE2.2020805@ebi.ac.uk> <5D3C5960-F802-4E26-9CA5-FB0933E0A4EC@cs.man.ac.uk> Message-ID: <4C066694.1060401@ebi.ac.uk> At one instant, I saw that 3 tables were locked but can't see which ones were those. But I will continue to investigate... Eric Franck Tanoh wrote: > I've tried again... any tracks? > > Try to delete the following service: > http://www.biocatalogue.org/rest_methods/87 if it doesn't work the > first time try again and again... > > Franck > > On 2 Jun 2010, at 14:30, Eric Nzuobontane wrote: > >> Can you try to reproduce the error please, I am observing the >> processes in the data base. The locks especially... >> >> Eric >> >> >> Jiten Bhagat wrote: >>> This database timeout issue is still ongoing.... >>> >>> Jits >>> >>> >>> -------- Original Message -------- >>> Subject: [Production ERROR] rest_methods#destroy >>> (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout >>> exceeded; try restarting transaction: DELETE FROM `annotation_versions` >>> WHERE `id` = 56400" >>> Date: Wed, 2 Jun 2010 14:07:03 +0100 >>> From: BioCatalogue Errors >>> To: ericnzuo at ebi.ac.uk, jits at cs.man.ac.uk >>> >>> >>> >>> A ActiveRecord::StatementInvalid occurred in rest_methods#destroy: >>> >>> Mysql::Error: Lock wait timeout exceeded; try restarting >>> transaction: DELETE FROM `annotation_versions` WHERE `id` = 56400 >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in >>> `log' >>> >>> ------------------------------- >>> Request: >>> ------------------------------- >>> >>> * URL : http://www.biocatalogue.org/rest_methods/80 >>> * Method : DELETE >>> * IP address: 130.88.195.202 >>> * Parameters: {"action"=>"destroy", "_method"=>"delete", >>> "authenticity_token"=>"0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=", >>> "id"=>"80", "controller"=>"rest_methods"} >>> * Rails root: >>> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue >>> >>> ------------------------------- >>> Session: >>> ------------------------------- >>> >>> * session id: nil >>> * data: nil >>> >>> ------------------------------- >>> Environment: >>> ------------------------------- >>> >>> * CONTENT_LENGTH : 82 >>> * CONTENT_TYPE : >>> application/x-www-form-urlencoded >>> * 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 : en-us,en;q=0.5 >>> * HTTP_CONNECTION : keep-alive >>> * HTTP_CONTENT_TYPE : >>> application/x-www-form-urlencoded >>> * HTTP_COOKIE : >>> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >>> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >>> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >>> search_results_tabber=0; stats-tabs_tabber=1; >>> __utmb=15951013.13.10.1275482785 >>> * HTTP_HOST : www.biocatalogue.org >>> * HTTP_KEEP_ALIVE : 300 >>> * HTTP_REFERER : >>> http://www.biocatalogue.org/rest_methods/80 >>> * HTTP_USER_AGENT : Mozilla/5.0 >>> (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) >>> Gecko/20100315 Firefox/3.5.9 >>> * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 >>> * PATH_INFO : /rest_methods/80 >>> * QUERY_STRING : * >>> REMOTE_ADDR : 130.88.195.202 >>> * REMOTE_PORT : 59702 >>> * REQUEST_METHOD : DELETE >>> * REQUEST_URI : /rest_methods/80 >>> * SCRIPT_NAME : * >>> SERVER_ADDR : 172.18.1.109 >>> * SERVER_ADMIN : root at localhost >>> * SERVER_NAME : www.biocatalogue.org >>> * SERVER_PORT : 80 >>> * SERVER_PROTOCOL : HTTP/1.1 >>> * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) >>> * _ : _ >>> * action_controller.request.query_parameters : * >>> action_controller.request.request_parameters: >>> authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=_methoddelete >>> >>> * action_controller.rescue.request : >>> # >>> * action_controller.rescue.response : >>> # >>> * rack.errors : # >>> * rack.input : >>> # >>> * rack.methodoverride.original_method : POST >>> * rack.multiprocess : true >>> * rack.multithread : false >>> * rack.request : >>> # >>> * rack.request.cookie_hash : >>> __utma15951013.396796326.1272273201.1275473442.1275482785.119stats-tabs_tabber1__utmb15951013.13.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations >>> >>> * rack.request.cookie_string : >>> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >>> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >>> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >>> search_results_tabber=0; stats-tabs_tabber=1; >>> __utmb=15951013.13.10.1275482785 >>> * rack.request.form_hash : >>> authenticity_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=_methoddelete >>> >>> * rack.request.form_input : >>> # >>> * rack.request.form_vars : >>> _method=delete&authenticity_token=0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d%2F0hNZ0%3D >>> >>> * rack.request.query_hash : * >>> rack.request.query_string : * >>> rack.routing_args : >>> actiondestroyid80controllerrest_methods >>> * rack.run_once : false >>> * rack.session : >>> search_show_listing_typesimpleprevious_url/rest_methods/80use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=user_id27flashlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= >>> >>> * rack.session.options : >>> securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath/ >>> >>> * rack.session.record : >>> # >>> * rack.url_scheme : http >>> * rack.version : 10 >>> * Process: 14304 >>> * Server : pweb-4a >>> * request.format: text/html >>> >>> ------------------------------- >>> Backtrace: >>> ------------------------------- >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in >>> `log' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:320:in >>> `execute' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:265:in >>> `update_sql' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:335:in >>> `update_sql' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:270:in >>> `delete_sql' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:54:in >>> `delete_without_query_dirty' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:18:in >>> `delete' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:2578:in >>> `destroy_without_lock' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/locking/optimistic.rb:113:in >>> `destroy_without_callbacks' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:337:in >>> `destroy_without_transactions' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >>> `send' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >>> `with_transaction_returning_status' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >>> `transaction' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >>> `transaction' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in >>> `with_transaction_returning_status' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in >>> `destroy' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >>> `has_many_dependent_destroy_for_versions' >>> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >>> `method_missing' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >>> `method_missing_without_paginate' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >>> `method_missing' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >>> `each' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >>> `send' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >>> `method_missing' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >>> `method_missing_without_paginate' >>> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >>> `method_missing' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >>> `has_many_dependent_destroy_for_versions' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >>> `send' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >>> `evaluate_method' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in >>> `run' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >>> `each' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >>> `send' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >>> `run' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in >>> `run_callbacks' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in >>> `callback' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in >>> `destroy_without_transactions' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >>> `send' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >>> `with_transaction_returning_status' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >>> `transaction' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >>> `transaction' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in >>> `with_transaction_returning_status' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in >>> `destroy_without_trash' >>> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in >>> `destroy' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >>> `transaction' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >>> `transaction' >>> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in >>> `destroy' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >>> `has_many_dependent_destroy_for_annotations' >>> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >>> `method_missing' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >>> `method_missing_without_paginate' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >>> `method_missing' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >>> `each' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >>> `send' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >>> `method_missing' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >>> `method_missing_without_paginate' >>> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >>> `method_missing' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >>> `has_many_dependent_destroy_for_annotations' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >>> `send' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >>> `evaluate_method' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in >>> `run' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >>> `each' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >>> `send' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >>> `run' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in >>> `run_callbacks' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in >>> `callback' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in >>> `destroy_without_transactions' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >>> `send' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >>> `with_transaction_returning_status' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >>> `transaction' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >>> `transaction' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in >>> `with_transaction_returning_status' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in >>> `destroy_without_trash' >>> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in >>> `destroy' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >>> `transaction' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >>> `transaction' >>> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in >>> `destroy' >>> [RAILS_ROOT]/app/controllers/rest_methods_controller.rb:136:in >>> `destroy' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in >>> `send' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in >>> `perform_action_without_filters' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:617:in >>> `call_filters' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:610:in >>> `perform_action_without_benchmark' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in >>> `perform_action_without_rescue' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in >>> `ms' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:10:in >>> `realtime' >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in >>> `ms' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in >>> `perform_action_without_rescue' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rescue.rb:160:in >>> `perform_action_without_flash' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb:141:in >>> `perform_action' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in >>> `send' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in >>> `process_without_filters' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:606:in >>> `process' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:391:in >>> `process' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:386:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/route_set.rb:433:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:88:in >>> `dispatch' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:111:in >>> `_call' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:82:in >>> `initialize' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/methodoverride.rb:24:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/params_parser.rb:15:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rewindable_input.rb:25:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in >>> `cache' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in >>> `cache' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >>> `synchronize' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in >>> `call' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in >>> `process_request' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in >>> `main_loop' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in >>> `start_request_handler' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in >>> `handle_spawn_application' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in >>> `safe_fork' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in >>> `handle_spawn_application' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >>> `__send__' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >>> `main_loop' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in >>> `start_synchronously' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in >>> `start' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in >>> `start' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in >>> `spawn_rails_application' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in >>> `lookup_or_add' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in >>> `spawn_rails_application' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in >>> `synchronize' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in >>> `synchronize' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in >>> `spawn_rails_application' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in >>> `spawn_application' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in >>> `handle_spawn_application' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >>> `__send__' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >>> `main_loop' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in >>> `start_synchronously' >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >> ================================== >> >> _______________________________________________ >> 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 Jun 2 12:32:51 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 02 Jun 2010 17:32:51 +0100 Subject: [BioCatalogue-developers] [Production ERROR] application#show (ActionView::TemplateError) "undefined method `service' for nil:NilClass" In-Reply-To: <4C066511.2070003@ebi.ac.uk> References: <4c0663df4cb16_66501558cf4fd7c81ba@pweb-3b.ebi.ac.uk.tmail> <4C066511.2070003@ebi.ac.uk> Message-ID: <4C0687B3.6090908@cs.man.ac.uk> There is a bigger problem here; we're getting errors exactly like this for a number of different things. Usually this shouldn't happen because Model.find(..) calls in the controller would trap bad URLs and give an appropriate 404. So it could be the data is inconsistent (orphaned objects etc) but I have added sanity checks for that. So in the end, I don't know. And I cannot reproduce this locally (for SoapOperations), even with the latest data. I have asked Mannie to at least investigate the RestService issues. As for "crowding the error messages with the possibility of important mails being missed!" ... this is an important error email. Just having checks in the UI might temporarily stop it, but would possibly hide bigger issues that could get forgotten. Note, I use email thread views to automatically group emails so I don't miss important ones. Jits Eric Nzuobontane wrote: > BioCatalogue Errors wrote: >> A ActionView::TemplateError occurred in application#show: >> >> undefined method `service' for nil:NilClass >> On line #16 of app/views/rest_methods/_breadcrumbs.html.erb >> >> 13: <% if controller.action_name.downcase == "show" -%> >> 14:
  • »
    • >> 15: 16:
  • <%= link_to >> display_name(@rest_service.service), @rest_service.service >> -%>
    • >> 17: >> 18:
  • »
    • >> 19: >> > > I think this bit of code could check if the @rest_service object is > valid before attempting to call the service method on it. Could issue > a warning and stop these error messages. > > Eric > > > > > > > > > >> app/views/rest_methods/_breadcrumbs.html.erb:16 >> app/helpers/application_helper.rb:510:in >> `render_breadcrumbs_after_home' >> app/views/widgets/_breadcrumbs_bar.html.erb:18 >> app/views/layouts/application_wide.html.erb:52 >> passenger (2.2.4) >> lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' >> passenger (2.2.4) >> lib/phusion_passenger/railz/application_spawner.rb:376:in >> `start_request_handler' >> passenger (2.2.4) >> lib/phusion_passenger/railz/application_spawner.rb:334:in >> `handle_spawn_application' >> passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in `safe_fork' >> passenger (2.2.4) >> lib/phusion_passenger/railz/application_spawner.rb:332:in >> `handle_spawn_application' >> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >> `__send__' >> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >> `main_loop' >> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in >> `start_synchronously' >> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in >> `start' >> passenger (2.2.4) >> lib/phusion_passenger/railz/application_spawner.rb:213:in `start' >> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in >> `spawn_rails_application' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_server_collection.rb:126:in >> `lookup_or_add' >> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in >> `spawn_rails_application' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' >> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in >> `spawn_rails_application' >> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in >> `spawn_application' >> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in >> `handle_spawn_application' >> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >> `__send__' >> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >> `main_loop' >> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in >> `start_synchronously' >> >> ------------------------------- >> Request: >> ------------------------------- >> >> * URL : http://www.biocatalogue.org/rest_methods/87 >> * Method : GET >> * IP address: 130.88.195.202 >> * Parameters: {"action"=>"show", "id"=>"87", >> "controller"=>"rest_methods"} >> * 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 : en-us,en;q=0.5 >> * HTTP_CACHE_CONTROL : max-age=0 >> * HTTP_CONNECTION : keep-alive >> * HTTP_COOKIE : >> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >> search_results_tabber=0; stats-tabs_tabber=1; >> __utmb=15951013.47.10.1275482785 >> * HTTP_HOST : www.biocatalogue.org >> * HTTP_IF_NONE_MATCH : >> "0180f1b3e6396d6c123bc9e0100888a9" >> * HTTP_KEEP_ALIVE : 300 >> * HTTP_REFERER : >> http://www.biocatalogue.org/services/2699 >> * HTTP_USER_AGENT : Mozilla/5.0 >> (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 >> Firefox/3.5.9 >> * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 >> * PATH_INFO : /rest_methods/87 >> * QUERY_STRING : * >> REMOTE_ADDR : 130.88.195.202 >> * REMOTE_PORT : 47246 >> * REQUEST_METHOD : GET >> * REQUEST_URI : /rest_methods/87 >> * SCRIPT_NAME : * >> SERVER_ADDR : 172.18.1.108 >> * SERVER_ADMIN : root at localhost >> * SERVER_NAME : www.biocatalogue.org >> * SERVER_PORT : 80 >> * SERVER_PROTOCOL : HTTP/1.1 >> * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) >> * _ : _ >> * action_controller.request.query_parameters : * >> action_controller.request.request_parameters: * >> action_controller.rescue.request : >> # >> * action_controller.rescue.response : >> # >> * rack.errors : # >> * rack.input : >> # >> * rack.multiprocess : true >> * rack.multithread : false >> * rack.request : >> # >> * rack.request.cookie_hash : >> __utma15951013.396796326.1272273201.1275473442.1275482785.119stats-tabs_tabber1__utmb15951013.47.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations >> >> * rack.request.cookie_string : >> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >> search_results_tabber=0; stats-tabs_tabber=1; >> __utmb=15951013.47.10.1275482785 >> * rack.request.query_hash : * >> rack.request.query_string : * >> rack.routing_args : >> actionshowid87controllerrest_methods >> * rack.run_once : false >> * rack.session : >> search_show_listing_typesimpleprevious_url/rest_methods/87use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=user_id27flashnoticeEndpoint >> GET /goTerms has been >> deletedlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= >> * rack.session.options : >> securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath/ >> >> * rack.session.record : >> # >> * rack.url_scheme : http >> * rack.version : 10 >> * Process: 26192 >> * Server : pweb-3b >> * request.format: text/html >> >> ------------------------------- >> Backtrace: >> ------------------------------- >> >> On line #16 of app/views/rest_methods/_breadcrumbs.html.erb >> 13: <% if controller.action_name.downcase == "show" -%> >> 14:
  • »
    • >> 15: 16:
  • <%= link_to >> display_name(@rest_service.service), @rest_service.service >> -%>
    • >> 17: >> 18:
  • »
    • >> 19: >> app/views/rest_methods/_breadcrumbs.html.erb:16 >> app/helpers/application_helper.rb:510:in >> `render_breadcrumbs_after_home' >> app/views/widgets/_breadcrumbs_bar.html.erb:18 >> app/views/layouts/application_wide.html.erb:52 >> passenger (2.2.4) >> lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' >> passenger (2.2.4) >> lib/phusion_passenger/railz/application_spawner.rb:376:in >> `start_request_handler' >> passenger (2.2.4) >> lib/phusion_passenger/railz/application_spawner.rb:334:in >> `handle_spawn_application' >> passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in >> `safe_fork' >> passenger (2.2.4) >> lib/phusion_passenger/railz/application_spawner.rb:332:in >> `handle_spawn_application' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_server.rb:351:in `__send__' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_server.rb:351:in `main_loop' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_server.rb:162:in `start' >> passenger (2.2.4) >> lib/phusion_passenger/railz/application_spawner.rb:213:in `start' >> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in >> `spawn_rails_application' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_server_collection.rb:126:in >> `lookup_or_add' >> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in >> `spawn_rails_application' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' >> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in >> `spawn_rails_application' >> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in >> `spawn_application' >> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in >> `handle_spawn_application' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_server.rb:351:in `__send__' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_server.rb:351:in `main_loop' >> passenger (2.2.4) >> lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' >> >> > > From noreply at rubyforge.org Wed Jun 2 12:42:06 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 2 Jun 2010 12:42:06 -0400 (EDT) Subject: [BioCatalogue-developers] [2075] trunk: REST API work: added favourites and views counts to the < counts> section in the section of . Message-ID: <20100602164206.7E489185835D@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Jun 2 14:17:47 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 02 Jun 2010 19:17:47 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parseAminoAcidSequenceFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parseAminoAcidSequenceFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/990 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 Jun 2 15:27:55 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 02 Jun 2010 20:27:55 +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 Wed Jun 2 17:48:57 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 02 Jun 2010 22:48:57 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:getPDBFromTransfac' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:getPDBFromTransfac' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1012 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Thu Jun 3 04:19:47 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 03 Jun 2010 09:19:47 +0100 Subject: [BioCatalogue-developers] [Production ERROR] application#show (ActionView::TemplateError) "undefined method `service' for nil:NilClass" In-Reply-To: <4C0687B3.6090908@cs.man.ac.uk> References: <4c0663df4cb16_66501558cf4fd7c81ba@pweb-3b.ebi.ac.uk.tmail> <4C066511.2070003@ebi.ac.uk> <4C0687B3.6090908@cs.man.ac.uk> Message-ID: <4C0765A3.3030803@ebi.ac.uk> Jiten Bhagat wrote: > There is a bigger problem here; we're getting errors exactly like this > for a number of different things. Usually this shouldn't happen because > Model.find(..) calls in the controller would trap bad URLs and give an > appropriate 404. So it could be the data is inconsistent (orphaned > objects etc) but I have added sanity checks for that. So in the end, I > don't know. And I cannot reproduce this locally (for SoapOperations), > even with the latest data. I have asked Mannie to at least investigate > the RestService issues. > As far as I see it is not about the inconsistency of data (though that might have an effect as well) but rather an application level issue. I believe the mails are generated often by robots as the little investigation I made last time pointed towards google bot. Right now, if you hit any url like http://www.biocatalogue.org/soap_operations/10000 (or any id which does not exist in the db), this will generate one of those errors. If generating an error is OK functionally, then we should expect these mails with the possibility of being flooded when something just keeps hitting one such url. Eric > Jits > > > Eric Nzuobontane wrote: > >> BioCatalogue Errors wrote: >> >>> A ActionView::TemplateError occurred in application#show: >>> >>> undefined method `service' for nil:NilClass >>> On line #16 of app/views/rest_methods/_breadcrumbs.html.erb >>> >>> 13: <% if controller.action_name.downcase == "show" -%> >>> 14:
  • »
    • >>> 15: 16:
  • <%= link_to >>> display_name(@rest_service.service), @rest_service.service >>> -%>
    • >>> 17: >>> 18:
  • »
    • >>> 19: >>> >>> >> I think this bit of code could check if the @rest_service object is >> valid before attempting to call the service method on it. Could issue >> a warning and stop these error messages. >> >> Eric >> >> >> >> >> >> >> >> >> >> >>> app/views/rest_methods/_breadcrumbs.html.erb:16 >>> app/helpers/application_helper.rb:510:in >>> `render_breadcrumbs_after_home' >>> app/views/widgets/_breadcrumbs_bar.html.erb:18 >>> app/views/layouts/application_wide.html.erb:52 >>> passenger (2.2.4) >>> lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' >>> passenger (2.2.4) >>> lib/phusion_passenger/railz/application_spawner.rb:376:in >>> `start_request_handler' >>> passenger (2.2.4) >>> lib/phusion_passenger/railz/application_spawner.rb:334:in >>> `handle_spawn_application' >>> passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in `safe_fork' >>> passenger (2.2.4) >>> lib/phusion_passenger/railz/application_spawner.rb:332:in >>> `handle_spawn_application' >>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>> `__send__' >>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>> `main_loop' >>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in >>> `start_synchronously' >>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in >>> `start' >>> passenger (2.2.4) >>> lib/phusion_passenger/railz/application_spawner.rb:213:in `start' >>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in >>> `spawn_rails_application' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_server_collection.rb:126:in >>> `lookup_or_add' >>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in >>> `spawn_rails_application' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' >>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in >>> `spawn_rails_application' >>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in >>> `spawn_application' >>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in >>> `handle_spawn_application' >>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>> `__send__' >>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>> `main_loop' >>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in >>> `start_synchronously' >>> >>> ------------------------------- >>> Request: >>> ------------------------------- >>> >>> * URL : http://www.biocatalogue.org/rest_methods/87 >>> * Method : GET >>> * IP address: 130.88.195.202 >>> * Parameters: {"action"=>"show", "id"=>"87", >>> "controller"=>"rest_methods"} >>> * 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 : en-us,en;q=0.5 >>> * HTTP_CACHE_CONTROL : max-age=0 >>> * HTTP_CONNECTION : keep-alive >>> * HTTP_COOKIE : >>> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >>> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >>> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >>> search_results_tabber=0; stats-tabs_tabber=1; >>> __utmb=15951013.47.10.1275482785 >>> * HTTP_HOST : www.biocatalogue.org >>> * HTTP_IF_NONE_MATCH : >>> "0180f1b3e6396d6c123bc9e0100888a9" >>> * HTTP_KEEP_ALIVE : 300 >>> * HTTP_REFERER : >>> http://www.biocatalogue.org/services/2699 >>> * HTTP_USER_AGENT : Mozilla/5.0 >>> (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 >>> Firefox/3.5.9 >>> * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 >>> * PATH_INFO : /rest_methods/87 >>> * QUERY_STRING : * >>> REMOTE_ADDR : 130.88.195.202 >>> * REMOTE_PORT : 47246 >>> * REQUEST_METHOD : GET >>> * REQUEST_URI : /rest_methods/87 >>> * SCRIPT_NAME : * >>> SERVER_ADDR : 172.18.1.108 >>> * SERVER_ADMIN : root at localhost >>> * SERVER_NAME : www.biocatalogue.org >>> * SERVER_PORT : 80 >>> * SERVER_PROTOCOL : HTTP/1.1 >>> * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) >>> * _ : _ >>> * action_controller.request.query_parameters : * >>> action_controller.request.request_parameters: * >>> action_controller.rescue.request : >>> # >>> * action_controller.rescue.response : >>> # >>> * rack.errors : # >>> * rack.input : >>> # >>> * rack.multiprocess : true >>> * rack.multithread : false >>> * rack.request : >>> # >>> * rack.request.cookie_hash : >>> __utma15951013.396796326.1272273201.1275473442.1275482785.119stats-tabs_tabber1__utmb15951013.47.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations >>> >>> * rack.request.cookie_string : >>> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >>> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >>> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >>> search_results_tabber=0; stats-tabs_tabber=1; >>> __utmb=15951013.47.10.1275482785 >>> * rack.request.query_hash : * >>> rack.request.query_string : * >>> rack.routing_args : >>> actionshowid87controllerrest_methods >>> * rack.run_once : false >>> * rack.session : >>> search_show_listing_typesimpleprevious_url/rest_methods/87use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=user_id27flashnoticeEndpoint >>> GET /goTerms has been >>> deletedlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= >>> * rack.session.options : >>> securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath/ >>> >>> * rack.session.record : >>> # >>> * rack.url_scheme : http >>> * rack.version : 10 >>> * Process: 26192 >>> * Server : pweb-3b >>> * request.format: text/html >>> >>> ------------------------------- >>> Backtrace: >>> ------------------------------- >>> >>> On line #16 of app/views/rest_methods/_breadcrumbs.html.erb >>> 13: <% if controller.action_name.downcase == "show" -%> >>> 14:
  • »
    • >>> 15: 16:
  • <%= link_to >>> display_name(@rest_service.service), @rest_service.service >>> -%>
    • >>> 17: >>> 18:
  • »
    • >>> 19: >>> app/views/rest_methods/_breadcrumbs.html.erb:16 >>> app/helpers/application_helper.rb:510:in >>> `render_breadcrumbs_after_home' >>> app/views/widgets/_breadcrumbs_bar.html.erb:18 >>> app/views/layouts/application_wide.html.erb:52 >>> passenger (2.2.4) >>> lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' >>> passenger (2.2.4) >>> lib/phusion_passenger/railz/application_spawner.rb:376:in >>> `start_request_handler' >>> passenger (2.2.4) >>> lib/phusion_passenger/railz/application_spawner.rb:334:in >>> `handle_spawn_application' >>> passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in >>> `safe_fork' >>> passenger (2.2.4) >>> lib/phusion_passenger/railz/application_spawner.rb:332:in >>> `handle_spawn_application' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_server.rb:351:in `__send__' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_server.rb:351:in `main_loop' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_server.rb:162:in `start' >>> passenger (2.2.4) >>> lib/phusion_passenger/railz/application_spawner.rb:213:in `start' >>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in >>> `spawn_rails_application' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_server_collection.rb:126:in >>> `lookup_or_add' >>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in >>> `spawn_rails_application' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' >>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in >>> `spawn_rails_application' >>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in >>> `spawn_application' >>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in >>> `handle_spawn_application' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_server.rb:351:in `__send__' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_server.rb:351:in `main_loop' >>> passenger (2.2.4) >>> lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' >>> >>> >>> >> -- 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 Jun 3 04:34:09 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 03 Jun 2010 09:34:09 +0100 Subject: [BioCatalogue-developers] [Production ERROR] annotations#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded In-Reply-To: <4beab2bfd7101_6eb215a7c5afffc818a@pweb-3b.ebi.ac.uk.tmail> References: <4beab2bfd7101_6eb215a7c5afffc818a@pweb-3b.ebi.ac.uk.tmail> Message-ID: <4C076901.4000908@ebi.ac.uk> I made some investigations into this yesterday but did not get to the bottom of the story. However, it seems it is not the indexing that is the culprit here but the thrashing of records. So what I believe is happening is that when a delete operation occurs, the thrash table is locked by the first thing that needs to be deleted and other deletes in the transaction cannot get hold of the lock fast enough so that the transaction times out. I will try to experiment further to see if this can be confirmed and hence help find a solution to the problem. Eric BioCatalogue Errors wrote: > A ActiveRecord::StatementInvalid occurred in annotations#destroy: > > Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 55788 > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' > > ------------------------------- > Request: > ------------------------------- > > * URL : http://www.biocatalogue.org/annotations/53304 > * Method : DELETE > * IP address: 130.88.195.202 > * Parameters: {"action"=>"destroy", "_method"=>"delete", "authenticity_token"=>"NIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN+pj0g=", "id"=>"53304", "controller"=>"annotations"} > * Rails root: /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue > > ------------------------------- > Session: > ------------------------------- > > * session id: nil > * data: nil > > ------------------------------- > Environment: > ------------------------------- > > * CONTENT_LENGTH : 82 > * CONTENT_TYPE : application/x-www-form-urlencoded > * 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 : en-us,en;q=0.5 > * HTTP_CONNECTION : keep-alive > * HTTP_CONTENT_TYPE : application/x-www-form-urlencoded > * HTTP_COOKIE : __utma=15951013.396796326.1272273201.1273657462.1273661473.55; __utmz=15951013.1272273201.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none); _session_id=ce30b8a07947150391b00de88bd95130; __utmc=15951013; search_results_tabber=0 > * HTTP_HOST : www.biocatalogue.org > * HTTP_KEEP_ALIVE : 300 > * HTTP_REFERER : http://www.biocatalogue.org/soap_operations/13085 > * HTTP_USER_AGENT : Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 Firefox/3.5.9 > * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 > * PATH_INFO : /annotations/53304 > * QUERY_STRING : > * REMOTE_ADDR : 130.88.195.202 > * REMOTE_PORT : 42125 > * REQUEST_METHOD : DELETE > * REQUEST_URI : /annotations/53304 > * SCRIPT_NAME : > * SERVER_ADDR : 172.18.1.108 > * SERVER_ADMIN : root at localhost > * SERVER_NAME : www.biocatalogue.org > * SERVER_PORT : 80 > * SERVER_PROTOCOL : HTTP/1.1 > * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) > * _ : _ > * action_controller.request.query_parameters : > * action_controller.request.request_parameters: authenticity_tokenNIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN+pj0g=_methoddelete > * action_controller.rescue.request : # > * action_controller.rescue.response : # > * rack.errors : # > * rack.input : # > * rack.methodoverride.original_method : POST > * rack.multiprocess : true > * rack.multithread : false > * rack.request : # > * rack.request.cookie_hash : __utma15951013.396796326.1272273201.1273657462.1273661473.55_session_idce30b8a07947150391b00de88bd95130__utmc15951013search_results_tabber0__utmz15951013.1272273201.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none) > * rack.request.cookie_string : __utma=15951013.396796326.1272273201.1273657462.1273661473.55; __utmz=15951013.1272273201.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none); _session_id=ce30b8a07947150391b00de88bd95130; __utmc=15951013; search_results_tabber=0 > * rack.request.form_hash : authenticity_tokenNIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN+pj0g=_methoddelete > * rack.request.form_input : # > * rack.request.form_vars : _method=delete&authenticity_token=NIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN%2Bpj0g%3D > * rack.request.query_hash : > * rack.request.query_string : > * rack.routing_args : actiondestroyid53304controllerannotations > * rack.run_once : false > * rack.session : search_show_listing_typedetailed_csrf_tokenNIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN+pj0g=user_id27previous_url/annotations/53304use_tab_cookietrueservices_index_listing_typedetailedflashlast_searchhttp://www.biocatalogue.org/search?q=WSNetGlycate&commit= > * rack.session.options : expire_aftersecurefalsehttponlytruecookie_onlytruekey_session_ididce30b8a07947150391b00de88bd95130domainpath/ > * rack.session.record : # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 28338 > * Server : pweb-3b > > * request.format: text/html > > ------------------------------- > Backtrace: > ------------------------------- > > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:320:in `execute' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:265:in `update_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:335:in `update_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:270:in `delete_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:54:in `delete_without_query_dirty' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:18:in `delete' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:2578:in `destroy_without_lock' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/locking/optimistic.rb:113:in `destroy_without_callbacks' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:337:in `destroy_without_transactions' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_versions' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `each' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_versions' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `evaluate_method' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in `call' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `each' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in `run_callbacks' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in `callback' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in `destroy_without_transactions' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in `destroy_without_trash' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in `destroy' > [RAILS_ROOT]/vendor/plugins/annotations/lib/app/controllers/annotations_controller.rb:121:in `destroy' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in `send' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in `perform_action_without_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:617:in `call_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:610:in `perform_action_without_benchmark' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in `ms' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:10:in `realtime' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in `ms' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rescue.rb:160:in `perform_action_without_flash' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb:141:in `perform_action' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in `send' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in `process_without_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:606:in `process' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:391:in `process' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:386:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/route_set.rb:433:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:88:in `dispatch' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:111:in `_call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:82:in `initialize' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/methodoverride.rb:24:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/params_parser.rb:15:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rewindable_input.rb:25:in `call' > [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in `cache' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in `cache' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `synchronize' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in `call' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in `safe_fork' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in `start' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 > > -- 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 Thu Jun 3 04:36:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 3 Jun 2010 09:36:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-303) Investigate database timout errors when deleting entries Message-ID: <3550847.1957.1275554177143.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-303?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-303 started by Eric Nzuobontane. > Investigate database timout errors when deleting entries > -------------------------------------------------------- > > Key: BIOCAT-303 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-303 > Project: BioCatalogue > Issue Type: Bug > Components: Server Management > Environment: MySQL datatabase, RoR activerecord > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > When deleting some errors the following timeout error occurs > Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `service_versions` WHERE `id` = 609 > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 3 04:39:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 3 Jun 2010 09:39:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-303) Investigate database timout errors when deleting entries Message-ID: <15126593.1958.1275554357028.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-303?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15004#action_15004 ] Eric Nzuobontane commented on BIOCAT-303: ----------------------------------------- Further investigation reveals that the table locking may actually be due to the trashing of records. It is believed that when a delete transaction occurs, the first item to be deleted locks the trash table and further deletes cannot get hold of the lock fast enough that the transaction times out. Further investigation is needed to confirm this. > Investigate database timout errors when deleting entries > -------------------------------------------------------- > > Key: BIOCAT-303 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-303 > Project: BioCatalogue > Issue Type: Bug > Components: Server Management > Environment: MySQL datatabase, RoR activerecord > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > When deleting some errors the following timeout error occurs > Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `service_versions` WHERE `id` = 609 > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Thu Jun 3 05:15:30 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 03 Jun 2010 10:15:30 +0100 Subject: [BioCatalogue-developers] [Production ERROR] application#show (ActionView::TemplateError) "undefined method `service' for nil:NilClass" In-Reply-To: <4C0765A3.3030803@ebi.ac.uk> References: <4c0663df4cb16_66501558cf4fd7c81ba@pweb-3b.ebi.ac.uk.tmail> <4C066511.2070003@ebi.ac.uk> <4C0687B3.6090908@cs.man.ac.uk> <4C0765A3.3030803@ebi.ac.uk> Message-ID: <4C0772B2.6080200@cs.man.ac.uk> Eric, Normal 404 (resource does not exist) errors *should not* send out these error emails. If a bot (or anyone else) hits http://www.biocatalogue.org/services/300000 then an error email should not be sent out, because it is something we know about (ie: we don't care that the resource doesn't exist). To ensure that proper 404s are generated, Model.find(id) must be used in the controllers. This generates a RecordNotFound exception which the controller traps and then sends out a 404 to the client. In the case of /soap_operations... something is breaking this expected pattern and a proper 404 is not being generated. Instead, a nil @soap_operation and/or @soap_service is passed on to the views and then @soap_service.service is failing as a result (similar thing is happening with the /rest_methods). So something is not quite right, and needs to be investigated further. The error emails have, very usefully, flagged this up for us. Having bots access URLs and generate errors, which we then get an email for, is a valuable way of catching bugs. Jits Eric Nzuobontane wrote: > Jiten Bhagat wrote: >> There is a bigger problem here; we're getting errors exactly like this >> for a number of different things. Usually this shouldn't happen because >> Model.find(..) calls in the controller would trap bad URLs and give an >> appropriate 404. So it could be the data is inconsistent (orphaned >> objects etc) but I have added sanity checks for that. So in the end, I >> don't know. And I cannot reproduce this locally (for SoapOperations), >> even with the latest data. I have asked Mannie to at least investigate >> the RestService issues. >> > As far as I see it is not about the inconsistency of data (though that > might have an effect as well) but rather an application level issue. I > believe the mails are generated often by robots as the little > investigation I made last time pointed towards google bot. Right now, > if you hit any url like > http://www.biocatalogue.org/soap_operations/10000 (or any id which > does not exist in the db), this will generate one of those errors. If > generating an error is OK functionally, then we should expect these > mails with the possibility of being flooded when something just keeps > hitting one such url. > > Eric > >> Jits >> >> >> Eric Nzuobontane wrote: >> >>> BioCatalogue Errors wrote: >>> >>>> A ActionView::TemplateError occurred in application#show: >>>> >>>> undefined method `service' for nil:NilClass >>>> On line #16 of app/views/rest_methods/_breadcrumbs.html.erb >>>> >>>> 13: <% if controller.action_name.downcase == "show" -%> >>>> 14:
  • »
    • >>>> 15: 16:
  • <%= link_to >>>> display_name(@rest_service.service), @rest_service.service >>>> -%>
    • >>>> 17: 18:
  • »
    • >>>> 19: >>> I think this bit of code could check if the @rest_service object is >>> valid before attempting to call the service method on it. Could issue >>> a warning and stop these error messages. >>> >>> Eric >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>>> app/views/rest_methods/_breadcrumbs.html.erb:16 >>>> app/helpers/application_helper.rb:510:in >>>> `render_breadcrumbs_after_home' >>>> app/views/widgets/_breadcrumbs_bar.html.erb:18 >>>> app/views/layouts/application_wide.html.erb:52 >>>> passenger (2.2.4) >>>> lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/railz/application_spawner.rb:376:in >>>> `start_request_handler' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/railz/application_spawner.rb:334:in >>>> `handle_spawn_application' >>>> passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in >>>> `safe_fork' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/railz/application_spawner.rb:332:in >>>> `handle_spawn_application' >>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>> `__send__' >>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>> `main_loop' >>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in >>>> `start_synchronously' >>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in >>>> `start' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/railz/application_spawner.rb:213:in `start' >>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in >>>> `spawn_rails_application' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_server_collection.rb:126:in >>>> `lookup_or_add' >>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in >>>> `spawn_rails_application' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_server_collection.rb:80:in >>>> `synchronize' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_server_collection.rb:79:in >>>> `synchronize' >>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in >>>> `spawn_rails_application' >>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in >>>> `spawn_application' >>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in >>>> `handle_spawn_application' >>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>> `__send__' >>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>> `main_loop' >>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in >>>> `start_synchronously' >>>> >>>> ------------------------------- >>>> Request: >>>> ------------------------------- >>>> >>>> * URL : http://www.biocatalogue.org/rest_methods/87 >>>> * Method : GET >>>> * IP address: 130.88.195.202 >>>> * Parameters: {"action"=>"show", "id"=>"87", >>>> "controller"=>"rest_methods"} >>>> * 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 : en-us,en;q=0.5 >>>> * HTTP_CACHE_CONTROL : max-age=0 >>>> * HTTP_CONNECTION : keep-alive >>>> * HTTP_COOKIE : >>>> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >>>> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >>>> >>>> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >>>> search_results_tabber=0; stats-tabs_tabber=1; >>>> __utmb=15951013.47.10.1275482785 >>>> * HTTP_HOST : www.biocatalogue.org >>>> * HTTP_IF_NONE_MATCH : >>>> "0180f1b3e6396d6c123bc9e0100888a9" >>>> * HTTP_KEEP_ALIVE : 300 >>>> * HTTP_REFERER : >>>> http://www.biocatalogue.org/services/2699 >>>> * HTTP_USER_AGENT : Mozilla/5.0 >>>> (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 >>>> Firefox/3.5.9 >>>> * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 >>>> * PATH_INFO : /rest_methods/87 >>>> * QUERY_STRING : * >>>> REMOTE_ADDR : 130.88.195.202 >>>> * REMOTE_PORT : 47246 >>>> * REQUEST_METHOD : GET >>>> * REQUEST_URI : /rest_methods/87 >>>> * SCRIPT_NAME : * >>>> SERVER_ADDR : 172.18.1.108 >>>> * SERVER_ADMIN : root at localhost >>>> * SERVER_NAME : www.biocatalogue.org >>>> * SERVER_PORT : 80 >>>> * SERVER_PROTOCOL : HTTP/1.1 >>>> * SERVER_SOFTWARE : Apache/2.2.3 >>>> (CentOS) >>>> * _ : _ >>>> * action_controller.request.query_parameters : * >>>> action_controller.request.request_parameters: * >>>> action_controller.rescue.request : >>>> # >>>> * action_controller.rescue.response : >>>> # >>>> * rack.errors : # >>>> * rack.input : >>>> # >>>> * rack.multiprocess : true >>>> * rack.multithread : false >>>> * rack.request : >>>> # >>>> * rack.request.cookie_hash : >>>> __utma15951013.396796326.1272273201.1275473442.1275482785.119stats-tabs_tabber1__utmb15951013.47.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations >>>> >>>> >>>> * rack.request.cookie_string : >>>> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >>>> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >>>> >>>> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >>>> search_results_tabber=0; stats-tabs_tabber=1; >>>> __utmb=15951013.47.10.1275482785 >>>> * rack.request.query_hash : * >>>> rack.request.query_string : * >>>> rack.routing_args : >>>> actionshowid87controllerrest_methods >>>> * rack.run_once : false >>>> * rack.session : >>>> search_show_listing_typesimpleprevious_url/rest_methods/87use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=user_id27flashnoticeEndpoint >>>> >>>> GET /goTerms has been >>>> deletedlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= >>>> >>>> * rack.session.options : >>>> securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath/ >>>> >>>> >>>> * rack.session.record : >>>> # >>>> * rack.url_scheme : http >>>> * rack.version : 10 >>>> * Process: 26192 >>>> * Server : pweb-3b >>>> * request.format: text/html >>>> >>>> ------------------------------- >>>> Backtrace: >>>> ------------------------------- >>>> >>>> On line #16 of app/views/rest_methods/_breadcrumbs.html.erb >>>> 13: <% if controller.action_name.downcase == "show" -%> >>>> 14:
  • »
    • >>>> 15: 16:
  • <%= link_to >>>> display_name(@rest_service.service), @rest_service.service >>>> -%>
    • >>>> 17: 18:
  • »
    • >>>> 19: app/views/rest_methods/_breadcrumbs.html.erb:16 >>>> app/helpers/application_helper.rb:510:in >>>> `render_breadcrumbs_after_home' >>>> app/views/widgets/_breadcrumbs_bar.html.erb:18 >>>> app/views/layouts/application_wide.html.erb:52 >>>> passenger (2.2.4) >>>> lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/railz/application_spawner.rb:376:in >>>> `start_request_handler' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/railz/application_spawner.rb:334:in >>>> `handle_spawn_application' >>>> passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in >>>> `safe_fork' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/railz/application_spawner.rb:332:in >>>> `handle_spawn_application' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_server.rb:351:in `__send__' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_server.rb:351:in `main_loop' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_server.rb:162:in `start' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/railz/application_spawner.rb:213:in `start' >>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in >>>> `spawn_rails_application' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_server_collection.rb:126:in >>>> `lookup_or_add' >>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in >>>> `spawn_rails_application' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_server_collection.rb:80:in >>>> `synchronize' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_server_collection.rb:79:in >>>> `synchronize' >>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in >>>> `spawn_rails_application' >>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in >>>> `spawn_application' >>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in >>>> `handle_spawn_application' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_server.rb:351:in `__send__' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_server.rb:351:in `main_loop' >>>> passenger (2.2.4) >>>> lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' >>>> >>>> >>> > > From jits at cs.man.ac.uk Thu Jun 3 05:19:50 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 03 Jun 2010 10:19:50 +0100 Subject: [BioCatalogue-developers] recent error emails In-Reply-To: <4C0772B2.6080200@cs.man.ac.uk> References: <4c0663df4cb16_66501558cf4fd7c81ba@pweb-3b.ebi.ac.uk.tmail> <4C066511.2070003@ebi.ac.uk> <4C0687B3.6090908@cs.man.ac.uk> <4C0765A3.3030803@ebi.ac.uk> <4C0772B2.6080200@cs.man.ac.uk> Message-ID: <4C0773B6.4040000@cs.man.ac.uk> It just occurred to me now why this is happening... A 404 *is* being generated, but in the resulting error page the template *still* tries to build the breadcrumbs and thus causes another error. I will provide a global fix for this (ie: for error pages ignore building of breadcrumbs). Jits Jiten Bhagat wrote: > Eric, > > Normal 404 (resource does not exist) errors *should not* send out these > error emails. > > If a bot (or anyone else) hits > http://www.biocatalogue.org/services/300000 then an error email should > not be sent out, because it is something we know about (ie: we don't > care that the resource doesn't exist). > > To ensure that proper 404s are generated, Model.find(id) must be used in > the controllers. This generates a RecordNotFound exception which the > controller traps and then sends out a 404 to the client. > > In the case of /soap_operations... something is breaking this expected > pattern and a proper 404 is not being generated. Instead, a nil > @soap_operation and/or @soap_service is passed on to the views and then > @soap_service.service is failing as a result (similar thing is happening > with the /rest_methods). So something is not quite right, and needs to > be investigated further. The error emails have, very usefully, flagged > this up for us. > > Having bots access URLs and generate errors, which we then get an email > for, is a valuable way of catching bugs. > > Jits > > > > Eric Nzuobontane wrote: > >> Jiten Bhagat wrote: >> >>> There is a bigger problem here; we're getting errors exactly like this >>> for a number of different things. Usually this shouldn't happen because >>> Model.find(..) calls in the controller would trap bad URLs and give an >>> appropriate 404. So it could be the data is inconsistent (orphaned >>> objects etc) but I have added sanity checks for that. So in the end, I >>> don't know. And I cannot reproduce this locally (for SoapOperations), >>> even with the latest data. I have asked Mannie to at least investigate >>> the RestService issues. >>> >>> >> As far as I see it is not about the inconsistency of data (though that >> might have an effect as well) but rather an application level issue. I >> believe the mails are generated often by robots as the little >> investigation I made last time pointed towards google bot. Right now, >> if you hit any url like >> http://www.biocatalogue.org/soap_operations/10000 (or any id which >> does not exist in the db), this will generate one of those errors. If >> generating an error is OK functionally, then we should expect these >> mails with the possibility of being flooded when something just keeps >> hitting one such url. >> >> Eric >> >> >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>> >>> >>>> BioCatalogue Errors wrote: >>>> >>>> >>>>> A ActionView::TemplateError occurred in application#show: >>>>> >>>>> undefined method `service' for nil:NilClass >>>>> On line #16 of app/views/rest_methods/_breadcrumbs.html.erb >>>>> >>>>> 13: <% if controller.action_name.downcase == "show" -%> >>>>> 14:
  • »
    • >>>>> 15: 16:
  • <%= link_to >>>>> display_name(@rest_service.service), @rest_service.service >>>>> -%>
    • >>>>> 17: 18:
  • »
    • >>>>> 19: >>>>> >>>> I think this bit of code could check if the @rest_service object is >>>> valid before attempting to call the service method on it. Could issue >>>> a warning and stop these error messages. >>>> >>>> Eric >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>>> app/views/rest_methods/_breadcrumbs.html.erb:16 >>>>> app/helpers/application_helper.rb:510:in >>>>> `render_breadcrumbs_after_home' >>>>> app/views/widgets/_breadcrumbs_bar.html.erb:18 >>>>> app/views/layouts/application_wide.html.erb:52 >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/railz/application_spawner.rb:376:in >>>>> `start_request_handler' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/railz/application_spawner.rb:334:in >>>>> `handle_spawn_application' >>>>> passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in >>>>> `safe_fork' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/railz/application_spawner.rb:332:in >>>>> `handle_spawn_application' >>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>>> `__send__' >>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>>> `main_loop' >>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in >>>>> `start_synchronously' >>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in >>>>> `start' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/railz/application_spawner.rb:213:in `start' >>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in >>>>> `spawn_rails_application' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_server_collection.rb:126:in >>>>> `lookup_or_add' >>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in >>>>> `spawn_rails_application' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_server_collection.rb:80:in >>>>> `synchronize' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_server_collection.rb:79:in >>>>> `synchronize' >>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in >>>>> `spawn_rails_application' >>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in >>>>> `spawn_application' >>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in >>>>> `handle_spawn_application' >>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>>> `__send__' >>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>>> `main_loop' >>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in >>>>> `start_synchronously' >>>>> >>>>> ------------------------------- >>>>> Request: >>>>> ------------------------------- >>>>> >>>>> * URL : http://www.biocatalogue.org/rest_methods/87 >>>>> * Method : GET >>>>> * IP address: 130.88.195.202 >>>>> * Parameters: {"action"=>"show", "id"=>"87", >>>>> "controller"=>"rest_methods"} >>>>> * 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 : en-us,en;q=0.5 >>>>> * HTTP_CACHE_CONTROL : max-age=0 >>>>> * HTTP_CONNECTION : keep-alive >>>>> * HTTP_COOKIE : >>>>> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >>>>> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >>>>> >>>>> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >>>>> search_results_tabber=0; stats-tabs_tabber=1; >>>>> __utmb=15951013.47.10.1275482785 >>>>> * HTTP_HOST : www.biocatalogue.org >>>>> * HTTP_IF_NONE_MATCH : >>>>> "0180f1b3e6396d6c123bc9e0100888a9" >>>>> * HTTP_KEEP_ALIVE : 300 >>>>> * HTTP_REFERER : >>>>> http://www.biocatalogue.org/services/2699 >>>>> * HTTP_USER_AGENT : Mozilla/5.0 >>>>> (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 >>>>> Firefox/3.5.9 >>>>> * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 >>>>> * PATH_INFO : /rest_methods/87 >>>>> * QUERY_STRING : * >>>>> REMOTE_ADDR : 130.88.195.202 >>>>> * REMOTE_PORT : 47246 >>>>> * REQUEST_METHOD : GET >>>>> * REQUEST_URI : /rest_methods/87 >>>>> * SCRIPT_NAME : * >>>>> SERVER_ADDR : 172.18.1.108 >>>>> * SERVER_ADMIN : root at localhost >>>>> * SERVER_NAME : www.biocatalogue.org >>>>> * SERVER_PORT : 80 >>>>> * SERVER_PROTOCOL : HTTP/1.1 >>>>> * SERVER_SOFTWARE : Apache/2.2.3 >>>>> (CentOS) >>>>> * _ : _ >>>>> * action_controller.request.query_parameters : * >>>>> action_controller.request.request_parameters: * >>>>> action_controller.rescue.request : >>>>> # >>>>> * action_controller.rescue.response : >>>>> # >>>>> * rack.errors : # >>>>> * rack.input : >>>>> # >>>>> * rack.multiprocess : true >>>>> * rack.multithread : false >>>>> * rack.request : >>>>> # >>>>> * rack.request.cookie_hash : >>>>> __utma15951013.396796326.1272273201.1275473442.1275482785.119stats-tabs_tabber1__utmb15951013.47.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations >>>>> >>>>> >>>>> * rack.request.cookie_string : >>>>> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >>>>> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >>>>> >>>>> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >>>>> search_results_tabber=0; stats-tabs_tabber=1; >>>>> __utmb=15951013.47.10.1275482785 >>>>> * rack.request.query_hash : * >>>>> rack.request.query_string : * >>>>> rack.routing_args : >>>>> actionshowid87controllerrest_methods >>>>> * rack.run_once : false >>>>> * rack.session : >>>>> search_show_listing_typesimpleprevious_url/rest_methods/87use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=user_id27flashnoticeEndpoint >>>>> >>>>> GET /goTerms has been >>>>> deletedlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= >>>>> >>>>> * rack.session.options : >>>>> securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath/ >>>>> >>>>> >>>>> * rack.session.record : >>>>> # >>>>> * rack.url_scheme : http >>>>> * rack.version : 10 >>>>> * Process: 26192 >>>>> * Server : pweb-3b >>>>> * request.format: text/html >>>>> >>>>> ------------------------------- >>>>> Backtrace: >>>>> ------------------------------- >>>>> >>>>> On line #16 of app/views/rest_methods/_breadcrumbs.html.erb >>>>> 13: <% if controller.action_name.downcase == "show" -%> >>>>> 14:
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    • >>>>> 15: 16:
  • <%= link_to >>>>> display_name(@rest_service.service), @rest_service.service >>>>> -%>
    • >>>>> 17: 18:
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    • >>>>> 19: app/views/rest_methods/_breadcrumbs.html.erb:16 >>>>> app/helpers/application_helper.rb:510:in >>>>> `render_breadcrumbs_after_home' >>>>> app/views/widgets/_breadcrumbs_bar.html.erb:18 >>>>> app/views/layouts/application_wide.html.erb:52 >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/railz/application_spawner.rb:376:in >>>>> `start_request_handler' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/railz/application_spawner.rb:334:in >>>>> `handle_spawn_application' >>>>> passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in >>>>> `safe_fork' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/railz/application_spawner.rb:332:in >>>>> `handle_spawn_application' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_server.rb:351:in `__send__' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_server.rb:351:in `main_loop' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_server.rb:162:in `start' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/railz/application_spawner.rb:213:in `start' >>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in >>>>> `spawn_rails_application' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_server_collection.rb:126:in >>>>> `lookup_or_add' >>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in >>>>> `spawn_rails_application' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_server_collection.rb:80:in >>>>> `synchronize' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_server_collection.rb:79:in >>>>> `synchronize' >>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in >>>>> `spawn_rails_application' >>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in >>>>> `spawn_application' >>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in >>>>> `handle_spawn_application' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_server.rb:351:in `__send__' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_server.rb:351:in `main_loop' >>>>> passenger (2.2.4) >>>>> lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' >>>>> >>>>> >>>>> >>>> >>>> >> > > > From ericnzuo at ebi.ac.uk Thu Jun 3 05:23:36 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 03 Jun 2010 10:23:36 +0100 Subject: [BioCatalogue-developers] recent error emails In-Reply-To: <4C0773B6.4040000@cs.man.ac.uk> References: <4c0663df4cb16_66501558cf4fd7c81ba@pweb-3b.ebi.ac.uk.tmail> <4C066511.2070003@ebi.ac.uk> <4C0687B3.6090908@cs.man.ac.uk> <4C0765A3.3030803@ebi.ac.uk> <4C0772B2.6080200@cs.man.ac.uk> <4C0773B6.4040000@cs.man.ac.uk> Message-ID: <4C077498.4060808@ebi.ac.uk> Thanks! Eric Jiten Bhagat wrote: > It just occurred to me now why this is happening... > > A 404 *is* being generated, but in the resulting error page the template > *still* tries to build the breadcrumbs and thus causes another error. > > I will provide a global fix for this (ie: for error pages ignore > building of breadcrumbs). > > Jits > > > Jiten Bhagat wrote: > >> Eric, >> >> Normal 404 (resource does not exist) errors *should not* send out these >> error emails. >> >> If a bot (or anyone else) hits >> http://www.biocatalogue.org/services/300000 then an error email should >> not be sent out, because it is something we know about (ie: we don't >> care that the resource doesn't exist). >> >> To ensure that proper 404s are generated, Model.find(id) must be used in >> the controllers. This generates a RecordNotFound exception which the >> controller traps and then sends out a 404 to the client. >> >> In the case of /soap_operations... something is breaking this expected >> pattern and a proper 404 is not being generated. Instead, a nil >> @soap_operation and/or @soap_service is passed on to the views and then >> @soap_service.service is failing as a result (similar thing is happening >> with the /rest_methods). So something is not quite right, and needs to >> be investigated further. The error emails have, very usefully, flagged >> this up for us. >> >> Having bots access URLs and generate errors, which we then get an email >> for, is a valuable way of catching bugs. >> >> Jits >> >> >> >> Eric Nzuobontane wrote: >> >> >>> Jiten Bhagat wrote: >>> >>> >>>> There is a bigger problem here; we're getting errors exactly like this >>>> for a number of different things. Usually this shouldn't happen because >>>> Model.find(..) calls in the controller would trap bad URLs and give an >>>> appropriate 404. So it could be the data is inconsistent (orphaned >>>> objects etc) but I have added sanity checks for that. So in the end, I >>>> don't know. And I cannot reproduce this locally (for SoapOperations), >>>> even with the latest data. I have asked Mannie to at least investigate >>>> the RestService issues. >>>> >>>> >>>> >>> As far as I see it is not about the inconsistency of data (though that >>> might have an effect as well) but rather an application level issue. I >>> believe the mails are generated often by robots as the little >>> investigation I made last time pointed towards google bot. Right now, >>> if you hit any url like >>> http://www.biocatalogue.org/soap_operations/10000 (or any id which >>> does not exist in the db), this will generate one of those errors. If >>> generating an error is OK functionally, then we should expect these >>> mails with the possibility of being flooded when something just keeps >>> hitting one such url. >>> >>> Eric >>> >>> >>> >>>> Jits >>>> >>>> >>>> Eric Nzuobontane wrote: >>>> >>>> >>>> >>>>> BioCatalogue Errors wrote: >>>>> >>>>> >>>>> >>>>>> A ActionView::TemplateError occurred in application#show: >>>>>> >>>>>> undefined method `service' for nil:NilClass >>>>>> On line #16 of app/views/rest_methods/_breadcrumbs.html.erb >>>>>> >>>>>> 13: <% if controller.action_name.downcase == "show" -%> >>>>>> 14:
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    • >>>>>> 15: 16:
  • <%= link_to >>>>>> display_name(@rest_service.service), @rest_service.service >>>>>> -%>
    • >>>>>> 17: 18:
  • »
    • >>>>>> 19: >>>>>> >>>>>> >>>>> I think this bit of code could check if the @rest_service object is >>>>> valid before attempting to call the service method on it. Could issue >>>>> a warning and stop these error messages. >>>>> >>>>> Eric >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>> app/views/rest_methods/_breadcrumbs.html.erb:16 >>>>>> app/helpers/application_helper.rb:510:in >>>>>> `render_breadcrumbs_after_home' >>>>>> app/views/widgets/_breadcrumbs_bar.html.erb:18 >>>>>> app/views/layouts/application_wide.html.erb:52 >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:376:in >>>>>> `start_request_handler' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:334:in >>>>>> `handle_spawn_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in >>>>>> `safe_fork' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:332:in >>>>>> `handle_spawn_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>>>> `__send__' >>>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>>>> `main_loop' >>>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in >>>>>> `start_synchronously' >>>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in >>>>>> `start' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:213:in `start' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in >>>>>> `spawn_rails_application' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server_collection.rb:126:in >>>>>> `lookup_or_add' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in >>>>>> `spawn_rails_application' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server_collection.rb:80:in >>>>>> `synchronize' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server_collection.rb:79:in >>>>>> `synchronize' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in >>>>>> `spawn_rails_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in >>>>>> `spawn_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in >>>>>> `handle_spawn_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>>>> `__send__' >>>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>>>> `main_loop' >>>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in >>>>>> `start_synchronously' >>>>>> >>>>>> ------------------------------- >>>>>> Request: >>>>>> ------------------------------- >>>>>> >>>>>> * URL : http://www.biocatalogue.org/rest_methods/87 >>>>>> * Method : GET >>>>>> * IP address: 130.88.195.202 >>>>>> * Parameters: {"action"=>"show", "id"=>"87", >>>>>> "controller"=>"rest_methods"} >>>>>> * 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 : en-us,en;q=0.5 >>>>>> * HTTP_CACHE_CONTROL : max-age=0 >>>>>> * HTTP_CONNECTION : keep-alive >>>>>> * HTTP_COOKIE : >>>>>> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >>>>>> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >>>>>> >>>>>> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >>>>>> search_results_tabber=0; stats-tabs_tabber=1; >>>>>> __utmb=15951013.47.10.1275482785 >>>>>> * HTTP_HOST : www.biocatalogue.org >>>>>> * HTTP_IF_NONE_MATCH : >>>>>> "0180f1b3e6396d6c123bc9e0100888a9" >>>>>> * HTTP_KEEP_ALIVE : 300 >>>>>> * HTTP_REFERER : >>>>>> http://www.biocatalogue.org/services/2699 >>>>>> * HTTP_USER_AGENT : Mozilla/5.0 >>>>>> (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 >>>>>> Firefox/3.5.9 >>>>>> * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 >>>>>> * PATH_INFO : /rest_methods/87 >>>>>> * QUERY_STRING : * >>>>>> REMOTE_ADDR : 130.88.195.202 >>>>>> * REMOTE_PORT : 47246 >>>>>> * REQUEST_METHOD : GET >>>>>> * REQUEST_URI : /rest_methods/87 >>>>>> * SCRIPT_NAME : * >>>>>> SERVER_ADDR : 172.18.1.108 >>>>>> * SERVER_ADMIN : root at localhost >>>>>> * SERVER_NAME : www.biocatalogue.org >>>>>> * SERVER_PORT : 80 >>>>>> * SERVER_PROTOCOL : HTTP/1.1 >>>>>> * SERVER_SOFTWARE : Apache/2.2.3 >>>>>> (CentOS) >>>>>> * _ : _ >>>>>> * action_controller.request.query_parameters : * >>>>>> action_controller.request.request_parameters: * >>>>>> action_controller.rescue.request : >>>>>> # >>>>>> * action_controller.rescue.response : >>>>>> # >>>>>> * rack.errors : # >>>>>> * rack.input : >>>>>> # >>>>>> * rack.multiprocess : true >>>>>> * rack.multithread : false >>>>>> * rack.request : >>>>>> # >>>>>> * rack.request.cookie_hash : >>>>>> __utma15951013.396796326.1272273201.1275473442.1275482785.119stats-tabs_tabber1__utmb15951013.47.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations >>>>>> >>>>>> >>>>>> * rack.request.cookie_string : >>>>>> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >>>>>> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >>>>>> >>>>>> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >>>>>> search_results_tabber=0; stats-tabs_tabber=1; >>>>>> __utmb=15951013.47.10.1275482785 >>>>>> * rack.request.query_hash : * >>>>>> rack.request.query_string : * >>>>>> rack.routing_args : >>>>>> actionshowid87controllerrest_methods >>>>>> * rack.run_once : false >>>>>> * rack.session : >>>>>> search_show_listing_typesimpleprevious_url/rest_methods/87use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=user_id27flashnoticeEndpoint >>>>>> >>>>>> GET /goTerms has been >>>>>> deletedlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= >>>>>> >>>>>> * rack.session.options : >>>>>> securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath/ >>>>>> >>>>>> >>>>>> * rack.session.record : >>>>>> # >>>>>> * rack.url_scheme : http >>>>>> * rack.version : 10 >>>>>> * Process: 26192 >>>>>> * Server : pweb-3b >>>>>> * request.format: text/html >>>>>> >>>>>> ------------------------------- >>>>>> Backtrace: >>>>>> ------------------------------- >>>>>> >>>>>> On line #16 of app/views/rest_methods/_breadcrumbs.html.erb >>>>>> 13: <% if controller.action_name.downcase == "show" -%> >>>>>> 14:
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    • >>>>>> 15: 16:
  • <%= link_to >>>>>> display_name(@rest_service.service), @rest_service.service >>>>>> -%>
    • >>>>>> 17: 18:
  • »
    • >>>>>> 19: app/views/rest_methods/_breadcrumbs.html.erb:16 >>>>>> app/helpers/application_helper.rb:510:in >>>>>> `render_breadcrumbs_after_home' >>>>>> app/views/widgets/_breadcrumbs_bar.html.erb:18 >>>>>> app/views/layouts/application_wide.html.erb:52 >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:376:in >>>>>> `start_request_handler' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:334:in >>>>>> `handle_spawn_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in >>>>>> `safe_fork' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:332:in >>>>>> `handle_spawn_application' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server.rb:351:in `__send__' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server.rb:351:in `main_loop' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server.rb:162:in `start' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:213:in `start' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in >>>>>> `spawn_rails_application' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server_collection.rb:126:in >>>>>> `lookup_or_add' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in >>>>>> `spawn_rails_application' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server_collection.rb:80:in >>>>>> `synchronize' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server_collection.rb:79:in >>>>>> `synchronize' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in >>>>>> `spawn_rails_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in >>>>>> `spawn_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in >>>>>> `handle_spawn_application' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server.rb:351:in `__send__' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server.rb:351:in `main_loop' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>> >>> >> >> -- 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 Jun 3 05:24:46 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 03 Jun 2010 10:24:46 +0100 Subject: [BioCatalogue-developers] db timeout issues In-Reply-To: <4C076901.4000908@ebi.ac.uk> References: <4beab2bfd7101_6eb215a7c5afffc818a@pweb-3b.ebi.ac.uk.tmail> <4C076901.4000908@ebi.ac.uk> Message-ID: <4C0774DE.1030501@cs.man.ac.uk> Ahh, okay. One thing to look at is this particular bit (from: http://actsastrashable.rubyforge.org/) ... "To protect yourself, simply declare acts_as_trashable in any active record model. This will cause the record to be serialized to a trash_records table before it is deleted when you call destroy. In addition, any has_and_belongs_to_many associations or any has_many or has_one associations declared with :dependent => :destroy will also be serialized. These associations should not have acts_as_trashable (there?s no harm if they do, you just end up with twice as much trash)." Jits Eric Nzuobontane wrote: > I made some investigations into this yesterday but did not get to the > bottom of the story. However, it seems it is not the indexing that is > the culprit here but the thrashing of records. So what I believe is > happening is that when a delete operation occurs, the thrash table is > locked by the first thing that needs to be deleted and other deletes > in the transaction cannot get hold of the lock fast enough so that the > transaction times out. I will try to experiment further to see if this > can be confirmed and hence help find a solution to the problem. > > Eric > > > > BioCatalogue Errors wrote: >> A ActiveRecord::StatementInvalid occurred in annotations#destroy: >> >> Mysql::Error: Lock wait timeout exceeded; try restarting >> transaction: DELETE FROM `annotation_versions` WHERE `id` = 55788 >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in >> `log' >> >> ------------------------------- >> Request: >> ------------------------------- >> >> * URL : http://www.biocatalogue.org/annotations/53304 >> * Method : DELETE >> * IP address: 130.88.195.202 >> * Parameters: {"action"=>"destroy", "_method"=>"delete", >> "authenticity_token"=>"NIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN+pj0g=", >> "id"=>"53304", "controller"=>"annotations"} >> * Rails root: >> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue >> >> ------------------------------- >> Session: >> ------------------------------- >> >> * session id: nil >> * data: nil >> >> ------------------------------- >> Environment: >> ------------------------------- >> >> * CONTENT_LENGTH : 82 >> * CONTENT_TYPE : >> application/x-www-form-urlencoded >> * 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 : en-us,en;q=0.5 >> * HTTP_CONNECTION : keep-alive >> * HTTP_CONTENT_TYPE : >> application/x-www-form-urlencoded >> * HTTP_COOKIE : >> __utma=15951013.396796326.1272273201.1273657462.1273661473.55; >> __utmz=15951013.1272273201.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none); >> _session_id=ce30b8a07947150391b00de88bd95130; __utmc=15951013; >> search_results_tabber=0 >> * HTTP_HOST : www.biocatalogue.org >> * HTTP_KEEP_ALIVE : 300 >> * HTTP_REFERER : >> http://www.biocatalogue.org/soap_operations/13085 >> * HTTP_USER_AGENT : Mozilla/5.0 >> (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 >> Firefox/3.5.9 >> * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 >> * PATH_INFO : /annotations/53304 >> * QUERY_STRING : * >> REMOTE_ADDR : 130.88.195.202 >> * REMOTE_PORT : 42125 >> * REQUEST_METHOD : DELETE >> * REQUEST_URI : /annotations/53304 >> * SCRIPT_NAME : * >> SERVER_ADDR : 172.18.1.108 >> * SERVER_ADMIN : root at localhost >> * SERVER_NAME : www.biocatalogue.org >> * SERVER_PORT : 80 >> * SERVER_PROTOCOL : HTTP/1.1 >> * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) >> * _ : _ >> * action_controller.request.query_parameters : * >> action_controller.request.request_parameters: >> authenticity_tokenNIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN+pj0g=_methoddelete >> >> * action_controller.rescue.request : >> # >> * action_controller.rescue.response : >> # >> * rack.errors : # >> * rack.input : >> # >> * rack.methodoverride.original_method : POST >> * rack.multiprocess : true >> * rack.multithread : false >> * rack.request : >> # >> * rack.request.cookie_hash : >> __utma15951013.396796326.1272273201.1273657462.1273661473.55_session_idce30b8a07947150391b00de88bd95130__utmc15951013search_results_tabber0__utmz15951013.1272273201.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none) >> >> * rack.request.cookie_string : >> __utma=15951013.396796326.1272273201.1273657462.1273661473.55; >> __utmz=15951013.1272273201.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none); >> _session_id=ce30b8a07947150391b00de88bd95130; __utmc=15951013; >> search_results_tabber=0 >> * rack.request.form_hash : >> authenticity_tokenNIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN+pj0g=_methoddelete >> >> * rack.request.form_input : >> # >> * rack.request.form_vars : >> _method=delete&authenticity_token=NIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN%2Bpj0g%3D >> >> * rack.request.query_hash : * >> rack.request.query_string : * >> rack.routing_args : >> actiondestroyid53304controllerannotations >> * rack.run_once : false >> * rack.session : >> search_show_listing_typedetailed_csrf_tokenNIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN+pj0g=user_id27previous_url/annotations/53304use_tab_cookietrueservices_index_listing_typedetailedflashlast_searchhttp://www.biocatalogue.org/search?q=WSNetGlycate&commit= >> >> * rack.session.options : >> expire_aftersecurefalsehttponlytruecookie_onlytruekey_session_ididce30b8a07947150391b00de88bd95130domainpath/ >> >> * rack.session.record : >> # >> * rack.url_scheme : http >> * rack.version : 10 >> * Process: 28338 >> * Server : pweb-3b >> * request.format: text/html >> >> ------------------------------- >> Backtrace: >> ------------------------------- >> >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in >> `log' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:320:in >> `execute' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:265:in >> `update_sql' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:335:in >> `update_sql' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:270:in >> `delete_sql' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:54:in >> `delete_without_query_dirty' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:18:in >> `delete' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:2578:in >> `destroy_without_lock' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/locking/optimistic.rb:113:in >> `destroy_without_callbacks' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:337:in >> `destroy_without_transactions' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `send' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `with_transaction_returning_status' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >> `transaction' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in >> `with_transaction_returning_status' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in >> `destroy' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >> `has_many_dependent_destroy_for_versions' >> >> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >> `method_missing' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >> `method_missing_without_paginate' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `method_missing' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `each' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `send' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >> `method_missing' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >> `method_missing_without_paginate' >> >> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >> `method_missing' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >> `has_many_dependent_destroy_for_versions' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >> `send' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >> `evaluate_method' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in >> `run' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `each' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `send' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >> `run' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in >> `run_callbacks' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in >> `callback' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in >> `destroy_without_transactions' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `send' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >> `with_transaction_returning_status' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >> `transaction' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in >> `with_transaction_returning_status' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in >> `destroy_without_trash' >> >> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in >> `destroy' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >> `transaction' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >> `transaction' >> >> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in >> `destroy' >> >> [RAILS_ROOT]/vendor/plugins/annotations/lib/app/controllers/annotations_controller.rb:121:in >> `destroy' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in >> `send' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in >> `perform_action_without_filters' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:617:in >> `call_filters' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:610:in >> `perform_action_without_benchmark' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in >> `perform_action_without_rescue' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in >> `ms' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:10:in >> `realtime' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in >> `ms' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in >> `perform_action_without_rescue' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rescue.rb:160:in >> `perform_action_without_flash' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb:141:in >> `perform_action' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in >> `send' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in >> `process_without_filters' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:606:in >> `process' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:391:in >> `process' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:386:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/route_set.rb:433:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:88:in >> `dispatch' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:111:in >> `_call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:82:in >> `initialize' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/methodoverride.rb:24:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/params_parser.rb:15:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rewindable_input.rb:25:in >> `call' >> [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in >> `cache' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in >> `cache' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >> `synchronize' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in >> `call' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in >> `process_request' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in >> `main_loop' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in >> `start_request_handler' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in >> `handle_spawn_application' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in >> `safe_fork' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in >> `handle_spawn_application' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `__send__' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `main_loop' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in >> `start_synchronously' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in >> `start' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in >> `start' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in >> `spawn_rails_application' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in >> `lookup_or_add' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in >> `spawn_rails_application' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in >> `synchronize' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in >> `synchronize' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in >> `spawn_rails_application' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in >> `spawn_application' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in >> `handle_spawn_application' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `__send__' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `main_loop' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in >> `start_synchronously' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 >> >> >> > > From noreply at rubyforge.org Thu Jun 3 05:26:56 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 3 Jun 2010 05:26:56 -0400 (EDT) Subject: [BioCatalogue-developers] [2076] trunk: - updated the sanity checks to check the REST objects as well Message-ID: <20100603092656.65D971858372@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu Jun 3 05:31:46 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 03 Jun 2010 10:31:46 +0100 Subject: [BioCatalogue-developers] db timeout issues In-Reply-To: <4C0774DE.1030501@cs.man.ac.uk> References: <4beab2bfd7101_6eb215a7c5afffc818a@pweb-3b.ebi.ac.uk.tmail> <4C076901.4000908@ebi.ac.uk> <4C0774DE.1030501@cs.man.ac.uk> Message-ID: <4C077682.8040601@ebi.ac.uk> Jiten Bhagat wrote: > Ahh, okay. > > One thing to look at is this particular bit (from: > http://actsastrashable.rubyforge.org/) ... > > "To protect yourself, simply declare acts_as_trashable in any active > record model. This will cause the record to be serialized to a > trash_records table before it is deleted when you call destroy. In > addition, any has_and_belongs_to_many associations or any has_many or > has_one associations declared with :dependent => :destroy will also be > serialized. These associations should not have acts_as_trashable > (there?s no harm if they do, you just end up with twice as much trash)." > I saw this too but as they say, the effect should only be in the *size *of the trash table. So I am not sure. Though it will be good to be consistent with the advise here which we are currently not following. Eric > Jits > > > Eric Nzuobontane wrote: > >> I made some investigations into this yesterday but did not get to the >> bottom of the story. However, it seems it is not the indexing that is >> the culprit here but the thrashing of records. So what I believe is >> happening is that when a delete operation occurs, the thrash table is >> locked by the first thing that needs to be deleted and other deletes >> in the transaction cannot get hold of the lock fast enough so that the >> transaction times out. I will try to experiment further to see if this >> can be confirmed and hence help find a solution to the problem. >> >> Eric >> >> >> >> BioCatalogue Errors wrote: >> >>> A ActiveRecord::StatementInvalid occurred in annotations#destroy: >>> >>> Mysql::Error: Lock wait timeout exceeded; try restarting >>> transaction: DELETE FROM `annotation_versions` WHERE `id` = 55788 >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in >>> `log' >>> >>> ------------------------------- >>> Request: >>> ------------------------------- >>> >>> * URL : http://www.biocatalogue.org/annotations/53304 >>> * Method : DELETE >>> * IP address: 130.88.195.202 >>> * Parameters: {"action"=>"destroy", "_method"=>"delete", >>> "authenticity_token"=>"NIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN+pj0g=", >>> "id"=>"53304", "controller"=>"annotations"} >>> * Rails root: >>> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue >>> >>> ------------------------------- >>> Session: >>> ------------------------------- >>> >>> * session id: nil >>> * data: nil >>> >>> ------------------------------- >>> Environment: >>> ------------------------------- >>> >>> * CONTENT_LENGTH : 82 >>> * CONTENT_TYPE : >>> application/x-www-form-urlencoded >>> * 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 : en-us,en;q=0.5 >>> * HTTP_CONNECTION : keep-alive >>> * HTTP_CONTENT_TYPE : >>> application/x-www-form-urlencoded >>> * HTTP_COOKIE : >>> __utma=15951013.396796326.1272273201.1273657462.1273661473.55; >>> __utmz=15951013.1272273201.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none); >>> _session_id=ce30b8a07947150391b00de88bd95130; __utmc=15951013; >>> search_results_tabber=0 >>> * HTTP_HOST : www.biocatalogue.org >>> * HTTP_KEEP_ALIVE : 300 >>> * HTTP_REFERER : >>> http://www.biocatalogue.org/soap_operations/13085 >>> * HTTP_USER_AGENT : Mozilla/5.0 >>> (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 >>> Firefox/3.5.9 >>> * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 >>> * PATH_INFO : /annotations/53304 >>> * QUERY_STRING : * >>> REMOTE_ADDR : 130.88.195.202 >>> * REMOTE_PORT : 42125 >>> * REQUEST_METHOD : DELETE >>> * REQUEST_URI : /annotations/53304 >>> * SCRIPT_NAME : * >>> SERVER_ADDR : 172.18.1.108 >>> * SERVER_ADMIN : root at localhost >>> * SERVER_NAME : www.biocatalogue.org >>> * SERVER_PORT : 80 >>> * SERVER_PROTOCOL : HTTP/1.1 >>> * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) >>> * _ : _ >>> * action_controller.request.query_parameters : * >>> action_controller.request.request_parameters: >>> authenticity_tokenNIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN+pj0g=_methoddelete >>> >>> * action_controller.rescue.request : >>> # >>> * action_controller.rescue.response : >>> # >>> * rack.errors : # >>> * rack.input : >>> # >>> * rack.methodoverride.original_method : POST >>> * rack.multiprocess : true >>> * rack.multithread : false >>> * rack.request : >>> # >>> * rack.request.cookie_hash : >>> __utma15951013.396796326.1272273201.1273657462.1273661473.55_session_idce30b8a07947150391b00de88bd95130__utmc15951013search_results_tabber0__utmz15951013.1272273201.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none) >>> >>> * rack.request.cookie_string : >>> __utma=15951013.396796326.1272273201.1273657462.1273661473.55; >>> __utmz=15951013.1272273201.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none); >>> _session_id=ce30b8a07947150391b00de88bd95130; __utmc=15951013; >>> search_results_tabber=0 >>> * rack.request.form_hash : >>> authenticity_tokenNIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN+pj0g=_methoddelete >>> >>> * rack.request.form_input : >>> # >>> * rack.request.form_vars : >>> _method=delete&authenticity_token=NIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN%2Bpj0g%3D >>> >>> * rack.request.query_hash : * >>> rack.request.query_string : * >>> rack.routing_args : >>> actiondestroyid53304controllerannotations >>> * rack.run_once : false >>> * rack.session : >>> search_show_listing_typedetailed_csrf_tokenNIUruT4US5lyc616Lb4V4vgkwUlLw4pdve43WN+pj0g=user_id27previous_url/annotations/53304use_tab_cookietrueservices_index_listing_typedetailedflashlast_searchhttp://www.biocatalogue.org/search?q=WSNetGlycate&commit= >>> >>> * rack.session.options : >>> expire_aftersecurefalsehttponlytruecookie_onlytruekey_session_ididce30b8a07947150391b00de88bd95130domainpath/ >>> >>> * rack.session.record : >>> # >>> * rack.url_scheme : http >>> * rack.version : 10 >>> * Process: 28338 >>> * Server : pweb-3b >>> * request.format: text/html >>> >>> ------------------------------- >>> Backtrace: >>> ------------------------------- >>> >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in >>> `log' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:320:in >>> `execute' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:265:in >>> `update_sql' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:335:in >>> `update_sql' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:270:in >>> `delete_sql' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:54:in >>> `delete_without_query_dirty' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:18:in >>> `delete' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:2578:in >>> `destroy_without_lock' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/locking/optimistic.rb:113:in >>> `destroy_without_callbacks' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:337:in >>> `destroy_without_transactions' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >>> `send' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >>> `with_transaction_returning_status' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >>> `transaction' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >>> `transaction' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in >>> `with_transaction_returning_status' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in >>> `destroy' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >>> `has_many_dependent_destroy_for_versions' >>> >>> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >>> `method_missing' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >>> `method_missing_without_paginate' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >>> `method_missing' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >>> `each' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >>> `send' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in >>> `method_missing' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in >>> `method_missing_without_paginate' >>> >>> [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in >>> `method_missing' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in >>> `has_many_dependent_destroy_for_versions' >>> >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >>> `send' >>> >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >>> `evaluate_method' >>> >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in >>> `run' >>> >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >>> `each' >>> >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >>> `send' >>> >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in >>> `run' >>> >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in >>> `run_callbacks' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in >>> `callback' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in >>> `destroy_without_transactions' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >>> `send' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in >>> `with_transaction_returning_status' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >>> `transaction' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >>> `transaction' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in >>> `with_transaction_returning_status' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in >>> `destroy_without_trash' >>> >>> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in >>> `destroy' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in >>> `transaction' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in >>> `transaction' >>> >>> [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in >>> `destroy' >>> >>> [RAILS_ROOT]/vendor/plugins/annotations/lib/app/controllers/annotations_controller.rb:121:in >>> `destroy' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in >>> `send' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in >>> `perform_action_without_filters' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:617:in >>> `call_filters' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:610:in >>> `perform_action_without_benchmark' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in >>> `perform_action_without_rescue' >>> >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in >>> `ms' >>> >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:10:in >>> `realtime' >>> >>> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in >>> `ms' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in >>> `perform_action_without_rescue' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rescue.rb:160:in >>> `perform_action_without_flash' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb:141:in >>> `perform_action' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in >>> `send' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in >>> `process_without_filters' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:606:in >>> `process' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:391:in >>> `process' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:386:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/route_set.rb:433:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:88:in >>> `dispatch' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:111:in >>> `_call' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:82:in >>> `initialize' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/methodoverride.rb:24:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/params_parser.rb:15:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rewindable_input.rb:25:in >>> `call' >>> [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in >>> `cache' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in >>> `cache' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >>> `synchronize' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >>> `call' >>> >>> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in >>> `call' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in >>> `process_request' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in >>> `main_loop' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in >>> `start_request_handler' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in >>> `handle_spawn_application' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in >>> `safe_fork' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in >>> `handle_spawn_application' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >>> `__send__' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >>> `main_loop' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in >>> `start_synchronously' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in >>> `start' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in >>> `start' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in >>> `spawn_rails_application' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in >>> `lookup_or_add' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in >>> `spawn_rails_application' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in >>> `synchronize' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in >>> `synchronize' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in >>> `spawn_rails_application' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in >>> `spawn_application' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in >>> `handle_spawn_application' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >>> `__send__' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >>> `main_loop' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in >>> `start_synchronously' >>> >>> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 >>> >>> >>> >>> >> -- 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 Thu Jun 3 05:42:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 3 Jun 2010 10:42:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-367) Fix issue with breadcrumbs still being generated even on error pages Message-ID: <28275846.1959.1275558137646.JavaMail.jira@rosalind.cs.man.ac.uk> Fix issue with breadcrumbs still being generated even on error pages -------------------------------------------------------------------- Key: BIOCAT-367 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-367 Project: BioCatalogue Issue Type: Bug Components: Web Interface Reporter: Jiten Bhagat Assignee: Jiten Bhagat Currently, if an error page is rendered the system will still try to build the breadcrumbs bar. This is not good because further errors are then generated if objects are not accessible within the _breadcrumbs partial. This is causing lots of error emails to be sent for the /soap_operations and /rest_methods endpoints. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 3 09:42:05 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 3 Jun 2010 09:42:05 -0400 (EDT) Subject: [BioCatalogue-developers] [2077] trunk/app: [BIOCAT-367] Fixed issue with breadcrumbs still being generated even on error pages Message-ID: <20100603134205.6B42C1858356@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu Jun 3 09:43:22 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 03 Jun 2010 14:43:22 +0100 Subject: [BioCatalogue-developers] recent error emails In-Reply-To: <4C0773B6.4040000@cs.man.ac.uk> References: <4c0663df4cb16_66501558cf4fd7c81ba@pweb-3b.ebi.ac.uk.tmail> <4C066511.2070003@ebi.ac.uk> <4C0687B3.6090908@cs.man.ac.uk> <4C0765A3.3030803@ebi.ac.uk> <4C0772B2.6080200@cs.man.ac.uk> <4C0773B6.4040000@cs.man.ac.uk> Message-ID: <4C07B17A.4070903@cs.man.ac.uk> I have fixed this in revision 2077. Jits Jiten Bhagat wrote: > It just occurred to me now why this is happening... > > A 404 *is* being generated, but in the resulting error page the template > *still* tries to build the breadcrumbs and thus causes another error. > > I will provide a global fix for this (ie: for error pages ignore > building of breadcrumbs). > > Jits > > > Jiten Bhagat wrote: > >> Eric, >> >> Normal 404 (resource does not exist) errors *should not* send out these >> error emails. >> >> If a bot (or anyone else) hits >> http://www.biocatalogue.org/services/300000 then an error email should >> not be sent out, because it is something we know about (ie: we don't >> care that the resource doesn't exist). >> >> To ensure that proper 404s are generated, Model.find(id) must be used in >> the controllers. This generates a RecordNotFound exception which the >> controller traps and then sends out a 404 to the client. >> >> In the case of /soap_operations... something is breaking this expected >> pattern and a proper 404 is not being generated. Instead, a nil >> @soap_operation and/or @soap_service is passed on to the views and then >> @soap_service.service is failing as a result (similar thing is happening >> with the /rest_methods). So something is not quite right, and needs to >> be investigated further. The error emails have, very usefully, flagged >> this up for us. >> >> Having bots access URLs and generate errors, which we then get an email >> for, is a valuable way of catching bugs. >> >> Jits >> >> >> >> Eric Nzuobontane wrote: >> >> >>> Jiten Bhagat wrote: >>> >>> >>>> There is a bigger problem here; we're getting errors exactly like this >>>> for a number of different things. Usually this shouldn't happen because >>>> Model.find(..) calls in the controller would trap bad URLs and give an >>>> appropriate 404. So it could be the data is inconsistent (orphaned >>>> objects etc) but I have added sanity checks for that. So in the end, I >>>> don't know. And I cannot reproduce this locally (for SoapOperations), >>>> even with the latest data. I have asked Mannie to at least investigate >>>> the RestService issues. >>>> >>>> >>>> >>> As far as I see it is not about the inconsistency of data (though that >>> might have an effect as well) but rather an application level issue. I >>> believe the mails are generated often by robots as the little >>> investigation I made last time pointed towards google bot. Right now, >>> if you hit any url like >>> http://www.biocatalogue.org/soap_operations/10000 (or any id which >>> does not exist in the db), this will generate one of those errors. If >>> generating an error is OK functionally, then we should expect these >>> mails with the possibility of being flooded when something just keeps >>> hitting one such url. >>> >>> Eric >>> >>> >>> >>>> Jits >>>> >>>> >>>> Eric Nzuobontane wrote: >>>> >>>> >>>> >>>>> BioCatalogue Errors wrote: >>>>> >>>>> >>>>> >>>>>> A ActionView::TemplateError occurred in application#show: >>>>>> >>>>>> undefined method `service' for nil:NilClass >>>>>> On line #16 of app/views/rest_methods/_breadcrumbs.html.erb >>>>>> >>>>>> 13: <% if controller.action_name.downcase == "show" -%> >>>>>> 14:
  • »
    • >>>>>> 15: 16:
  • <%= link_to >>>>>> display_name(@rest_service.service), @rest_service.service >>>>>> -%>
    • >>>>>> 17: 18:
  • »
    • >>>>>> 19: >>>>>> >>>>>> >>>>> I think this bit of code could check if the @rest_service object is >>>>> valid before attempting to call the service method on it. Could issue >>>>> a warning and stop these error messages. >>>>> >>>>> Eric >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>> app/views/rest_methods/_breadcrumbs.html.erb:16 >>>>>> app/helpers/application_helper.rb:510:in >>>>>> `render_breadcrumbs_after_home' >>>>>> app/views/widgets/_breadcrumbs_bar.html.erb:18 >>>>>> app/views/layouts/application_wide.html.erb:52 >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:376:in >>>>>> `start_request_handler' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:334:in >>>>>> `handle_spawn_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in >>>>>> `safe_fork' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:332:in >>>>>> `handle_spawn_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>>>> `__send__' >>>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>>>> `main_loop' >>>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in >>>>>> `start_synchronously' >>>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:162:in >>>>>> `start' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:213:in `start' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in >>>>>> `spawn_rails_application' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server_collection.rb:126:in >>>>>> `lookup_or_add' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in >>>>>> `spawn_rails_application' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server_collection.rb:80:in >>>>>> `synchronize' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server_collection.rb:79:in >>>>>> `synchronize' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in >>>>>> `spawn_rails_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in >>>>>> `spawn_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in >>>>>> `handle_spawn_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>>>> `__send__' >>>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:351:in >>>>>> `main_loop' >>>>>> passenger (2.2.4) lib/phusion_passenger/abstract_server.rb:195:in >>>>>> `start_synchronously' >>>>>> >>>>>> ------------------------------- >>>>>> Request: >>>>>> ------------------------------- >>>>>> >>>>>> * URL : http://www.biocatalogue.org/rest_methods/87 >>>>>> * Method : GET >>>>>> * IP address: 130.88.195.202 >>>>>> * Parameters: {"action"=>"show", "id"=>"87", >>>>>> "controller"=>"rest_methods"} >>>>>> * 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 : en-us,en;q=0.5 >>>>>> * HTTP_CACHE_CONTROL : max-age=0 >>>>>> * HTTP_CONNECTION : keep-alive >>>>>> * HTTP_COOKIE : >>>>>> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >>>>>> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >>>>>> >>>>>> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >>>>>> search_results_tabber=0; stats-tabs_tabber=1; >>>>>> __utmb=15951013.47.10.1275482785 >>>>>> * HTTP_HOST : www.biocatalogue.org >>>>>> * HTTP_IF_NONE_MATCH : >>>>>> "0180f1b3e6396d6c123bc9e0100888a9" >>>>>> * HTTP_KEEP_ALIVE : 300 >>>>>> * HTTP_REFERER : >>>>>> http://www.biocatalogue.org/services/2699 >>>>>> * HTTP_USER_AGENT : Mozilla/5.0 >>>>>> (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.9) Gecko/20100315 >>>>>> Firefox/3.5.9 >>>>>> * HTTP_X_CLUSTER_CLIENT_IP : 130.88.195.202 >>>>>> * PATH_INFO : /rest_methods/87 >>>>>> * QUERY_STRING : * >>>>>> REMOTE_ADDR : 130.88.195.202 >>>>>> * REMOTE_PORT : 47246 >>>>>> * REQUEST_METHOD : GET >>>>>> * REQUEST_URI : /rest_methods/87 >>>>>> * SCRIPT_NAME : * >>>>>> SERVER_ADDR : 172.18.1.108 >>>>>> * SERVER_ADMIN : root at localhost >>>>>> * SERVER_NAME : www.biocatalogue.org >>>>>> * SERVER_PORT : 80 >>>>>> * SERVER_PROTOCOL : HTTP/1.1 >>>>>> * SERVER_SOFTWARE : Apache/2.2.3 >>>>>> (CentOS) >>>>>> * _ : _ >>>>>> * action_controller.request.query_parameters : * >>>>>> action_controller.request.request_parameters: * >>>>>> action_controller.rescue.request : >>>>>> # >>>>>> * action_controller.rescue.response : >>>>>> # >>>>>> * rack.errors : # >>>>>> * rack.input : >>>>>> # >>>>>> * rack.multiprocess : true >>>>>> * rack.multithread : false >>>>>> * rack.request : >>>>>> # >>>>>> * rack.request.cookie_hash : >>>>>> __utma15951013.396796326.1272273201.1275473442.1275482785.119stats-tabs_tabber1__utmb15951013.47.10.1275482785__utmc15951013_session_id44ec0108816cfb2dd65cf4b41fa5ecafsearch_results_tabber0__utmz15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations >>>>>> >>>>>> >>>>>> * rack.request.cookie_string : >>>>>> __utma=15951013.396796326.1272273201.1275473442.1275482785.119; >>>>>> __utmz=15951013.1274709230.92.4.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=CYGDAnnotations; >>>>>> >>>>>> __utmc=15951013; _session_id=44ec0108816cfb2dd65cf4b41fa5ecaf; >>>>>> search_results_tabber=0; stats-tabs_tabber=1; >>>>>> __utmb=15951013.47.10.1275482785 >>>>>> * rack.request.query_hash : * >>>>>> rack.request.query_string : * >>>>>> rack.routing_args : >>>>>> actionshowid87controllerrest_methods >>>>>> * rack.run_once : false >>>>>> * rack.session : >>>>>> search_show_listing_typesimpleprevious_url/rest_methods/87use_tab_cookiefalseservices_index_listing_typedetailed_csrf_token0kG6dBrYr1Ev8XeG6a1n6hsZ2W13c8trCaA7d/0hNZ0=user_id27flashnoticeEndpoint >>>>>> >>>>>> GET /goTerms has been >>>>>> deletedlast_searchhttp://www.biocatalogue.org/search?q=virginia+&commit= >>>>>> >>>>>> * rack.session.options : >>>>>> securefalseexpire_afterkey_session_idid44ec0108816cfb2dd65cf4b41fa5ecafhttponlytruedomaincookie_onlytruepath/ >>>>>> >>>>>> >>>>>> * rack.session.record : >>>>>> # >>>>>> * rack.url_scheme : http >>>>>> * rack.version : 10 >>>>>> * Process: 26192 >>>>>> * Server : pweb-3b >>>>>> * request.format: text/html >>>>>> >>>>>> ------------------------------- >>>>>> Backtrace: >>>>>> ------------------------------- >>>>>> >>>>>> On line #16 of app/views/rest_methods/_breadcrumbs.html.erb >>>>>> 13: <% if controller.action_name.downcase == "show" -%> >>>>>> 14:
  • »
    • >>>>>> 15: 16:
  • <%= link_to >>>>>> display_name(@rest_service.service), @rest_service.service >>>>>> -%>
    • >>>>>> 17: 18:
  • »
    • >>>>>> 19: app/views/rest_methods/_breadcrumbs.html.erb:16 >>>>>> app/helpers/application_helper.rb:510:in >>>>>> `render_breadcrumbs_after_home' >>>>>> app/views/widgets/_breadcrumbs_bar.html.erb:18 >>>>>> app/views/layouts/application_wide.html.erb:52 >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:376:in >>>>>> `start_request_handler' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:334:in >>>>>> `handle_spawn_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/utils.rb:182:in >>>>>> `safe_fork' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:332:in >>>>>> `handle_spawn_application' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server.rb:351:in `__send__' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server.rb:351:in `main_loop' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server.rb:162:in `start' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/railz/application_spawner.rb:213:in `start' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:261:in >>>>>> `spawn_rails_application' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server_collection.rb:126:in >>>>>> `lookup_or_add' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:255:in >>>>>> `spawn_rails_application' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server_collection.rb:80:in >>>>>> `synchronize' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server_collection.rb:79:in >>>>>> `synchronize' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:254:in >>>>>> `spawn_rails_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:153:in >>>>>> `spawn_application' >>>>>> passenger (2.2.4) lib/phusion_passenger/spawn_manager.rb:286:in >>>>>> `handle_spawn_application' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server.rb:351:in `__send__' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server.rb:351:in `main_loop' >>>>>> passenger (2.2.4) >>>>>> lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>> >>> >> >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From issues at mygrid.org.uk Thu Jun 3 09:44:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 3 Jun 2010 14:44:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-367) Fix issue with breadcrumbs still being generated even on error pages In-Reply-To: <28275846.1959.1275558137646.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27900973.1960.1275572657042.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-367?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10370 ] Jiten Bhagat logged work on BIOCAT-367: --------------------------------------- Author: Jiten Bhagat Created on: 2010-06-03 14:43 Start Date: 2010-06-03 10:33 Worklog Time Spent: 1 hour, 30 minutes Issue Time Tracking ------------------- Remaining Estimate: 30 minutes (was: 2 hours) Time Spent: 1 hour, 30 minutes > Fix issue with breadcrumbs still being generated even on error pages > -------------------------------------------------------------------- > > Key: BIOCAT-367 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-367 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 1 hour, 30 minutes > Remaining Estimate: 30 minutes > > Currently, if an error page is rendered the system will still try to build the breadcrumbs bar. This is not good because further errors are then generated if objects are not accessible within the _breadcrumbs partial. > This is causing lots of error emails to be sent for the /soap_operations and /rest_methods endpoints. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 3 09:44:21 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 3 Jun 2010 14:44:21 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-367) Fix issue with breadcrumbs still being generated even on error pages In-Reply-To: <28275846.1959.1275558137646.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21306200.1961.1275572661421.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-367?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-367. --------------------------------- Resolution: Fixed Fixed in revision 2077 > Fix issue with breadcrumbs still being generated even on error pages > -------------------------------------------------------------------- > > Key: BIOCAT-367 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-367 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 1 hour, 30 minutes > Remaining Estimate: 30 minutes > > Currently, if an error page is rendered the system will still try to build the breadcrumbs bar. This is not good because further errors are then generated if objects are not accessible within the _breadcrumbs partial. > This is causing lots of error emails to be sent for the /soap_operations and /rest_methods endpoints. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 3 10:24:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 3 Jun 2010 10:24:08 -0400 (EDT) Subject: [BioCatalogue-developers] [2078] trunk: [BIOCAT-365] Initial skeleton of the copy annotations feature for the Curation Dashboard . Message-ID: <20100603142408.9F7161858366@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Jun 3 10:28:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 3 Jun 2010 10:28:07 -0400 (EDT) Subject: [BioCatalogue-developers] [2079] trunk/app/views/widgets/_login_links.html.erb: [BIOCAT-363] Removed link on "Welcome [user name]" and added new "My Profile" link. Message-ID: <20100603142807.E37D7185834B@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jun 3 10:28:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 3 Jun 2010 15:28:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-365) Implement curation page for "Copy annotations from SOAP operation x to SOAP operation y" In-Reply-To: <16563352.1766.1275408497109.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20013046.1962.1275575297049.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-365?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10371 ] Jiten Bhagat logged work on BIOCAT-365: --------------------------------------- Author: Jiten Bhagat Created on: 2010-06-03 15:26 Start Date: 2010-06-03 14:26 Worklog Time Spent: 30 minutes Issue Time Tracking ------------------- Remaining Estimate: 3 hours, 30 minutes (was: 4 hours) Time Spent: 30 minutes > Implement curation page for "Copy annotations from SOAP operation x to SOAP operation y" > ---------------------------------------------------------------------------------------- > > Key: BIOCAT-365 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-365 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard > Environment: RoR > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 4 hours > Time Spent: 30 minutes > Remaining Estimate: 3 hours, 30 minutes > > Due to the recent additions of so many new SOAP operations (over 1000) due to the service updater, Franck needs a way to easily copy over annotations. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 3 10:30:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 3 Jun 2010 15:30:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (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: <14922554.1963.1275575417026.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 ] Jiten Bhagat resolved BIOCAT-363. --------------------------------- Resolution: Fixed Done in revision 2079 > 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 ericnzuo at ebi.ac.uk Thu Jun 3 11:08:54 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 03 Jun 2010 16:08:54 +0100 Subject: [BioCatalogue-developers] downtime for the test site Message-ID: <4C07C586.3070709@ebi.ac.uk> I want to reload the data on the test site with live data. I will need to bring it down for a couple of minutes. 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 issues at mygrid.org.uk Fri Jun 4 05:14:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 4 Jun 2010 10:14:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-368) Curate CNRS IBCP services (wsdl locations are currently wrong in catalogue) Message-ID: <9137376.2031.1275642857173.JavaMail.jira@rosalind.cs.man.ac.uk> Curate CNRS IBCP services (wsdl locations are currently wrong in catalogue) --------------------------------------------------------------------------- Key: BIOCAT-368 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-368 Project: BioCatalogue Issue Type: Task Components: Data Reporter: Eric Nzuobontane Assignee: Jiten Bhagat WSDL locations for these services have changes since they were registered in the catalogue. Need to manually correct these to bring them up to date. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 4 05:14:20 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 4 Jun 2010 10:14:20 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-368) Curate CNRS IBCP services (wsdl locations are currently wrong in catalogue) In-Reply-To: <9137376.2031.1275642857173.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <33378554.2032.1275642860126.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-368?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-368: --------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > Curate CNRS IBCP services (wsdl locations are currently wrong in catalogue) > --------------------------------------------------------------------------- > > Key: BIOCAT-368 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-368 > Project: BioCatalogue > Issue Type: Task > Components: Data > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 hour > Remaining Estimate: 1 hour > > WSDL locations for these services have changes since they were registered in the catalogue. Need to manually correct these to bring them up to date. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 4 05:14:21 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 4 Jun 2010 10:14:21 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-368) Curate CNRS IBCP services (wsdl locations are currently wrong in catalogue) In-Reply-To: <9137376.2031.1275642857173.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22325925.2033.1275642861470.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-368?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-368 started by Eric Nzuobontane. > Curate CNRS IBCP services (wsdl locations are currently wrong in catalogue) > --------------------------------------------------------------------------- > > Key: BIOCAT-368 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-368 > Project: BioCatalogue > Issue Type: Task > Components: Data > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 hour > Remaining Estimate: 1 hour > > WSDL locations for these services have changes since they were registered in the catalogue. Need to manually correct these to bring them up to date. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 4 05:45:26 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 4 Jun 2010 10:45:26 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-368) Curate CNRS IBCP services (wsdl locations are currently wrong in catalogue) In-Reply-To: <9137376.2031.1275642857173.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5531234.2148.1275644726084.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-368?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-368. ------------------------------------- Resolution: Fixed Now updated the wsdl locations and launched update checker for the services. > Curate CNRS IBCP services (wsdl locations are currently wrong in catalogue) > --------------------------------------------------------------------------- > > Key: BIOCAT-368 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-368 > Project: BioCatalogue > Issue Type: Task > Components: Data > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 hour > Remaining Estimate: 1 hour > > WSDL locations for these services have changes since they were registered in the catalogue. Need to manually correct these to bring them up to date. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri Jun 4 06:37:39 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 4 Jun 2010 06:37:39 -0400 (EDT) Subject: [BioCatalogue-developers] [2080] trunk/app/views/widgets/_action_bar.html.erb: Minor style fix Message-ID: <20100604103741.65BB9185836F@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 4 07:02:31 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 4 Jun 2010 12:02:31 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-369) Implement report for "Potential Duplicate SOAP Operations within a SOAP Service" In-Reply-To: <1531803.2327.1275649336991.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7136583.2328.1275649351478.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-369?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10375 ] Jiten Bhagat logged work on BIOCAT-369: --------------------------------------- Author: Jiten Bhagat Created on: 2010-06-04 12:02 Start Date: 2010-06-04 10:02 Worklog Time Spent: 2 hours Issue Time Tracking ------------------- Remaining Estimate: 2 hours (was: 4 hours) Time Spent: 2 hours > Implement report for "Potential Duplicate SOAP Operations within a SOAP Service" > -------------------------------------------------------------------------------- > > Key: BIOCAT-369 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-369 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 4 hours > Time Spent: 2 hours > Remaining Estimate: 2 hours > > Need a curation report page that allows a curator like Franck to see a list of potentially duplicate/similar SOAP operations that are candidates for copying over of annotations. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 4 07:02:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 4 Jun 2010 12:02:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-369) Implement report for "Potential Duplicate SOAP Operations within a SOAP Service" Message-ID: <1531803.2327.1275649336991.JavaMail.jira@rosalind.cs.man.ac.uk> Implement report for "Potential Duplicate SOAP Operations within a SOAP Service" -------------------------------------------------------------------------------- Key: BIOCAT-369 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-369 Project: BioCatalogue Issue Type: New Feature Components: Curation Dashboard Reporter: Jiten Bhagat Assignee: Jiten Bhagat Need a curation report page that allows a curator like Franck to see a list of potentially duplicate/similar SOAP operations that are candidates for copying over of annotations. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 4 07:04:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 4 Jun 2010 12:04:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-365) Implement curation page for "Copy annotations from SOAP operation x to SOAP operation y" In-Reply-To: <16563352.1766.1275408497109.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25154917.2329.1275649457026.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-365?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15017#action_15017 ] Jiten Bhagat commented on BIOCAT-365: ------------------------------------- When copying over annotations, should the original sources of the annotations be maintained, or should the curator get credit for copying over the annotation? > Implement curation page for "Copy annotations from SOAP operation x to SOAP operation y" > ---------------------------------------------------------------------------------------- > > Key: BIOCAT-365 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-365 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard > Environment: RoR > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 4 hours > Time Spent: 30 minutes > Remaining Estimate: 3 hours, 30 minutes > > Due to the recent additions of so many new SOAP operations (over 1000) due to the service updater, Franck needs a way to easily copy over annotations. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 4 07:18:17 2010 From: issues at mygrid.org.uk (Franck Tanoh (JIRA)) Date: Fri, 4 Jun 2010 12:18:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-365) Implement curation page for "Copy annotations from SOAP operation x to SOAP operation y" In-Reply-To: <16563352.1766.1275408497109.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28666585.2351.1275650297029.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-365?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Franck Tanoh updated BIOCAT-365: -------------------------------- I think whoever copy the annotation should get the credit either curator or BioCatalogue or any other users. That is, the person who added the annotation will be responsible if anyone else disagree with what he's added. But we could adopt the policy of encouraging the member who added the annotation in the first place. > Implement curation page for "Copy annotations from SOAP operation x to SOAP operation y" > ---------------------------------------------------------------------------------------- > > Key: BIOCAT-365 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-365 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard > Environment: RoR > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 4 hours > Time Spent: 30 minutes > Remaining Estimate: 3 hours, 30 minutes > > Due to the recent additions of so many new SOAP operations (over 1000) due to the service updater, Franck needs a way to easily copy over annotations. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 4 07:43:16 2010 From: issues at mygrid.org.uk (Franck Tanoh (JIRA)) Date: Fri, 4 Jun 2010 12:43:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-365) Implement curation page for "Copy annotations from SOAP operation x to SOAP operation y" In-Reply-To: <16563352.1766.1275408497109.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21960984.2403.1275651796999.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-365?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Franck Tanoh updated BIOCAT-365: -------------------------------- To clarify my previous comment. my view is that we should credit the person (e.g curator) who assigned the annotation to the other service or operation. > Implement curation page for "Copy annotations from SOAP operation x to SOAP operation y" > ---------------------------------------------------------------------------------------- > > Key: BIOCAT-365 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-365 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard > Environment: RoR > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 4 hours > Time Spent: 30 minutes > Remaining Estimate: 3 hours, 30 minutes > > Due to the recent additions of so many new SOAP operations (over 1000) due to the service updater, Franck needs a way to easily copy over annotations. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 4 09:32:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 4 Jun 2010 14:32:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-365) Implement curation page for "Copy annotations from SOAP operation x to SOAP operation y" In-Reply-To: <16563352.1766.1275408497109.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13248187.2404.1275658337128.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-365?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15026#action_15026 ] Jiten Bhagat commented on BIOCAT-365: ------------------------------------- Okay, so I will assign the curator/admin who performed the copy action as the "source" of the new annotation(s). I will also store a Relationship to say what the original annotation was for any copied annotations. > Implement curation page for "Copy annotations from SOAP operation x to SOAP operation y" > ---------------------------------------------------------------------------------------- > > Key: BIOCAT-365 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-365 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard > Environment: RoR > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 4 hours > Time Spent: 30 minutes > Remaining Estimate: 3 hours, 30 minutes > > Due to the recent additions of so many new SOAP operations (over 1000) due to the service updater, Franck needs a way to easily copy over annotations. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Fri Jun 4 09:38:02 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 04 Jun 2010 14:38:02 +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 Fri Jun 4 11:55:34 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 04 Jun 2010 16:55:34 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'GOR III protein secondary structure prediction (CNRS IBCP)' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'GOR III protein secondary structure prediction (CNRS IBCP)' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/269 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Jun 4 12:02:05 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 4 Jun 2010 12:02:05 -0400 (EDT) Subject: [BioCatalogue-developers] [2081] trunk/vendor/plugins/annotations: Update Annotations plugin to latest from master repository. Message-ID: <20100604160205.876043C8043@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Jun 4 12:42:30 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 4 Jun 2010 12:42:30 -0400 (EDT) Subject: [BioCatalogue-developers] [2082] trunk: [BIOCAT-365] [BIOCAT-369] Initial working implementations of the "Copy Annotations From Item to Item " curation tool and the " Potential Duplicate SOAP Operations within a SOAP Service" curation report. Message-ID: <20100604164230.CB03B1858351@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Fri Jun 4 12:46:29 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 04 Jun 2010 17:46:29 +0100 Subject: [BioCatalogue-developers] New curation features Message-ID: <4C092DE5.1040809@cs.man.ac.uk> Hi Franck, For when you get in on Monday - I've have added a curation tool and report on http://sandbox.biocatalogue.org. Please can you have a play? When you log on, you should now see a "Curation Dashboard" link at the top right. Click on this and have a play with the various things and let me know how you get on please. Cheers, Jits From utopia at cs.man.ac.uk Sat Jun 5 04:53:27 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 05 Jun 2010 09:53:27 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'BLAST blastp protein similarity search (CNRS IBCP)' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'BLAST blastp protein similarity search (CNRS IBCP)' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/92 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Jun 5 10:00:25 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 05 Jun 2010 15:00:25 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getPubMed' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getPubMed' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1090 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 Jun 5 11:33:24 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 05 Jun 2010 16:33:24 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:translateNucleoSeqToAminoSeq' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:translateNucleoSeqToAminoSeq' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1074 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 Jun 5 14:27:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 05 Jun 2010 19:27:28 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getSymbolInteractionsXML' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getSymbolInteractionsXML' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1087 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 Jun 6 08:21:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 06 Jun 2010 13:21:06 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'FASTA protein similarity search (CNRS IBCP)' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'FASTA protein similarity search (CNRS IBCP)' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/264 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Jun 6 08:40:07 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 06 Jun 2010 13:40:07 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:getAminoAcidSequenceFromPDB' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:getAminoAcidSequenceFromPDB' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/988 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 Jun 6 13:10:04 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 06 Jun 2010 18:10:04 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToMD_TrajectoryCRD' changed to Passed 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 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1120 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Mon Jun 7 06:39:32 2010 From: issues at mygrid.org.uk (Franck Tanoh (JIRA)) Date: Mon, 7 Jun 2010 11:39:32 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-370) In the curation dashboard possibility to compare each archived soap operation to all existing soap operations of a service. Message-ID: <11617150.2514.1275907172502.JavaMail.jira@rosalind.cs.man.ac.uk> In the curation dashboard possibility to compare each archived soap operation to all existing soap operations of a service. ---------------------------------------------------------------------------------------------------------------------------- Key: BIOCAT-370 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-370 Project: BioCatalogue Issue Type: New Feature Components: Curation Dashboard Reporter: Franck Tanoh Assignee: Jiten Bhagat In the curation dashboard possibility to compare each archived soap operation to all existing soap operations of a service. If we can do a 1(archived operation) to all (existing operations) comparison, we can then easily transfer any descriptions from archived services that are still valid. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ytanoh at cs.man.ac.uk Mon Jun 7 06:47:46 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 7 Jun 2010 11:47:46 +0100 Subject: [BioCatalogue-developers] New curation features In-Reply-To: <4C092DE5.1040809@cs.man.ac.uk> References: <4C092DE5.1040809@cs.man.ac.uk> Message-ID: Hi Jits, Thanks for the effort... this is a good path toward the curation dashboard. The issue we discussed is here: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-370 Some easy ways to fill in the ID on the 'copy annotation page' will be useful. for example, auto-complete when I tick a service on the 'report' page. Cheers, Franck On 4 June 2010 17:46, Jiten Bhagat wrote: > Hi Franck, > > For when you get in on Monday - > > I've have added a curation tool and report on > http://sandbox.biocatalogue.org. Please can you have a play? > > When you log on, you should now see a "Curation Dashboard" link at the > top right. Click on this and have a play with the various things and let > me know how you get on please. > > Cheers, > Jits > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Mon Jun 7 06:57:06 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 07 Jun 2010 11:57:06 +0100 Subject: [BioCatalogue-developers] New curation features In-Reply-To: References: <4C092DE5.1040809@cs.man.ac.uk> Message-ID: <4C0CD082.2070405@cs.man.ac.uk> > Some easy ways to fill in the ID on the 'copy annotation page' will be > useful. for example, auto-complete when I tick a service on the > 'report' page. This is a very good idea, but very tricky to implement unfortunately (because the ID fields are dependant on the type of item you want to copy annotations on). Please could you add to the task list? Thanks, Jits Franck Tanoh wrote: > Hi Jits, > > Thanks for the effort... this is a good path toward the curation > dashboard. > The issue we discussed is here: > http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-370 > Some easy ways to fill in the ID on the 'copy annotation page' will be > useful. for example, auto-complete when I tick a service on the > 'report' page. > > Cheers, > Franck > > On 4 June 2010 17:46, Jiten Bhagat > wrote: > > Hi Franck, > > For when you get in on Monday - > > I've have added a curation tool and report on > http://sandbox.biocatalogue.org. Please can you have a play? > > When you log on, you should now see a "Curation Dashboard" link at the > top right. Click on this and have a play with the various things > and let > me know how you get on please. > > Cheers, > Jits > > > > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Mon Jun 7 07:03:12 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 7 Jun 2010 07:03:12 -0400 (EDT) Subject: [BioCatalogue-developers] [2083] trunk/vendor/plugins/annotations: Update Annotations plugin to latest from master repository. Message-ID: <20100607110312.E9250185835D@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jun 7 07:07:56 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 7 Jun 2010 07:07:56 -0400 (EDT) Subject: [BioCatalogue-developers] [2084] trunk/lib/bio_catalogue/annotations.rb: Added a check to BioCatalogue:: Annotations#bulk_create for when an empty annotations input is provided. Message-ID: <20100607110756.6FB853C8039@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jun 7 07:54:17 2010 From: issues at mygrid.org.uk (Franck Tanoh (JIRA)) Date: Mon, 7 Jun 2010 12:54:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-371) Some easy ways to fill in the ID on the 'copy annotation page' will be useful. for example, auto-complete when I tick a service on the 'report' page. Message-ID: <8889938.2562.1275911657025.JavaMail.jira@rosalind.cs.man.ac.uk> Some easy ways to fill in the ID on the 'copy annotation page' will be useful. for example, auto-complete when I tick a service on the 'report' page. ----------------------------------------------------------------------------------------------------------------------------------------------------- Key: BIOCAT-371 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-371 Project: BioCatalogue Issue Type: Sub-task Components: Curation Dashboard Reporter: Franck Tanoh Assignee: Jiten Bhagat (Franck) > Some easy ways to fill in the ID on the 'copy annotation page' will be > useful. for example, auto-complete when I tick a service on the > 'report' page. (Jits) This is a very good idea, but very tricky to implement unfortunately (because the ID fields are dependant on the type of item you want to copy annotations on). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 7 12:15:49 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 7 Jun 2010 12:15:49 -0400 (EDT) Subject: [BioCatalogue-developers] [2085] trunk/app/views/services/show.html.erb: On the service page, don' t highlight the activity list when it loads up. Message-ID: <20100607161549.858061858354@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jun 7 12:50:35 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 7 Jun 2010 12:50:35 -0400 (EDT) Subject: [BioCatalogue-developers] [2086] trunk/vendor/plugins/annotations: Update Annotations plugin to latest from master repository, to fix a major bug in the create_annotations method ( but that only affected the output, not the actual creation process). Message-ID: <20100607165035.3948A1858354@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jun 7 12:51:21 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 7 Jun 2010 12:51:21 -0400 (EDT) Subject: [BioCatalogue-developers] [2087] trunk/app/controllers/annotations_controller.rb: Disabled the / annotations/ bulk_create XML endpoint as it is not outputting the correct thing. Message-ID: <20100607165121.28A46167829F@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jun 7 13:07:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 7 Jun 2010 18:07:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-372) Documentation URL not being picked up by the WSDL parser Message-ID: <22066438.2608.1275930437035.JavaMail.jira@rosalind.cs.man.ac.uk> Documentation URL not being picked up by the WSDL parser -------------------------------------------------------- Key: BIOCAT-372 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-372 Project: BioCatalogue Issue Type: Bug Components: Service Submission Reporter: Jiten Bhagat Assignee: Eric Nzuobontane Priority: Critical As reported by Olivier Sallou: bq. I just submitted a new service (wsdl interproscan) but we have some errors: at submission, documentation tag is not recognized, and as a consequence is not filled automatically (though used to do so). I manually added 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 Jun 7 13:07:19 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 7 Jun 2010 18:07:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-372) Documentation URL not being picked up by the WSDL parser In-Reply-To: <22066438.2608.1275930437035.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26724941.2609.1275930439984.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-372?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-372: -------------------------------- Description: As reported by Olivier Sallou: bq. I just submitted a new service (wsdl interproscan) but we have some errors: at submission, documentation tag is not recognized, and as a consequence is not filled automatically (though used to do so). I manually added it. was: As reported by Olivier Sallou: bq. I just submitted a new service (wsdl interproscan) but we have some errors: at submission, documentation tag is not recognized, and as a consequence is not filled automatically (though used to do so). I manually added it. > Documentation URL not being picked up by the WSDL parser > -------------------------------------------------------- > > Key: BIOCAT-372 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-372 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > Priority: Critical > > As reported by Olivier Sallou: > bq. I just submitted a new service (wsdl interproscan) but we have some errors: at submission, documentation tag is not recognized, and as a consequence is not filled automatically (though used to do so). I manually added 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 utopia at cs.man.ac.uk Mon Jun 7 19:25:02 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 08 Jun 2010 00:25:02 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:translateGeneIDGFFPredictions' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:translateGeneIDGFFPredictions' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/768 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Tue Jun 8 04:08:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 8 Jun 2010 09:08:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-372) Documentation URL not being picked up by the WSDL parser In-Reply-To: <22066438.2608.1275930437035.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24984484.2645.1275984497178.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-372?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-372 started by Eric Nzuobontane. > Documentation URL not being picked up by the WSDL parser > -------------------------------------------------------- > > Key: BIOCAT-372 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-372 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > Priority: Critical > > As reported by Olivier Sallou: > bq. I just submitted a new service (wsdl interproscan) but we have some errors: at submission, documentation tag is not recognized, and as a consequence is not filled automatically (though used to do so). I manually added it. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 8 04:58:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 8 Jun 2010 09:58:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-373) Issue with < and > characters within annotations when rendered in the UI Message-ID: <2931027.2646.1275987497061.JavaMail.jira@rosalind.cs.man.ac.uk> Issue with < and > characters within annotations when rendered in the UI ------------------------------------------------------------------------ Key: BIOCAT-373 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-373 Project: BioCatalogue Issue Type: Bug Components: Web Interface Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical Currently, if users add annotations like: bq. usage: iprscan [-appl ...] [-nocrc] [-seqtype p|n] [-trlen ] [-trtable ]\r\n [-iprlookup] [-goterms] -i [-o ]\r\n\r\n -i ... then the annotation is displayed incorrectly and breaks the page layout. This is not good! It seems that only a rich text editor will solve this particular issue. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Tue Jun 8 05:30:17 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 08 Jun 2010 10:30:17 +0100 Subject: [BioCatalogue-developers] Recent BioCatalogue features Message-ID: <4C0E0DA9.2030005@cs.man.ac.uk> Hi Marco, As mentioned, here are some of the most recent new features in the BioCatalogue, that might be interesting to mention in your interview tomorrow: - Activity/news feeds for services (also in ATOM) - Monitoring test changes feed (also in ATOM) - Service responsibility request mechanism (you can now request responsibility for a service) - Service update checker (check for WSDL updates for now and updates the catalogue automatically) - Service archival (can mark a service as archived) - REST endpoints returned in search - Service provider curation - (the service providers in the catalogue now make more "sense") - Various service monitoring updates (show since when a URL is being monitored; better REST service monitoring - we now monitor some example endpoints automatically) - New API features (get all WSDL locations; favourites and viewings count; alpha release of bulk annotations API) The previous release also had: - Public read only REST API - Better support for describing REST Services. You can now describe in detail the exact endpoints available for a REST service, together with the input and output parameters and representations. This will also be used to describe the BioCatalogue REST API. - A more streamlined UI for browsing the SOAP operations and REST endpoints of a service. - SOAP operations are now directly returned in search. We also have an alpha version plugin for Taverna that integrates the BioCatalogue into the workflow building process. This will be further developed this summer to make it production ready and released bundled with Taverna. In terms of future functionality that might be useful to bioinformaticians, we are working on: - Being able to run services directly within the BioCatalogue, in order to test out things quickly. - Integration with myExperiment (a new "Services" tab in myexp and things like "other workflows that use the services in this workflow") - Functional Units of Services- Ability to present services in terms of their biological functions, biological data types and biological resources. Hope this is useful. Jits From jits at cs.man.ac.uk Tue Jun 8 05:34:31 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 08 Jun 2010 10:34:31 +0100 Subject: [BioCatalogue-developers] Recent BioCatalogue features In-Reply-To: <4C0E0DA9.2030005@cs.man.ac.uk> References: <4C0E0DA9.2030005@cs.man.ac.uk> Message-ID: <4C0E0EA7.7070402@cs.man.ac.uk> Guys, I am drafting a detailed announcement based on the below. I will send this out by end of today. Once the release goes through tomorrow I'll publish the full announcement. Jits PS: Eric, can you update the test server please? I'll look through the logs and see if any custom deployment actions are required. Otherwise, just assume the normal set of deployment actions, apart from a full reindex. Jiten Bhagat wrote: > Hi Marco, > > As mentioned, here are some of the most recent new features in the > BioCatalogue, that might be interesting to mention in your interview > tomorrow: > > - Activity/news feeds for services (also in ATOM) > - Monitoring test changes feed (also in ATOM) > - Service responsibility request mechanism (you can now request > responsibility for a service) > - Service update checker (check for WSDL updates for now and updates the > catalogue automatically) > - Service archival (can mark a service as archived) > - REST endpoints returned in search > - Service provider curation - (the service providers in the catalogue > now make more "sense") > - Various service monitoring updates (show since when a URL is being > monitored; better REST service monitoring - we now monitor some example > endpoints automatically) > - New API features (get all WSDL locations; favourites and viewings > count; alpha release of bulk annotations API) > > The previous release also had: > > - Public read only REST API > - Better support for describing REST Services. You can now describe in > detail the exact endpoints available for a REST service, together with > the input and output parameters and representations. This will also be > used to describe the BioCatalogue REST API. > - A more streamlined UI for browsing the SOAP operations and REST > endpoints of a service. > - SOAP operations are now directly returned in search. > > We also have an alpha version plugin for Taverna that integrates the > BioCatalogue into the workflow building process. This will be further > developed this summer to make it production ready and released bundled > with Taverna. > > In terms of future functionality that might be useful to > bioinformaticians, we are working on: > > - Being able to run services directly within the BioCatalogue, in order > to test out things quickly. > - Integration with myExperiment (a new "Services" tab in myexp and > things like "other workflows that use the services in this workflow") > - Functional Units of Services- Ability to present services in terms of > their biological functions, biological data types and biological resources. > > Hope this is useful. > > Jits > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From ytanoh at cs.man.ac.uk Tue Jun 8 05:59:17 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 8 Jun 2010 10:59:17 +0100 Subject: [BioCatalogue-developers] Recent BioCatalogue features In-Reply-To: <4C0E0EA7.7070402@cs.man.ac.uk> References: <4C0E0DA9.2030005@cs.man.ac.uk> <4C0E0EA7.7070402@cs.man.ac.uk> Message-ID: Hi Jits, It will be useful if you can point to some examples to illustrate some of the features. Things like "Activity/news feeds" are difficult to understand until you see one. You could also show the importance of the "service responsibility request" e.g. ...that is, more than one person can maintain the same web service in the Biocatalogue not only the submitter as previously. is the soaplab annotation import part the release tomorrow? Franck On 8 June 2010 10:34, Jiten Bhagat wrote: > Guys, > > I am drafting a detailed announcement based on the below. I will send > this out by end of today. > > Once the release goes through tomorrow I'll publish the full announcement. > > Jits > > PS: Eric, can you update the test server please? I'll look through the > logs and see if any custom deployment actions are required. Otherwise, > just assume the normal set of deployment actions, apart from a full > reindex. > > > Jiten Bhagat wrote: > > Hi Marco, > > > > As mentioned, here are some of the most recent new features in the > > BioCatalogue, that might be interesting to mention in your interview > > tomorrow: > > > > - Activity/news feeds for services (also in ATOM) > > - Monitoring test changes feed (also in ATOM) > > - Service responsibility request mechanism (you can now request > > responsibility for a service) > > - Service update checker (check for WSDL updates for now and updates the > > catalogue automatically) > > - Service archival (can mark a service as archived) > > - REST endpoints returned in search > > - Service provider curation - (the service providers in the catalogue > > now make more "sense") > > - Various service monitoring updates (show since when a URL is being > > monitored; better REST service monitoring - we now monitor some example > > endpoints automatically) > > - New API features (get all WSDL locations; favourites and viewings > > count; alpha release of bulk annotations API) > > > > The previous release also had: > > > > - Public read only REST API > > - Better support for describing REST Services. You can now describe in > > detail the exact endpoints available for a REST service, together with > > the input and output parameters and representations. This will also be > > used to describe the BioCatalogue REST API. > > - A more streamlined UI for browsing the SOAP operations and REST > > endpoints of a service. > > - SOAP operations are now directly returned in search. > > > > We also have an alpha version plugin for Taverna that integrates the > > BioCatalogue into the workflow building process. This will be further > > developed this summer to make it production ready and released bundled > > with Taverna. > > > > In terms of future functionality that might be useful to > > bioinformaticians, we are working on: > > > > - Being able to run services directly within the BioCatalogue, in order > > to test out things quickly. > > - Integration with myExperiment (a new "Services" tab in myexp and > > things like "other workflows that use the services in this workflow") > > - Functional Units of Services- Ability to present services in terms of > > their biological functions, biological data types and biological > resources. > > > > Hope this is useful. > > > > Jits > > _______________________________________________ > > BioCatalogue-developers mailing list > > BioCatalogue-developers at rubyforge.org > > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue Jun 8 07:54:47 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 08 Jun 2010 12:54:47 +0100 Subject: [BioCatalogue-developers] Recent BioCatalogue features In-Reply-To: References: <4C0E0DA9.2030005@cs.man.ac.uk> <4C0E0EA7.7070402@cs.man.ac.uk> Message-ID: <4C0E2F87.8050405@ebi.ac.uk> > > > is the soaplab annotation import part the release tomorrow? I just need to get the UI ready for it and it will be ready to go. Not all soaplab services return the description though. I think the manchester one is one of those that don't. Eric > > Franck > > On 8 June 2010 10:34, Jiten Bhagat > wrote: > > Guys, > > I am drafting a detailed announcement based on the below. I will send > this out by end of today. > > Once the release goes through tomorrow I'll publish the full > announcement. > > Jits > > PS: Eric, can you update the test server please? I'll look through the > logs and see if any custom deployment actions are required. Otherwise, > just assume the normal set of deployment actions, apart from a > full reindex. > > > Jiten Bhagat wrote: > > Hi Marco, > > > > As mentioned, here are some of the most recent new features in the > > BioCatalogue, that might be interesting to mention in your interview > > tomorrow: > > > > - Activity/news feeds for services (also in ATOM) > > - Monitoring test changes feed (also in ATOM) > > - Service responsibility request mechanism (you can now request > > responsibility for a service) > > - Service update checker (check for WSDL updates for now and > updates the > > catalogue automatically) > > - Service archival (can mark a service as archived) > > - REST endpoints returned in search > > - Service provider curation - (the service providers in the > catalogue > > now make more "sense") > > - Various service monitoring updates (show since when a URL is being > > monitored; better REST service monitoring - we now monitor some > example > > endpoints automatically) > > - New API features (get all WSDL locations; favourites and viewings > > count; alpha release of bulk annotations API) > > > > The previous release also had: > > > > - Public read only REST API > > - Better support for describing REST Services. You can now > describe in > > detail the exact endpoints available for a REST service, > together with > > the input and output parameters and representations. This will > also be > > used to describe the BioCatalogue REST API. > > - A more streamlined UI for browsing the SOAP operations and REST > > endpoints of a service. > > - SOAP operations are now directly returned in search. > > > > We also have an alpha version plugin for Taverna that integrates the > > BioCatalogue into the workflow building process. This will be > further > > developed this summer to make it production ready and released > bundled > > with Taverna. > > > > In terms of future functionality that might be useful to > > bioinformaticians, we are working on: > > > > - Being able to run services directly within the BioCatalogue, > in order > > to test out things quickly. > > - Integration with myExperiment (a new "Services" tab in myexp and > > things like "other workflows that use the services in this > workflow") > > - Functional Units of Services- Ability to present services in > terms of > > their biological functions, biological data types and biological > resources. > > > > Hope this is useful. > > > > Jits > > _______________________________________________ > > BioCatalogue-developers mailing list > > BioCatalogue-developers at rubyforge.org > > > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > > > > -- > "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 noreply at rubyforge.org Tue Jun 8 09:27:57 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 8 Jun 2010 09:27:57 -0400 (EDT) Subject: [BioCatalogue-developers] [2088] trunk: update soaplab services with descriptions from the soaplab server Message-ID: <20100608132757.9A4B4185835A@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Tue Jun 8 10:21:08 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 8 Jun 2010 15:21:08 +0100 Subject: [BioCatalogue-developers] Recent BioCatalogue features In-Reply-To: <4C0E2F87.8050405@ebi.ac.uk> References: <4C0E0DA9.2030005@cs.man.ac.uk> <4C0E0EA7.7070402@cs.man.ac.uk> <4C0E2F87.8050405@ebi.ac.uk> Message-ID: >Not all soaplab services return the description though. I think the manchester one is one of those that don't. Oh no! Can you investigate please? Paul's just told me that those services have descriptions 100% Franck On 8 June 2010 12:54, Eric Nzuobontane wrote: > > >> >> is the soaplab annotation import part the release tomorrow? >> > I just need to get the UI ready for it and it will be ready to go. Not all > soaplab services return the description though. I think the manchester one > is one of those that don't. > > Eric > > > >> Franck >> >> >> On 8 June 2010 10:34, Jiten Bhagat > jits at cs.man.ac.uk>> wrote: >> >> Guys, >> >> I am drafting a detailed announcement based on the below. I will send >> this out by end of today. >> >> Once the release goes through tomorrow I'll publish the full >> announcement. >> >> Jits >> >> PS: Eric, can you update the test server please? I'll look through the >> logs and see if any custom deployment actions are required. Otherwise, >> just assume the normal set of deployment actions, apart from a >> full reindex. >> >> >> Jiten Bhagat wrote: >> > Hi Marco, >> > >> > As mentioned, here are some of the most recent new features in the >> > BioCatalogue, that might be interesting to mention in your interview >> > tomorrow: >> > >> > - Activity/news feeds for services (also in ATOM) >> > - Monitoring test changes feed (also in ATOM) >> > - Service responsibility request mechanism (you can now request >> > responsibility for a service) >> > - Service update checker (check for WSDL updates for now and >> updates the >> > catalogue automatically) >> > - Service archival (can mark a service as archived) >> > - REST endpoints returned in search >> > - Service provider curation - (the service providers in the >> catalogue >> > now make more "sense") >> > - Various service monitoring updates (show since when a URL is being >> > monitored; better REST service monitoring - we now monitor some >> example >> > endpoints automatically) >> > - New API features (get all WSDL locations; favourites and viewings >> > count; alpha release of bulk annotations API) >> > >> > The previous release also had: >> > >> > - Public read only REST API >> > - Better support for describing REST Services. You can now >> describe in >> > detail the exact endpoints available for a REST service, >> together with >> > the input and output parameters and representations. This will >> also be >> > used to describe the BioCatalogue REST API. >> > - A more streamlined UI for browsing the SOAP operations and REST >> > endpoints of a service. >> > - SOAP operations are now directly returned in search. >> > >> > We also have an alpha version plugin for Taverna that integrates the >> > BioCatalogue into the workflow building process. This will be >> further >> > developed this summer to make it production ready and released >> bundled >> > with Taverna. >> > >> > In terms of future functionality that might be useful to >> > bioinformaticians, we are working on: >> > >> > - Being able to run services directly within the BioCatalogue, >> in order >> > to test out things quickly. >> > - Integration with myExperiment (a new "Services" tab in myexp and >> > things like "other workflows that use the services in this >> workflow") >> > - Functional Units of Services- Ability to present services in >> terms of >> > their biological functions, biological data types and biological >> resources. >> > >> > Hope this is useful. >> > >> > Jits >> > _______________________________________________ >> > BioCatalogue-developers mailing list >> > BioCatalogue-developers at rubyforge.org >> >> >> > http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> >> >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> >> >> >> -- >> "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 > ================================== > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Jun 8 10:57:25 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 08 Jun 2010 15:57:25 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'ProDomCG_evoscen' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'ProDomCG_evoscen' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1871 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Tue Jun 8 11:44:53 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 8 Jun 2010 16:44:53 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-372) Documentation URL not being picked up by the WSDL parser In-Reply-To: <22066438.2608.1275930437035.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29789052.2747.1276011893142.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-372?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15036#action_15036 ] Eric Nzuobontane commented on BIOCAT-372: ----------------------------------------- The WSDL parser expected documentation for the service level to be enclosed with the service tags. The reason these are not pick up is because they are defined outside to the service elements. Maybe users should be developers should be encouraged to scope these documentations within the service elements though this definition is perfectly legal. > Documentation URL not being picked up by the WSDL parser > -------------------------------------------------------- > > Key: BIOCAT-372 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-372 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > Priority: Critical > > As reported by Olivier Sallou: > bq. I just submitted a new service (wsdl interproscan) but we have some errors: at submission, documentation tag is not recognized, and as a consequence is not filled automatically (though used to do so). I manually added 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 ericnzuo at ebi.ac.uk Tue Jun 8 11:55:05 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 08 Jun 2010 16:55:05 +0100 Subject: [BioCatalogue-developers] Recent BioCatalogue features In-Reply-To: References: <4C0E0DA9.2030005@cs.man.ac.uk> <4C0E0EA7.7070402@cs.man.ac.uk> <4C0E2F87.8050405@ebi.ac.uk> Message-ID: <4C0E67D9.50409@ebi.ac.uk> I am not sure if we are talking about the same soaplab. The one I mean is http://soaplab.taverna.org.uk/soaplab2/services/ Can you verify with Paul that this should be working fine? The other soaplab from Manchester is fine as far as I can see Eric Franck Tanoh wrote: > >Not all soaplab services return the description though. I think the > manchester one is one of those that don't. > Oh no! Can you investigate please? Paul's just told me that those > services have descriptions 100% > > Franck > > On 8 June 2010 12:54, Eric Nzuobontane > wrote: > > > > > is the soaplab annotation import part the release tomorrow? > > I just need to get the UI ready for it and it will be ready to go. > Not all soaplab services return the description though. I think > the manchester one is one of those that don't. > > Eric > > > > Franck > > > On 8 June 2010 10:34, Jiten Bhagat >> wrote: > > Guys, > > I am drafting a detailed announcement based on the below. I > will send > this out by end of today. > > Once the release goes through tomorrow I'll publish the full > announcement. > > Jits > > PS: Eric, can you update the test server please? I'll look > through the > logs and see if any custom deployment actions are required. > Otherwise, > just assume the normal set of deployment actions, apart from a > full reindex. > > > Jiten Bhagat wrote: > > Hi Marco, > > > > As mentioned, here are some of the most recent new > features in the > > BioCatalogue, that might be interesting to mention in > your interview > > tomorrow: > > > > - Activity/news feeds for services (also in ATOM) > > - Monitoring test changes feed (also in ATOM) > > - Service responsibility request mechanism (you can now > request > > responsibility for a service) > > - Service update checker (check for WSDL updates for now and > updates the > > catalogue automatically) > > - Service archival (can mark a service as archived) > > - REST endpoints returned in search > > - Service provider curation - (the service providers in the > catalogue > > now make more "sense") > > - Various service monitoring updates (show since when a > URL is being > > monitored; better REST service monitoring - we now > monitor some > example > > endpoints automatically) > > - New API features (get all WSDL locations; favourites > and viewings > > count; alpha release of bulk annotations API) > > > > The previous release also had: > > > > - Public read only REST API > > - Better support for describing REST Services. You can now > describe in > > detail the exact endpoints available for a REST service, > together with > > the input and output parameters and representations. This > will > also be > > used to describe the BioCatalogue REST API. > > - A more streamlined UI for browsing the SOAP operations > and REST > > endpoints of a service. > > - SOAP operations are now directly returned in search. > > > > We also have an alpha version plugin for Taverna that > integrates the > > BioCatalogue into the workflow building process. This will be > further > > developed this summer to make it production ready and > released > bundled > > with Taverna. > > > > In terms of future functionality that might be useful to > > bioinformaticians, we are working on: > > > > - Being able to run services directly within the > BioCatalogue, > in order > > to test out things quickly. > > - Integration with myExperiment (a new "Services" tab in > myexp and > > things like "other workflows that use the services in this > workflow") > > - Functional Units of Services- Ability to present > services in > terms of > > their biological functions, biological data types and > biological > resources. > > > > Hope this is useful. > > > > Jits > > _______________________________________________ > > BioCatalogue-developers mailing list > > BioCatalogue-developers at rubyforge.org > > > > > > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > > > > > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > > > > -- > "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 > ================================== > > > > > -- > "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 Tue Jun 8 12:03:25 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 08 Jun 2010 17:03:25 +0100 Subject: [BioCatalogue-developers] Recent BioCatalogue features In-Reply-To: References: <4C0E0DA9.2030005@cs.man.ac.uk> <4C0E0EA7.7070402@cs.man.ac.uk> Message-ID: <4C0E69CD.9020902@cs.man.ac.uk> Franck Tanoh wrote: > Hi Jits, > > It will be useful if you can point to some examples to illustrate some > of the features. > Things like "Activity/news feeds" are difficult to understand until > you see one. > You could also show the importance of the "service responsibility > request" e.g. ...that is, more than one person can maintain the same > web service in the Biocatalogue not only the submitter as previously. I intend to elaborate on each new feature with a full explanation of that feature. Expect some text first thing tomorrow morning. Jits > > is the soaplab annotation import part the release tomorrow? > > Franck > > On 8 June 2010 10:34, Jiten Bhagat > wrote: > > Guys, > > I am drafting a detailed announcement based on the below. I will send > this out by end of today. > > Once the release goes through tomorrow I'll publish the full > announcement. > > Jits > > PS: Eric, can you update the test server please? I'll look through the > logs and see if any custom deployment actions are required. Otherwise, > just assume the normal set of deployment actions, apart from a > full reindex. > > > Jiten Bhagat wrote: > > Hi Marco, > > > > As mentioned, here are some of the most recent new features in the > > BioCatalogue, that might be interesting to mention in your interview > > tomorrow: > > > > - Activity/news feeds for services (also in ATOM) > > - Monitoring test changes feed (also in ATOM) > > - Service responsibility request mechanism (you can now request > > responsibility for a service) > > - Service update checker (check for WSDL updates for now and > updates the > > catalogue automatically) > > - Service archival (can mark a service as archived) > > - REST endpoints returned in search > > - Service provider curation - (the service providers in the > catalogue > > now make more "sense") > > - Various service monitoring updates (show since when a URL is being > > monitored; better REST service monitoring - we now monitor some > example > > endpoints automatically) > > - New API features (get all WSDL locations; favourites and viewings > > count; alpha release of bulk annotations API) > > > > The previous release also had: > > > > - Public read only REST API > > - Better support for describing REST Services. You can now > describe in > > detail the exact endpoints available for a REST service, > together with > > the input and output parameters and representations. This will > also be > > used to describe the BioCatalogue REST API. > > - A more streamlined UI for browsing the SOAP operations and REST > > endpoints of a service. > > - SOAP operations are now directly returned in search. > > > > We also have an alpha version plugin for Taverna that integrates the > > BioCatalogue into the workflow building process. This will be > further > > developed this summer to make it production ready and released > bundled > > with Taverna. > > > > In terms of future functionality that might be useful to > > bioinformaticians, we are working on: > > > > - Being able to run services directly within the BioCatalogue, > in order > > to test out things quickly. > > - Integration with myExperiment (a new "Services" tab in myexp and > > things like "other workflows that use the services in this > workflow") > > - Functional Units of Services- Ability to present services in > terms of > > their biological functions, biological data types and biological > resources. > > > > Hope this is useful. > > > > Jits > > _______________________________________________ > > BioCatalogue-developers mailing list > > BioCatalogue-developers at rubyforge.org > > > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > > > > -- > "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 Jun 8 12:23:42 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 8 Jun 2010 17:23:42 +0100 Subject: [BioCatalogue-developers] Recent BioCatalogue features In-Reply-To: <4C0E67D9.50409@ebi.ac.uk> References: <4C0E0DA9.2030005@cs.man.ac.uk> <4C0E0EA7.7070402@cs.man.ac.uk> <4C0E2F87.8050405@ebi.ac.uk> <4C0E67D9.50409@ebi.ac.uk> Message-ID: The different between those 2 soaplab servers is that http://soaplab.taverna.org.uk/soaplab2/services/ is the soaplab2 version of http://phoebus.cs.man.ac.uk:1977/axis/services (soaplab1). So they are both working fine but use different version of soaplab. Franck Both soaplab services are from different server but they are the same services according to Paul ( and ). On 8 June 2010 16:55, Eric Nzuobontane wrote: > I am not sure if we are talking about the same soaplab. The one I mean is > http://soaplab.taverna.org.uk/soaplab2/services/ > > Can you verify with Paul that this should be working fine? The other > soaplab from Manchester is fine as far as I can see > > Eric > > > Franck Tanoh wrote: > >> >Not all soaplab services return the description though. I think the >> manchester one is one of those that don't. >> Oh no! Can you investigate please? Paul's just told me that those services >> have descriptions 100% >> >> Franck >> >> On 8 June 2010 12:54, Eric Nzuobontane > ericnzuo at ebi.ac.uk>> wrote: >> >> >> >> >> is the soaplab annotation import part the release tomorrow? >> >> I just need to get the UI ready for it and it will be ready to go. >> Not all soaplab services return the description though. I think >> the manchester one is one of those that don't. >> >> Eric >> >> >> >> Franck >> >> >> On 8 June 2010 10:34, Jiten Bhagat > > >> >> wrote: >> >> Guys, >> >> I am drafting a detailed announcement based on the below. I >> will send >> this out by end of today. >> >> Once the release goes through tomorrow I'll publish the full >> announcement. >> >> Jits >> >> PS: Eric, can you update the test server please? I'll look >> through the >> logs and see if any custom deployment actions are required. >> Otherwise, >> just assume the normal set of deployment actions, apart from a >> full reindex. >> >> >> Jiten Bhagat wrote: >> > Hi Marco, >> > >> > As mentioned, here are some of the most recent new >> features in the >> > BioCatalogue, that might be interesting to mention in >> your interview >> > tomorrow: >> > >> > - Activity/news feeds for services (also in ATOM) >> > - Monitoring test changes feed (also in ATOM) >> > - Service responsibility request mechanism (you can now >> request >> > responsibility for a service) >> > - Service update checker (check for WSDL updates for now and >> updates the >> > catalogue automatically) >> > - Service archival (can mark a service as archived) >> > - REST endpoints returned in search >> > - Service provider curation - (the service providers in the >> catalogue >> > now make more "sense") >> > - Various service monitoring updates (show since when a >> URL is being >> > monitored; better REST service monitoring - we now >> monitor some >> example >> > endpoints automatically) >> > - New API features (get all WSDL locations; favourites >> and viewings >> > count; alpha release of bulk annotations API) >> > >> > The previous release also had: >> > >> > - Public read only REST API >> > - Better support for describing REST Services. You can now >> describe in >> > detail the exact endpoints available for a REST service, >> together with >> > the input and output parameters and representations. This >> will >> also be >> > used to describe the BioCatalogue REST API. >> > - A more streamlined UI for browsing the SOAP operations >> and REST >> > endpoints of a service. >> > - SOAP operations are now directly returned in search. >> > >> > We also have an alpha version plugin for Taverna that >> integrates the >> > BioCatalogue into the workflow building process. This will be >> further >> > developed this summer to make it production ready and >> released >> bundled >> > with Taverna. >> > >> > In terms of future functionality that might be useful to >> > bioinformaticians, we are working on: >> > >> > - Being able to run services directly within the >> BioCatalogue, >> in order >> > to test out things quickly. >> > - Integration with myExperiment (a new "Services" tab in >> myexp and >> > things like "other workflows that use the services in this >> workflow") >> > - Functional Units of Services- Ability to present >> services in >> terms of >> > their biological functions, biological data types and >> biological >> resources. >> > >> > Hope this is useful. >> > >> > Jits >> > _______________________________________________ >> > BioCatalogue-developers mailing list >> > BioCatalogue-developers at rubyforge.org >> >> > > >> >> > http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> >> > > >> >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> >> >> >> -- "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 >> >> ================================== >> >> >> >> >> -- >> "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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Jun 8 18:56:58 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 08 Jun 2010 23:56:58 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runSignalPDAS' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runSignalPDAS' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1092 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 Jun 8 20:55:57 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 09 Jun 2010 01:55:57 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runDisruptionPhysicalProperties' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runDisruptionPhysicalProperties' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1020 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 Jun 9 04:37:50 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 09 Jun 2010 09:37:50 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMatScanGFF' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMatScanGFF' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/776 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Jun 9 05:04:37 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 9 Jun 2010 05:04:37 -0400 (EDT) Subject: [BioCatalogue-developers] [2089] trunk/app: build UI for descriptions from soaplab server. Message-ID: <20100609090437.E04851858361@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jun 9 05:18:17 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 9 Jun 2010 05:18:17 -0400 (EDT) Subject: [BioCatalogue-developers] [2090] trunk/app/views/soap_services/_description_from_soaplab.html.erb: minor change for when no description is available Message-ID: <20100609091817.651351858361@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jun 9 05:33:48 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 9 Jun 2010 05:33:48 -0400 (EDT) Subject: [BioCatalogue-developers] [2091] trunk/app/models/soap_service.rb: Index the new description from soaplab. Message-ID: <20100609093348.D2015185831A@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Wed Jun 9 06:09:56 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 09 Jun 2010 11:09:56 +0100 Subject: [BioCatalogue-developers] Descriptions from soaplab Message-ID: <4C0F6874.2060401@ebi.ac.uk> Hi, I have now updated the test site for the descriptions from soaplab code. Also tested on one of the soaplab servers. Here is an example of a service with the description obtained http://test.biocatalogue.org/services/2157 Please have a look 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 issues at mygrid.org.uk Wed Jun 9 06:54:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 9 Jun 2010 11:54:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-344) Update soaplab services descriptions by calling the describe method In-Reply-To: <7031632.523.1274179577000.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10299024.2864.1276080857008.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-344?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-344 started by Eric Nzuobontane. > Update soaplab services descriptions by calling the describe method > ------------------------------------------------------------------- > > Key: BIOCAT-344 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-344 > Project: BioCatalogue > Issue Type: Task > Components: Content Acquisition > Environment: SAOP, Soaplab, soapclients > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > Call the describe method for the soaplab services and add the content to the service description -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 9 06:56:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 9 Jun 2010 11:56:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-374) use teaser of the description from soaplab Message-ID: <9984711.2865.1276080977016.JavaMail.jira@rosalind.cs.man.ac.uk> use teaser of the description from soaplab ------------------------------------------ Key: BIOCAT-374 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-374 Project: BioCatalogue Issue Type: Sub-task Reporter: Eric Nzuobontane Assignee: Jiten Bhagat As descriptions from soaplab can be long, a teaser is needed to show a bit of the description and the whole lot on click. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 9 06:56:18 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 9 Jun 2010 11:56:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-374) use teaser of the description from soaplab In-Reply-To: <9984711.2865.1276080977016.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22044969.2866.1276080978176.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-374?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-374: --------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > use teaser of the description from soaplab > ------------------------------------------ > > Key: BIOCAT-374 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-374 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > As descriptions from soaplab can be long, a teaser is needed to show a bit of the description and the whole lot on click. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 9 07:21:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 9 Jun 2010 12:21:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-374) use teaser of the description from soaplab In-Reply-To: <9984711.2865.1276080977016.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3615345.2867.1276082477023.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-374?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat reassigned BIOCAT-374: ----------------------------------- Assignee: Jiten Bhagat (was: Eric Nzuobontane) > use teaser of the description from soaplab > ------------------------------------------ > > Key: BIOCAT-374 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-374 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > As descriptions from soaplab can be long, a teaser is needed to show a bit of the description and the whole lot on click. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 9 08:09:25 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 09 Jun 2010 13:09:25 +0100 Subject: [BioCatalogue-developers] Draft announcement... Message-ID: <4C0F8475.1020501@cs.man.ac.uk> ... for after the next release: Please provide all changes in the form of text diffs, so I can update my master copy easily, thanks! Jits Title/Subject: Latest updates - service responsibility, monitoring status changes, service activity, service update checker and many more. Message: Hello all, We have updated the BioCatalogue (http://www.biocatalogue.org) with a number of new features and improvements in the last six weeks. Below we highlight and describe some of these: - Service responsibility request mechanism - Monitoring test changes feed - New activity feeds for individual services - Service update checker (WSDL updates for now) - Archiving services - REST endpoints in search - Service provider curation - Various service monitoring updates - New API features Service responsibility request mechanism Previously, the submitter of a service was the only one (together with site curators and admins) who had finer control on a service entry in the catalogue. They could delete the service or delete individual annotations on the service, and so on. But now, other members can request responsibility for a service in the catalogue. Thereby allowing more than one person to maintain a service entry. Requests can then be approved or denied by the submitter. * To request responsibility for a service: - You need to log in first - Browse to the service's profile page - Select the 'Take Responsibility' option from the 'Actions' drop down menu (the blue button on the left hand side next to the title of the service) - Follow the instructions on the subsequent page(s) * Note: in cases where no action has been taken on these requests, a site curator or admin can step in and take action. Monitoring test changes feed Service monitoring is a key feature offered by the BioCatalogue. Now you have the ability to see the latest monitoring status changes that have been logged for the individual service tests we carry out. This allows providers and consumers to easily keep track of monitoring changes across the catalogue. A short list can be seen on the homepage, towards the bottom list. With a more detailed list here: http://www.biocatalogue.org/latest#monitoring You can also subscribe to the ATOM feed for this: http://www.biocatalogue.org/status_changes.atom New activity feeds for individual services The 'Latest Activity' lists are a nice way of seeing what is happening in the catalogue. And now, as part of a new "News" tab on each service's profile page, we have introduced an activity list for each individual service. Here you can see the latest annotations, monitoring status changes, favourites, updates and so on. You can also subscribe to the ATOM feed, allowing you get instant notifications of new activity on any services that you are interested in. For example, for the EBI DBFetch service: http://www.biocatalogue.org/services/4#news (ATOM feed is: http://www.biocatalogue.org/services/4/activity.atom) Service update checker (WSDL updates for now) The interface for SOAP services - WSDL files - may often be updated by service providers. These updates can range from metadata changes/additions to substantial structural changes in the service and it's operations. The BioCatalogue now has the ability to pick up these changes and update service entries automatically. Any removed operations, inputs or outputs are still kept, but are marked as "archived". All changes are logged and shown under the new "News" tab on a service's profile page. See for example: http://www.biocatalogue.org/services/8#updates_from_wsdl_5. This allows service consumers to see a changelog of a service over time. Archiving services Services can now be marked as archived/deprecated by anyone who has responsibility for it in the catalogue. Archived services will still show up in search and other listings but will be greyed out and with a warning notice. You can archive/unarchive services via the 'Actions' menu on a service's profile page. In the future, we will allow you to filter out archived services from search and other listings. As well as links to alternative services that users should use when they come across archived/deprecated services. REST endpoints in search We now show matching REST endpoints in keyword searches. This complements the SOAP operations results and allows users to directly find matching REST endpoints that an be used in their scripts/tools. Service provider curation We have carried out a major curation exercise of the service provider entries in the catalogue. The majority of service providers should now have friendly display names, which makes it easier to browse and filter. As part of this work, we introduced the notion of service provider hostnames. These map on to the service providers, allowing us to easily configure and control what services belong to what service provider. If you are a service provider and would like us to fix any issues with this then please let us know. Various service monitoring updates We are continually tweaking and improving our service monitoring. We now show the exact the URLs that are monitored for availability checks together with the date since the monitoring began for that particular check. For REST services monitoring we now monitor some example endpoints automatically. So please do provide add example endpoints on REST services (this can be done by adding endpoints to a REST service entry and then adding example annotations). New API features We have added viewings and favourites counts to the REST API, as well as a new endpoint - /soap_services/wsdl_locations that allows you to get a list of all the WSDL locations of all the SOAP based services in the catalogue. We also have an alpha version bulk annotations submission API which we are trialling out with a new curation app we are developing. Let us know if you would like more information on using this right now. Please do not hesitate to provide us with any feedback. Regards, - The BioCatalogue Team From ericnzuo at ebi.ac.uk Wed Jun 9 08:30:53 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 09 Jun 2010 13:30:53 +0100 Subject: [BioCatalogue-developers] Draft announcement... In-Reply-To: <4C0F8475.1020501@cs.man.ac.uk> References: <4C0F8475.1020501@cs.man.ac.uk> Message-ID: <4C0F897D.3040503@ebi.ac.uk> That is quite elaborate. Very good. The only thing I would add is probably a little screen shot with the actions menu. That would help people that have not really used the catalogue much before find it quickly. Eric Jiten Bhagat wrote: > ... for after the next release: > > Please provide all changes in the form of text diffs, so I can update my > master copy easily, thanks! > > Jits > > > Title/Subject: Latest updates - service responsibility, monitoring > status changes, service activity, service update checker and many more. > > Message: > > Hello all, > > We have updated the BioCatalogue (http://www.biocatalogue.org) with a > number of new features and improvements in the last six weeks. Below we > highlight and describe some of these: > > - Service responsibility request mechanism > - Monitoring test changes feed > - New activity feeds for individual services > - Service update checker (WSDL updates for now) > - Archiving services > - REST endpoints in search > - Service provider curation > - Various service monitoring updates > - New API features > > > Service responsibility request mechanism > > Previously, the submitter of a service was the only one (together with > site curators and admins) who had finer control on a service entry in > the catalogue. They could delete the service or delete individual > annotations on the service, and so on. But now, other members can > request responsibility for a service in the catalogue. Thereby > allowing more than one person to maintain a service entry. Requests can > then be approved or denied by the submitter. * > > To request responsibility for a service: > - You need to log in first > - Browse to the service's profile page > - Select the 'Take Responsibility' option from the 'Actions' drop down > menu (the blue button on the left hand side next to the title of the > service) > - Follow the instructions on the subsequent page(s) > > * Note: in cases where no action has been taken on these requests, a > site curator or admin can step in and take action. > > > Monitoring test changes feed > > Service monitoring is a key feature offered by the BioCatalogue. Now you > have the ability to see the latest monitoring status changes that have > been logged for the individual service tests we carry out. This allows > providers and consumers to easily keep track of monitoring changes > across the catalogue. > > A short list can be seen on the homepage, towards the bottom list. With > a more detailed list here: http://www.biocatalogue.org/latest#monitoring > > You can also subscribe to the ATOM feed for this: > http://www.biocatalogue.org/status_changes.atom > > > New activity feeds for individual services > > The 'Latest Activity' lists are a nice way of seeing what is happening > in the catalogue. And now, as part of a new "News" tab on each service's > profile page, we have introduced an activity list for each individual > service. Here you can see the latest annotations, monitoring status > changes, favourites, updates and so on. You can also subscribe to the > ATOM feed, allowing you get instant notifications of new activity on any > services that you are interested in. > > For example, for the EBI DBFetch service: > http://www.biocatalogue.org/services/4#news (ATOM feed is: > http://www.biocatalogue.org/services/4/activity.atom) > > > Service update checker (WSDL updates for now) > > The interface for SOAP services - WSDL files - may often be updated by > service providers. These updates can range from metadata > changes/additions to substantial structural changes in the service and > it's operations. The BioCatalogue now has the ability to pick up these > changes and update service entries automatically. Any removed > operations, inputs or outputs are still kept, but are marked as "archived". > > All changes are logged and shown under the new "News" tab on a service's > profile page. See for example: > http://www.biocatalogue.org/services/8#updates_from_wsdl_5. This allows > service consumers to see a changelog of a service over time. > > > Archiving services > > Services can now be marked as archived/deprecated by anyone who has > responsibility for it in the catalogue. Archived services will still > show up in search and other listings but will be greyed out and with a > warning notice. > > You can archive/unarchive services via the 'Actions' menu on a service's > profile page. > > In the future, we will allow you to filter out archived services from > search and other listings. As well as links to alternative services that > users should use when they come across archived/deprecated services. > > > REST endpoints in search > > We now show matching REST endpoints in keyword searches. This > complements the SOAP operations results and allows users to directly > find matching REST endpoints that an be used in their scripts/tools. > > > Service provider curation > > We have carried out a major curation exercise of the service provider > entries in the catalogue. The majority of service providers should now > have friendly display names, which makes it easier to browse and filter. > > As part of this work, we introduced the notion of service provider > hostnames. These map on to the service providers, allowing us to easily > configure and control what services belong to what service provider. If > you are a service provider and would like us to fix any issues with this > then please let us know. > > > Various service monitoring updates > > We are continually tweaking and improving our service monitoring. We now > show the exact the URLs that are monitored for availability checks > together with the date since the monitoring began for that particular check. > > For REST services monitoring we now monitor some example endpoints > automatically. So please do provide add example endpoints on REST > services (this can be done by adding endpoints to a REST service entry > and then adding example annotations). > > > New API features > > We have added viewings and favourites counts to the REST API, as well as > a new endpoint - /soap_services/wsdl_locations that allows you to get a > list of all the WSDL locations of all the SOAP based services in the > catalogue. > > We also have an alpha version bulk annotations submission API which we > are trialling out with a new curation app we are developing. Let us know > if you would like more information on using this right now. > > > Please do not hesitate to provide us with any feedback. > > Regards, > - The BioCatalogue Team > > _______________________________________________ > 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 Jun 9 08:35:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 9 Jun 2010 08:35:22 -0400 (EDT) Subject: [BioCatalogue-developers] [2092] trunk/script/biocatalogue/ update_descriptions_for_all_soaplab_services.rb: script to run soaplab descriptions updater Message-ID: <20100609123522.D8C591858361@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Wed Jun 9 08:51:30 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 09 Jun 2010 13:51:30 +0100 Subject: [BioCatalogue-developers] [Fwd: [2092] trunk/script/biocatalogue/ update_descriptions_for_all_soaplab_services.rb: script to run soaplab descriptions updater] Message-ID: <4C0F8E52.50006@cs.man.ac.uk> Why not just make this a rake task? Jits -------- Original Message -------- Subject: [BioCatalogue-developers] [2092] trunk/script/biocatalogue/ update_descriptions_for_all_soaplab_services.rb: script to run soaplab descriptions updater Date: Wed, 9 Jun 2010 08:35:22 -0400 (EDT) From: noreply at rubyforge.org To: biocatalogue-developers at rubyforge.org Revision 2092 Author ebontane Date 2010-06-09 08:35:22 -0400 (Wed, 09 Jun 2010) Log Message script to run soaplab descriptions updater Added Paths * trunk/script/biocatalogue/update_descriptions_for_all_soaplab_services.rb <#trunkscriptbiocatalogueupdate_descriptions_for_all_soaplab_servicesrb> Diff Added: trunk/script/biocatalogue/update_descriptions_for_all_soaplab_services.rb (0 => 2092) --- trunk/script/biocatalogue/update_descriptions_for_all_soaplab_services.rb (rev 0) +++ trunk/script/biocatalogue/update_descriptions_for_all_soaplab_services.rb 2010-06-09 12:35:22 UTC (rev 2092) @@ -0,0 +1,60 @@ +#!/usr/bin/env ruby + +# This script will lunch background jobs, one for each soaplab service, +# that will update the description of the service by calling the describe +# operation implemented by soaplab services +# +# Usage: update_descriptions_for_all_soaplab_services.rb [options] +# +# -e, --environment=name Specifies the environment to run this script under (test|development|production). +# Default: development +# +# -h, --help Show this help message. +# +# Depedencies: +# - Rails (v2.3.2) + +require 'optparse' +require 'benchmark' + +class UpdateSoaplabServiceDescriptions + + attr_accessor :options + + def initialize(args) + @options = { + :environment => (ENV['RAILS_ENV'] || "production").dup, + } + + args.options do |opts| + opts.on("-e", "--environment=name", String, + "Specifies the environment to run this script under (test|development|production).", + "Default: development") { |v| @options[:environment] = v } + + opts.separator "" + + opts.on("-h", "--help", "Show this help message.") { puts opts; exit } + + opts.parse! + end + + # Start the Rails app + + ENV["RAILS_ENV"] = @options[:environment] + RAILS_ENV.replace(@options[:environment]) if defined?(RAILS_ENV) + + require File.join(File.dirname(__FILE__), '..', '..', 'config', 'environment') + end + + def run + SoaplabServer.all.each do |server| + server.update_descriptions_from_soaplab! + end + end +end + + +puts Benchmark.measure { + UpdateSoaplabServiceDescriptions.new(ARGV.clone).run +} + -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Attached Message Part URL: From jits at cs.man.ac.uk Wed Jun 9 08:52:53 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 09 Jun 2010 13:52:53 +0100 Subject: [BioCatalogue-developers] Draft announcement... In-Reply-To: <4C0F897D.3040503@ebi.ac.uk> References: <4C0F8475.1020501@cs.man.ac.uk> <4C0F897D.3040503@ebi.ac.uk> Message-ID: <4C0F8EA5.4010808@cs.man.ac.uk> I'd like to avoid screenshots. Since it's often tricky to get correct in emails. Especially since we send out plain text emails. Also, I'll reuse this text for an announcement too. Jits Eric Nzuobontane wrote: > That is quite elaborate. Very good. The only thing I would add is > probably a little screen shot with the actions menu. That would help > people that have not really used the catalogue much before find it > quickly. > > Eric > > > > Jiten Bhagat wrote: >> ... for after the next release: >> >> Please provide all changes in the form of text diffs, so I can update my >> master copy easily, thanks! >> >> Jits >> >> >> Title/Subject: Latest updates - service responsibility, monitoring >> status changes, service activity, service update checker and many more. >> >> Message: >> >> Hello all, >> >> We have updated the BioCatalogue (http://www.biocatalogue.org) with a >> number of new features and improvements in the last six weeks. Below we >> highlight and describe some of these: >> >> - Service responsibility request mechanism >> - Monitoring test changes feed >> - New activity feeds for individual services >> - Service update checker (WSDL updates for now) >> - Archiving services >> - REST endpoints in search >> - Service provider curation >> - Various service monitoring updates >> - New API features >> >> >> Service responsibility request mechanism >> >> Previously, the submitter of a service was the only one (together with >> site curators and admins) who had finer control on a service entry in >> the catalogue. They could delete the service or delete individual >> annotations on the service, and so on. But now, other members can >> request responsibility for a service in the catalogue. Thereby >> allowing more than one person to maintain a service entry. Requests can >> then be approved or denied by the submitter. * >> >> To request responsibility for a service: >> - You need to log in first >> - Browse to the service's profile page >> - Select the 'Take Responsibility' option from the 'Actions' drop down >> menu (the blue button on the left hand side next to the title of the >> service) >> - Follow the instructions on the subsequent page(s) >> >> * Note: in cases where no action has been taken on these requests, a >> site curator or admin can step in and take action. >> >> >> Monitoring test changes feed >> >> Service monitoring is a key feature offered by the BioCatalogue. Now you >> have the ability to see the latest monitoring status changes that have >> been logged for the individual service tests we carry out. This allows >> providers and consumers to easily keep track of monitoring changes >> across the catalogue. >> >> A short list can be seen on the homepage, towards the bottom list. With >> a more detailed list here: http://www.biocatalogue.org/latest#monitoring >> >> You can also subscribe to the ATOM feed for this: >> http://www.biocatalogue.org/status_changes.atom >> >> >> New activity feeds for individual services >> >> The 'Latest Activity' lists are a nice way of seeing what is happening >> in the catalogue. And now, as part of a new "News" tab on each service's >> profile page, we have introduced an activity list for each individual >> service. Here you can see the latest annotations, monitoring status >> changes, favourites, updates and so on. You can also subscribe to the >> ATOM feed, allowing you get instant notifications of new activity on any >> services that you are interested in. >> >> For example, for the EBI DBFetch service: >> http://www.biocatalogue.org/services/4#news (ATOM feed is: >> http://www.biocatalogue.org/services/4/activity.atom) >> >> >> Service update checker (WSDL updates for now) >> >> The interface for SOAP services - WSDL files - may often be updated by >> service providers. These updates can range from metadata >> changes/additions to substantial structural changes in the service and >> it's operations. The BioCatalogue now has the ability to pick up these >> changes and update service entries automatically. Any removed >> operations, inputs or outputs are still kept, but are marked as >> "archived". >> >> All changes are logged and shown under the new "News" tab on a service's >> profile page. See for example: >> http://www.biocatalogue.org/services/8#updates_from_wsdl_5. This allows >> service consumers to see a changelog of a service over time. >> >> >> Archiving services >> >> Services can now be marked as archived/deprecated by anyone who has >> responsibility for it in the catalogue. Archived services will still >> show up in search and other listings but will be greyed out and with a >> warning notice. >> >> You can archive/unarchive services via the 'Actions' menu on a service's >> profile page. >> >> In the future, we will allow you to filter out archived services from >> search and other listings. As well as links to alternative services that >> users should use when they come across archived/deprecated services. >> >> >> REST endpoints in search >> >> We now show matching REST endpoints in keyword searches. This >> complements the SOAP operations results and allows users to directly >> find matching REST endpoints that an be used in their scripts/tools. >> >> >> Service provider curation >> >> We have carried out a major curation exercise of the service provider >> entries in the catalogue. The majority of service providers should now >> have friendly display names, which makes it easier to browse and filter. >> >> As part of this work, we introduced the notion of service provider >> hostnames. These map on to the service providers, allowing us to easily >> configure and control what services belong to what service provider. If >> you are a service provider and would like us to fix any issues with this >> then please let us know. >> >> >> Various service monitoring updates >> >> We are continually tweaking and improving our service monitoring. We now >> show the exact the URLs that are monitored for availability checks >> together with the date since the monitoring began for that particular >> check. >> >> For REST services monitoring we now monitor some example endpoints >> automatically. So please do provide add example endpoints on REST >> services (this can be done by adding endpoints to a REST service entry >> and then adding example annotations). >> >> >> New API features >> >> We have added viewings and favourites counts to the REST API, as well as >> a new endpoint - /soap_services/wsdl_locations that allows you to get a >> list of all the WSDL locations of all the SOAP based services in the >> catalogue. >> >> We also have an alpha version bulk annotations submission API which we >> are trialling out with a new curation app we are developing. Let us know >> if you would like more information on using this right now. >> >> >> Please do not hesitate to provide us with any feedback. >> >> Regards, >> - The BioCatalogue Team >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > > From noreply at rubyforge.org Wed Jun 9 10:38:57 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 9 Jun 2010 10:38:57 -0400 (EDT) Subject: [BioCatalogue-developers] [2093] trunk: Improved UI for Soaplab descriptions. Message-ID: <20100609143857.5CB071858372@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Wed Jun 9 11:00:23 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 09 Jun 2010 16:00:23 +0100 Subject: [BioCatalogue-developers] Curating Soaplab Services Message-ID: <4C0FAC87.1050604@ebi.ac.uk> I would go with something like this for the soaplab curation... Curating Soaplab Services Previously soaplab services registered in the BioCatalogue had only the descriptions available in the wsdl. In many cases there were no descriptions at all in the wsdl and consequently not in the catalogue as well. However, soaplab services implement the 'describe' operation which returns a detailed description of the analysis. BioCatalogue now harvests these descriptions from soaplab services thereby enriching the catalogue with reliable descriptions from the providers. An example of a soaplab service with provider annotations from server : -- 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 Jun 9 11:05:25 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 09 Jun 2010 16:05:25 +0100 Subject: [BioCatalogue-developers] Curating Soaplab Services In-Reply-To: <4C0FAC87.1050604@ebi.ac.uk> References: <4C0FAC87.1050604@ebi.ac.uk> Message-ID: <4C0FADB5.3030404@cs.man.ac.uk> Sounds good to me! Only thing - I would change the heading to "Harvesting soaplab service details". What do you think? Jits Eric Nzuobontane wrote: > I would go with something like this for the soaplab curation... > > Curating Soaplab Services > > Previously soaplab services registered in the BioCatalogue had only > the descriptions available in the wsdl. In many cases there were no > descriptions at all in the wsdl and consequently not in the catalogue > as well. However, soaplab services implement the 'describe' operation > which returns a detailed description of the analysis. BioCatalogue now > harvests these descriptions from soaplab services thereby enriching > the catalogue with reliable descriptions from the providers. > An example of a soaplab service with provider annotations from server > : > From ericnzuo at ebi.ac.uk Wed Jun 9 11:08:43 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 09 Jun 2010 16:08:43 +0100 Subject: [BioCatalogue-developers] Curating Soaplab Services In-Reply-To: <4C0FADB5.3030404@cs.man.ac.uk> References: <4C0FAC87.1050604@ebi.ac.uk> <4C0FADB5.3030404@cs.man.ac.uk> Message-ID: <4C0FAE7B.7070500@ebi.ac.uk> Yeah, that sounds good. And maybe add that we harvest the descriptions where possible! We now know that things are not always what we expect so people should contact us if they do not find descriptions for their soaplab services and we will investigate. Eric Jiten Bhagat wrote: > Sounds good to me! > > Only thing - I would change the heading to "Harvesting soaplab service > details". What do you think? > > Jits > > > Eric Nzuobontane wrote: > >> I would go with something like this for the soaplab curation... >> >> Curating Soaplab Services >> >> Previously soaplab services registered in the BioCatalogue had only >> the descriptions available in the wsdl. In many cases there were no >> descriptions at all in the wsdl and consequently not in the catalogue >> as well. However, soaplab services implement the 'describe' operation >> which returns a detailed description of the analysis. BioCatalogue now >> harvests these descriptions from soaplab services thereby enriching >> the catalogue with reliable descriptions from the providers. >> An example of a soaplab service with provider annotations from server >> : >> >> -- 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 Jun 9 11:13:31 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 09 Jun 2010 16:13:31 +0100 Subject: [BioCatalogue-developers] Curating Soaplab Services In-Reply-To: <4C0FAE7B.7070500@ebi.ac.uk> References: <4C0FAC87.1050604@ebi.ac.uk> <4C0FADB5.3030404@cs.man.ac.uk> <4C0FAE7B.7070500@ebi.ac.uk> Message-ID: <4C0FAF9B.1000608@cs.man.ac.uk> Please could you amend your text to add that in. Thanks, Jits Eric Nzuobontane wrote: > Yeah, that sounds good. And maybe add that we harvest the descriptions > where possible! We now know that things are not always what we expect > so people should contact us if they do not find descriptions for their > soaplab services and we will investigate. > > Eric > > > Jiten Bhagat wrote: > >> Sounds good to me! >> >> Only thing - I would change the heading to "Harvesting soaplab service >> details". What do you think? >> >> Jits >> >> >> Eric Nzuobontane wrote: >> >>> I would go with something like this for the soaplab curation... >>> >>> Curating Soaplab Services >>> >>> Previously soaplab services registered in the BioCatalogue had only >>> the descriptions available in the wsdl. In many cases there were no >>> descriptions at all in the wsdl and consequently not in the catalogue >>> as well. However, soaplab services implement the 'describe' operation >>> which returns a detailed description of the analysis. BioCatalogue now >>> harvests these descriptions from soaplab services thereby enriching >>> the catalogue with reliable descriptions from the providers. >>> An example of a soaplab service with provider annotations from server >>> : >>> >>> > > From ytanoh at cs.man.ac.uk Wed Jun 9 11:17:53 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 9 Jun 2010 16:17:53 +0100 Subject: [BioCatalogue-developers] Fwd: soaplab2 References: Message-ID: <8C331FE5-65D0-4A22-AC43-8876A80F3719@cs.man.ac.uk> Franck Begin forwarded message: > From: Stian Soiland-Reyes > Date: 9 June 2010 16:03:02 BST > To: Franck Tanoh > Subject: soaplab2 > > http://soaplab.taverna.org.uk/soaplab2/ > http://soaplab.taverna.org.uk/soaplab2/services/ > http://soaplab.taverna.org.uk/soaplab2/services/list?wsdl > http://soaplab.taverna.org.uk/soaplab2/services?wsdl > > last one has methods like 'describe' - but you'll have to run it to > see if anything makes sense, the returned data types are quite crude, > like: > > > > > > > > > so just a string called 'return' - typical sign that someone has > clicked the auto-generate button to make their web service :) > > -- > Stian Soiland-Reyes, myGrid team > School of Computer Science > The University of Manchester -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jun 9 11:17:06 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 9 Jun 2010 11:17:06 -0400 (EDT) Subject: [BioCatalogue-developers] [2094] trunk/script/biocatalogue/service_annotation_report.rb: Updated service annotation report script to take into account the new description from soaplab server field . Message-ID: <20100609151706.1BFBA1858373@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jun 9 12:14:20 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 9 Jun 2010 12:14:20 -0400 (EDT) Subject: [BioCatalogue-developers] [2095] trunk: Implemented "Services Missing Annotations" curation report. Message-ID: <20100609161420.8C9541858366@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu Jun 10 04:42:51 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 10 Jun 2010 09:42:51 +0100 Subject: [BioCatalogue-developers] Test site updated Message-ID: <4C10A58B.4040901@ebi.ac.uk> Hi, I have updated the test site already. Please test and let me know if it is clear to go ahead with the update. 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 issues at mygrid.org.uk Thu Jun 10 05:18:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 10 Jun 2010 10:18:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-324) Archived services should not be monitored anymore In-Reply-To: <5845695.58.1273658296994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1616817.39.1276161495328.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-324?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15122#action_15122 ] Jiten Bhagat commented on BIOCAT-324: ------------------------------------- The monitoring "subsystem" should be as decoupled as possible from the core system. The process that updates the UrlMonitors/TestScripts to monitor should look through for archived services and disable the ServiceTest(s) accordingly. > 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 jits at cs.man.ac.uk Thu Jun 10 05:53:17 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 10 Jun 2010 10:53:17 +0100 Subject: [BioCatalogue-developers] [Biocatalogue-support] [BioCatalogue] Service 'BinarySearchService' has a test change status from PASSED to FAILED In-Reply-To: <4C10AFF6.4000006@ebi.ac.uk> References: <4c106a8d2b73b_63c415aa541b2fc475e2@pweb-4a.ebi.ac.uk.tmail> <4C10AAD4.1030408@ebi.ac.uk> <4C10AFF6.4000006@ebi.ac.uk> Message-ID: <4C10B60D.8080107@cs.man.ac.uk> [Moving to dev list...] The second way is exactly what I am suggesting too (see my previous emails and comment on the JIRA task - http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-324). Always be conscious of adding ANY after_save / after_create callbacks to any models. They have the potential to: - slow things down considerably. - cause errors that would disrupt the save/create process. Jits Eric Nzuobontane wrote: > Well you can look at this from two ways. Either the archiving process > needs to set the appropriate flags for all services that depend on the > service entry being active or all of those services needs to check the > status of the service and take the appropriate action. I think maybe > the second way is better as archiving does not need to know what else > is listening. > > Eric > > > > Franck Tanoh wrote: >> >Does archiving disable the service test associated with the service? >> No it doesn't. I don't think that should be done manually. >> >> Franck >> >> >> On 10 June 2010 10:05, Eric Nzuobontane > > wrote: >> >> No we should not. Does archiving disable the service test >> associated with the service? But if the service tests are not >> disabled, then they are certainly still monitored! >> >> Eric >> >> >> >> Franck Tanoh wrote: >> >> Hi Eric, >> >> Are we monitoring archived services? the service mentioned >> below has been archived for a while. >> >> Cheers, >> Franck >> >> On 10 June 2010 05:31, > >> > >> wrote: >> >> >> >> A monitoring test status change has occurred! Service >> 'BinarySearchService' has a test (UrlMonitor, ID: 2331) >> change >> status from PASSED to FAILED. Last test result message: >> This check >> failed. Go to Service: >> http://www.biocatalogue.org/services/2159 >> >> >> >> >> -- "Science knows no country, because knowledge >> belongs to >> humanity, and is the torch which illuminates the world." - >> Louis Pasteur >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> ================================== >> >> >> >> >> -- >> "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 Jun 10 06:10:04 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 10 Jun 2010 11:10:04 +0100 Subject: [BioCatalogue-developers] [Fwd: [BioCatalogue] Service Reponsibility Request] Message-ID: <4C10B9FC.8030309@cs.man.ac.uk> Hi guys, You probably know this already, but... When causing any action on the test/sandbox servers that require sending out an email, make sure you don't choose a service that will cause an email to be sent out to someone outside of the team. You can imagine how bad it would look if someone got an email from test.biocatalogue.org.... Jits -------- Original Message -------- Subject: [BioCatalogue] Service Reponsibility Request Date: Thu, 10 Jun 2010 11:04:22 +0100 From: contact at biocatalogue.org To: jits at cs.man.ac.uk Dear Jiten Bhagat, We have received a request from tanoh that they would like to be given permissions for the service, WSTMHMM_2_0 for which you are currently responsible. Granting this request will give the user full permissions on the service including the possibility to remove it from the BioCatalogue. Please visit http://test.biocatalogue.org/responsibility_requests to grant or turn down this request. Kind Regards, - The BioCatalogue Team http://test.biocatalogue.org From ytanoh at cs.man.ac.uk Thu Jun 10 06:39:30 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 10 Jun 2010 11:39:30 +0100 Subject: [BioCatalogue-developers] [Fwd: [BioCatalogue] Service Reponsibility Request] In-Reply-To: <4C10B9FC.8030309@cs.man.ac.uk> References: <4C10B9FC.8030309@cs.man.ac.uk> Message-ID: >You probably know this already, but... oh yeah, I think we all learnt from the Embrace user import blunder last year :-) ... but a reminder in never bad Franck On 10 June 2010 11:10, Jiten Bhagat wrote: > Hi guys, > > You probably know this already, but... > > When causing any action on the test/sandbox servers that require sending > out an email, make sure you don't choose a service that will cause an > email to be sent out to someone outside of the team. > > You can imagine how bad it would look if someone got an email from > test.biocatalogue.org.... > > Jits > > > -------- Original Message -------- > Subject: [BioCatalogue] Service Reponsibility Request > Date: Thu, 10 Jun 2010 11:04:22 +0100 > From: contact at biocatalogue.org > To: jits at cs.man.ac.uk > > > > Dear Jiten Bhagat, > > We have received a request from tanoh > that they would like to be > given permissions for the service, WSTMHMM_2_0 > for which you are currently > responsible. Granting this request will give the user full permissions > on the service including the possibility to remove it from the > BioCatalogue. > > Please visit http://test.biocatalogue.org/responsibility_requests to > grant or turn down this request. > > Kind Regards, > - The BioCatalogue Team > > http://test.biocatalogue.org > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Thu Jun 10 06:33:20 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 10 Jun 2010 11:33:20 +0100 Subject: [BioCatalogue-developers] Test site updated In-Reply-To: <4C10A58B.4040901@ebi.ac.uk> References: <4C10A58B.4040901@ebi.ac.uk> Message-ID: Hi, some little things to report apart from that it's working fine. 1- Soaplab service with description (from soaplab server) are considered as missing description by the curation dashboard 2- the service category on the left (http://www.biocatalogue.org/services) the actual number of services for each category is most of the time different from the number between parenthesis. e.g. Text Mining category show 9 services but in reality if you select that category there are 19 services . Same thing applies to 'System Biology' category etc... 3- the 'enable tag filter' doesn't work ( that's a known issue i think) ... returns error 500 after a while. Cheers, Franck On 10 June 2010 09:42, Eric Nzuobontane wrote: > Hi, > > I have updated the test site already. Please test and let me know if it is > clear to go ahead with the update. > > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu Jun 10 06:57:30 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 10 Jun 2010 11:57:30 +0100 Subject: [BioCatalogue-developers] [Fwd: [BioCatalogue] Service Reponsibility Request] In-Reply-To: References: <4C10B9FC.8030309@cs.man.ac.uk> Message-ID: <4C10C51A.40306@ebi.ac.uk> Well, right now there is still a problem. At least with the test site as the user accounts are available there as well as on live. Nothing really stops anyone outside of the group making those request from there now. Maybe we need to do something which indicates that is a test site and only send mails to admins. Eric Franck Tanoh wrote: > >You probably know this already, but... > oh yeah, I think we all learnt from the Embrace user import blunder > last year :-) ... but a reminder in never bad > > Franck > > On 10 June 2010 11:10, Jiten Bhagat > wrote: > > Hi guys, > > You probably know this already, but... > > When causing any action on the test/sandbox servers that require > sending > out an email, make sure you don't choose a service that will cause an > email to be sent out to someone outside of the team. > > You can imagine how bad it would look if someone got an email from > test.biocatalogue.org.... > > Jits > > > -------- Original Message -------- > Subject: [BioCatalogue] Service Reponsibility Request > Date: Thu, 10 Jun 2010 11:04:22 +0100 > From: contact at biocatalogue.org > To: jits at cs.man.ac.uk > > > > Dear Jiten Bhagat, > > We have received a request from tanoh > that they would like to be > given permissions for the service, WSTMHMM_2_0 > for which you are > currently > responsible. Granting this request will give the user full permissions > on the service including the possibility to remove it from the > BioCatalogue. > > Please visit http://test.biocatalogue.org/responsibility_requests to > grant or turn down this request. > > Kind Regards, > - The BioCatalogue Team > > http://test.biocatalogue.org > > > > > -- > "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 Thu Jun 10 07:05:09 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 10 Jun 2010 12:05:09 +0100 Subject: [BioCatalogue-developers] [Fwd: [BioCatalogue] Service Reponsibility Request] In-Reply-To: <4C10C51A.40306@ebi.ac.uk> References: <4C10B9FC.8030309@cs.man.ac.uk> <4C10C51A.40306@ebi.ac.uk> Message-ID: <4C10C6E5.3020208@cs.man.ac.uk> True. Weird. I'm pretty sure I had created a script to cleanup dev/test databases. I can't seem to find it in the codebase anywhere though. It would basically change the email addresses of all users in the database to {random_number}@example.org. We should adapt that kind of script to keep certain email addresses (ours) but obfuscate all others. Jits Eric Nzuobontane wrote: > Well, right now there is still a problem. At least with the test site > as the user accounts are available there as well as on live. Nothing > really stops anyone outside of the group making those request from > there now. Maybe we need to do something which indicates that is a > test site and only send mails to admins. > > Eric > > > Franck Tanoh wrote: >> >You probably know this already, but... >> oh yeah, I think we all learnt from the Embrace user import blunder >> last year :-) ... but a reminder in never bad >> >> Franck >> >> On 10 June 2010 11:10, Jiten Bhagat > > wrote: >> >> Hi guys, >> >> You probably know this already, but... >> >> When causing any action on the test/sandbox servers that require >> sending >> out an email, make sure you don't choose a service that will >> cause an >> email to be sent out to someone outside of the team. >> >> You can imagine how bad it would look if someone got an email from >> test.biocatalogue.org.... >> >> Jits >> >> >> -------- Original Message -------- >> Subject: [BioCatalogue] Service Reponsibility Request >> Date: Thu, 10 Jun 2010 11:04:22 +0100 >> From: contact at biocatalogue.org >> To: jits at cs.man.ac.uk >> >> >> >> Dear Jiten Bhagat, >> >> We have received a request from tanoh >> that they would like to be >> given permissions for the service, WSTMHMM_2_0 >> for which you are >> currently >> responsible. Granting this request will give the user full >> permissions >> on the service including the possibility to remove it from the >> BioCatalogue. >> >> Please visit http://test.biocatalogue.org/responsibility_requests to >> grant or turn down this request. >> >> Kind Regards, >> - The BioCatalogue Team >> >> http://test.biocatalogue.org >> >> >> >> >> -- >> "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 Jun 10 07:13:46 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 10 Jun 2010 12:13:46 +0100 Subject: [BioCatalogue-developers] [Fwd: [BioCatalogue] Service Reponsibility Request] In-Reply-To: <4C10C6E5.3020208@cs.man.ac.uk> References: <4C10B9FC.8030309@cs.man.ac.uk> <4C10C51A.40306@ebi.ac.uk> <4C10C6E5.3020208@cs.man.ac.uk> Message-ID: <4C10C8EA.7080408@ebi.ac.uk> Jiten Bhagat wrote: > True. > > Weird. I'm pretty sure I had created a script to cleanup dev/test > databases. I can't seem to find it in the codebase anywhere though. > > It would basically change the email addresses of all users in the > database to {random_number}@example.org. > that is one idea. The problem with that is that the application will still send mail and the mail server will be attempting to deliver to an invalid address and keep trying until it gives up. Maybe this in combination with some custom code which ignores non admin emails. Eric > We should adapt that kind of script to keep certain email addresses > (ours) but obfuscate all others. > > Jits > > > Eric Nzuobontane wrote: > >> Well, right now there is still a problem. At least with the test site >> as the user accounts are available there as well as on live. Nothing >> really stops anyone outside of the group making those request from >> there now. Maybe we need to do something which indicates that is a >> test site and only send mails to admins. >> >> Eric >> >> >> Franck Tanoh wrote: >> >>>> You probably know this already, but... >>>> >>> oh yeah, I think we all learnt from the Embrace user import blunder >>> last year :-) ... but a reminder in never bad >>> >>> Franck >>> >>> On 10 June 2010 11:10, Jiten Bhagat >> > wrote: >>> >>> Hi guys, >>> >>> You probably know this already, but... >>> >>> When causing any action on the test/sandbox servers that require >>> sending >>> out an email, make sure you don't choose a service that will >>> cause an >>> email to be sent out to someone outside of the team. >>> >>> You can imagine how bad it would look if someone got an email from >>> test.biocatalogue.org.... >>> >>> Jits >>> >>> >>> -------- Original Message -------- >>> Subject: [BioCatalogue] Service Reponsibility Request >>> Date: Thu, 10 Jun 2010 11:04:22 +0100 >>> From: contact at biocatalogue.org >>> To: jits at cs.man.ac.uk >>> >>> >>> >>> Dear Jiten Bhagat, >>> >>> We have received a request from tanoh >>> that they would like to be >>> given permissions for the service, WSTMHMM_2_0 >>> for which you are >>> currently >>> responsible. Granting this request will give the user full >>> permissions >>> on the service including the possibility to remove it from the >>> BioCatalogue. >>> >>> Please visit http://test.biocatalogue.org/responsibility_requests to >>> grant or turn down this request. >>> >>> Kind Regards, >>> - The BioCatalogue Team >>> >>> http://test.biocatalogue.org >>> >>> >>> >>> >>> -- >>> "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 Thu Jun 10 07:19:01 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 10 Jun 2010 12:19:01 +0100 Subject: [BioCatalogue-developers] Test site updated In-Reply-To: References: <4C10A58B.4040901@ebi.ac.uk> Message-ID: <4C10CA25.4030108@cs.man.ac.uk> Thanks Franck. See inline below.... Franck Tanoh wrote: > Hi, > > some little things to report apart from that it's working fine. > 1- Soaplab service with description (from soaplab server) are > considered as missing description by the curation dashboard I will fix now. > 2- the service category on the left > (http://www.biocatalogue.org/services) the actual number of services > for each category is most of the time different from the number > between parenthesis. e.g. Text Mining category show 9 services but in > reality if you select that category there are 19 services . Same thing > applies to 'System Biology' category etc... Those numbers are cached, so it seems like the cache is not refreshing. I will also take a closer look right now. > 3- the 'enable tag filter' doesn't work ( that's a known issue i > think) ... returns error 500 after a while. Hmm... generating the tag filters is a really time consuming process unfortunately, so this seems to timeout a lot. I need some proper time to look at this, so I'm afraid it won' be solved any time soon :-( Jits > > Cheers, > Franck > > On 10 June 2010 09:42, Eric Nzuobontane > wrote: > > Hi, > > I have updated the test site already. Please test and let me know > if it is clear to go ahead with the update. > > 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 > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From jits at cs.man.ac.uk Thu Jun 10 07:20:30 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 10 Jun 2010 12:20:30 +0100 Subject: [BioCatalogue-developers] [Fwd: [BioCatalogue] Service Reponsibility Request] In-Reply-To: <4C10C8EA.7080408@ebi.ac.uk> References: <4C10B9FC.8030309@cs.man.ac.uk> <4C10C51A.40306@ebi.ac.uk> <4C10C6E5.3020208@cs.man.ac.uk> <4C10C8EA.7080408@ebi.ac.uk> Message-ID: <4C10CA7E.5000605@cs.man.ac.uk> Eric Nzuobontane wrote: > Jiten Bhagat wrote: >> True. >> >> Weird. I'm pretty sure I had created a script to cleanup dev/test >> databases. I can't seem to find it in the codebase anywhere though. >> >> It would basically change the email addresses of all users in the >> database to {random_number}@example.org. >> > that is one idea. The problem with that is that the application will > still send mail and the mail server will be attempting to deliver to > an invalid address and keep trying until it gives up. Maybe this in > combination with some custom code which ignores non admin emails. Yeap, we need something more elaborate like that to prevent any unwanted emails being set out at all. Jits > > Eric > >> We should adapt that kind of script to keep certain email addresses >> (ours) but obfuscate all others. >> >> Jits >> >> >> Eric Nzuobontane wrote: >> >>> Well, right now there is still a problem. At least with the test site >>> as the user accounts are available there as well as on live. Nothing >>> really stops anyone outside of the group making those request from >>> there now. Maybe we need to do something which indicates that is a >>> test site and only send mails to admins. >>> >>> Eric >>> >>> >>> Franck Tanoh wrote: >>> >>>>> You probably know this already, but... >>>>> >>>> oh yeah, I think we all learnt from the Embrace user import blunder >>>> last year :-) ... but a reminder in never bad >>>> >>>> Franck >>>> >>>> On 10 June 2010 11:10, Jiten Bhagat >>> > wrote: >>>> >>>> Hi guys, >>>> >>>> You probably know this already, but... >>>> >>>> When causing any action on the test/sandbox servers that require >>>> sending >>>> out an email, make sure you don't choose a service that will >>>> cause an >>>> email to be sent out to someone outside of the team. >>>> >>>> You can imagine how bad it would look if someone got an email from >>>> test.biocatalogue.org.... >>>> >>>> Jits >>>> >>>> >>>> -------- Original Message -------- >>>> Subject: [BioCatalogue] Service Reponsibility Request >>>> Date: Thu, 10 Jun 2010 11:04:22 +0100 >>>> From: contact at biocatalogue.org >>>> To: jits at cs.man.ac.uk >>>> >>>> >>>> >>>> Dear Jiten Bhagat, >>>> >>>> We have received a request from tanoh >>>> that they would like >>>> to be >>>> given permissions for the service, WSTMHMM_2_0 >>>> for which you are >>>> currently >>>> responsible. Granting this request will give the user full >>>> permissions >>>> on the service including the possibility to remove it from the >>>> BioCatalogue. >>>> >>>> Please visit >>>> http://test.biocatalogue.org/responsibility_requests to >>>> grant or turn down this request. >>>> >>>> Kind Regards, >>>> - The BioCatalogue Team >>>> >>>> http://test.biocatalogue.org >>>> >>>> >>>> >>>> >>>> -- >>>> "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 Jun 10 07:41:09 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 10 Jun 2010 12:41:09 +0100 Subject: [BioCatalogue-developers] Test site updated In-Reply-To: <4C10CA25.4030108@cs.man.ac.uk> References: <4C10A58B.4040901@ebi.ac.uk> <4C10CA25.4030108@cs.man.ac.uk> Message-ID: <4C10CF55.1000806@cs.man.ac.uk> Franck, Thinking about this some more... Surely the "description" from soaplab is not really a "description"? You still need a human readable description in the "description" section. Even if it's just a case of copying and pasting the value from the "details from Soaplab server" data? Jits Jiten Bhagat wrote: > Thanks Franck. > > See inline below.... > > Franck Tanoh wrote: > >> Hi, >> >> some little things to report apart from that it's working fine. >> 1- Soaplab service with description (from soaplab server) are >> considered as missing description by the curation dashboard >> > > I will fix now. > > >> 2- the service category on the left >> (http://www.biocatalogue.org/services) the actual number of services >> for each category is most of the time different from the number >> between parenthesis. e.g. Text Mining category show 9 services but in >> reality if you select that category there are 19 services . Same thing >> applies to 'System Biology' category etc... >> > > Those numbers are cached, so it seems like the cache is not refreshing. > I will also take a closer look right now. > > >> 3- the 'enable tag filter' doesn't work ( that's a known issue i >> think) ... returns error 500 after a while. >> > > Hmm... generating the tag filters is a really time consuming process > unfortunately, so this seems to timeout a lot. I need some proper time > to look at this, so I'm afraid it won' be solved any time soon :-( > > Jits > > >> Cheers, >> Franck >> >> On 10 June 2010 09:42, Eric Nzuobontane > > wrote: >> >> Hi, >> >> I have updated the test site already. Please test and let me know >> if it is clear to go ahead with the update. >> >> 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 >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From noreply at rubyforge.org Thu Jun 10 07:53:25 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 10 Jun 2010 07:53:25 -0400 (EDT) Subject: [BioCatalogue-developers] [2096] trunk/lib/bio_catalogue: Refactored the mechanism for finding services for the missing annotation curation report Message-ID: <20100610115325.5FB1D1858366@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu Jun 10 07:59:01 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 10 Jun 2010 12:59:01 +0100 Subject: [BioCatalogue-developers] Test site updated In-Reply-To: <4C10CF55.1000806@cs.man.ac.uk> References: <4C10A58B.4040901@ebi.ac.uk> <4C10CA25.4030108@cs.man.ac.uk> <4C10CF55.1000806@cs.man.ac.uk> Message-ID: <4C10D385.4040200@ebi.ac.uk> I think it is also sometimes desirable for the developer to have different levels of details for their service documentation. So some things might not be appropriate to go into a wsdl for example, but might be available from a meta data method like describe. Eric Jiten Bhagat wrote: > Franck, > > Thinking about this some more... > > Surely the "description" from soaplab is not really a "description"? You > still need a human readable description in the "description" section. > Even if it's just a case of copying and pasting the value from the > "details from Soaplab server" data? > > Jits > > > > Jiten Bhagat wrote: > >> Thanks Franck. >> >> See inline below.... >> >> Franck Tanoh wrote: >> >> >>> Hi, >>> >>> some little things to report apart from that it's working fine. >>> 1- Soaplab service with description (from soaplab server) are >>> considered as missing description by the curation dashboard >>> >>> >> I will fix now. >> >> >> >>> 2- the service category on the left >>> (http://www.biocatalogue.org/services) the actual number of services >>> for each category is most of the time different from the number >>> between parenthesis. e.g. Text Mining category show 9 services but in >>> reality if you select that category there are 19 services . Same thing >>> applies to 'System Biology' category etc... >>> >>> >> Those numbers are cached, so it seems like the cache is not refreshing. >> I will also take a closer look right now. >> >> >> >>> 3- the 'enable tag filter' doesn't work ( that's a known issue i >>> think) ... returns error 500 after a while. >>> >>> >> Hmm... generating the tag filters is a really time consuming process >> unfortunately, so this seems to timeout a lot. I need some proper time >> to look at this, so I'm afraid it won' be solved any time soon :-( >> >> Jits >> >> >> >>> Cheers, >>> Franck >>> >>> On 10 June 2010 09:42, Eric Nzuobontane >> > wrote: >>> >>> Hi, >>> >>> I have updated the test site already. Please test and let me know >>> if it is clear to go ahead with the update. >>> >>> 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 >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >>> >>> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> > > _______________________________________________ > 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 Jun 10 08:01:57 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 10 Jun 2010 08:01:57 -0400 (EDT) Subject: [BioCatalogue-developers] [2097] trunk/lib/bio_catalogue/categorising.rb: Ensure that the cache for the counts of services per category is regularly refreshed Message-ID: <20100610120158.05DE21858381@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Jun 10 08:42:57 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 10 Jun 2010 13:42:57 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'pathfinding' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'pathfinding' has changed status from 'Untested' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/2810 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Thu Jun 10 10:03:45 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 10 Jun 2010 15:03:45 +0100 Subject: [BioCatalogue-developers] Not available tomorrow Message-ID: <4C10F0C1.30700@ebi.ac.uk> Hi Guys, I am not available tomorrow and on Monday. 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 Thu Jun 10 10:54:15 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 10 Jun 2010 15:54:15 +0100 Subject: [BioCatalogue-developers] Harvesting Soaplab Service Details In-Reply-To: <4C0FAE7B.7070500@ebi.ac.uk> References: <4C0FAC87.1050604@ebi.ac.uk> <4C0FADB5.3030404@cs.man.ac.uk> <4C0FAE7B.7070500@ebi.ac.uk> Message-ID: <4C10FC97.80500@ebi.ac.uk> Harvesting Soaplab Service Details Previously soaplab services registered in the BioCatalogue had only the descriptions available in the wsdl. In many cases there were no descriptions at all in the wsdl and consequently not in the catalogue as well. However, soaplab services implement the 'describe' operation which returns a detailed description of the analysis. BioCatalogue now harvests these descriptions (where possible) from soaplab services thereby enriching the catalogue with reliable descriptions from the providers. Those descriptions can be seen for these services for example, http://www.biocatalogue.org/soaplab_servers/3 . We have failed to obtain the descriptions for some soaplab services and will be contacting the providers these services so that we could investigate together. Eric Eric Nzuobontane wrote: > Yeah, that sounds good. And maybe add that we harvest the descriptions > where possible! We now know that things are not always what we expect > so people should contact us if they do not find descriptions for their > soaplab services and we will investigate. > > Eric > > > Jiten Bhagat wrote: > >> Sounds good to me! >> >> Only thing - I would change the heading to "Harvesting soaplab service >> details". What do you think? >> >> Jits >> >> >> Eric Nzuobontane wrote: >> >>> I would go with something like this for the soaplab curation... >>> >>> Curating Soaplab Services >>> >>> Previously soaplab services registered in the BioCatalogue had only >>> the descriptions available in the wsdl. In many cases there were no >>> descriptions at all in the wsdl and consequently not in the catalogue >>> as well. However, soaplab services implement the 'describe' operation >>> which returns a detailed description of the analysis. BioCatalogue now >>> harvests these descriptions from soaplab services thereby enriching >>> the catalogue with reliable descriptions from the providers. >>> An example of a soaplab service with provider annotations from server >>> : >>> >>> > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From utopia at cs.man.ac.uk Thu Jun 10 12:50:19 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 10 Jun 2010 17:50:19 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'pathwayinference' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'pathwayinference' has changed status from 'Untested' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/2812 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Jun 10 13:16:07 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 10 Jun 2010 18:16:07 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'metabolicgraphconstruction' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'metabolicgraphconstruction' has changed status from 'Untested' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/2814 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Jun 10 13:34:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 10 Jun 2010 18:34:06 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'graphconversion' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'graphconversion' has changed status from 'Untested' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/2816 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jun 11 08:08:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 11 Jun 2010 13:08:28 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parseMultipleAlignFromBLASTText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parseMultipleAlignFromBLASTText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/989 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 Jun 11 08:15:30 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 11 Jun 2010 13:15:30 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromFASTAToDNASequenceCollection' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromFASTAToDNASequenceCollection' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/786 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Jun 12 23:35:45 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 13 Jun 2010 04:35:45 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMultiPairwiseMetaAlignmentGFF' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMultiPairwiseMetaAlignmentGFF' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/783 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Jun 13 13:10:03 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 13 Jun 2010 18:10:03 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getStructureFromMD_Trajectory' changed to Failed 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 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1165 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 Tue Jun 15 05:00:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 10:00:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-378) Develop app for mass curation via spreadsheets Message-ID: <21283392.5166.1276592415369.JavaMail.jira@rosalind.cs.man.ac.uk> Develop app for mass curation via spreadsheets ---------------------------------------------- Key: BIOCAT-378 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-378 Project: BioCatalogue Issue Type: New Feature Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 15 05:59:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 10:59:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-379) decide on which graphics framework to use for the app Message-ID: <17105394.5175.1276595955405.JavaMail.jira@rosalind.cs.man.ac.uk> decide on which graphics framework to use for the app ----------------------------------------------------- Key: BIOCAT-379 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-379 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 15 05:59:17 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 10:59:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-379) decide on which graphics framework to use for the app In-Reply-To: <17105394.5175.1276595955405.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8573854.5176.1276595957447.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-379?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-379. ------------------------------------ Resolution: Fixed > decide on which graphics framework to use for the app > ----------------------------------------------------- > > Key: BIOCAT-379 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-379 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 15 06:02:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:02:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-380) generate structure Message-ID: <32038048.5177.1276596135310.JavaMail.jira@rosalind.cs.man.ac.uk> generate structure ------------------ Key: BIOCAT-380 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-380 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira Priority: Critical -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 15 06:04:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:04:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-380) generate structure In-Reply-To: <32038048.5177.1276596135310.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2475071.5178.1276596255326.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-380?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15249#action_15249 ] Mannie Tagarira commented on BIOCAT-380: ---------------------------------------- modularize the application, create separations between the source files, resources, and libraries > generate structure > ------------------ > > Key: BIOCAT-380 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-380 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 15 06:12:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:12:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-380) generate structure In-Reply-To: <32038048.5177.1276596135310.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2724366.5179.1276596735311.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-380?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15250#action_15250 ] Mannie Tagarira commented on BIOCAT-380: ---------------------------------------- The following structure has been put into place; this will most probably change... Application Root Dir - Event-Handlers - User-Interface - Models - Libraries - Other-Sources - Resources > generate structure > ------------------ > > Key: BIOCAT-380 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-380 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 15 06:17:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:17:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-380) generate structure In-Reply-To: <32038048.5177.1276596135310.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31044037.5180.1276597035489.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-380?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15251#action_15251 ] Mannie Tagarira commented on BIOCAT-380: ---------------------------------------- Changed the application's structure to a more generic structure (this is to allow for easier packing and deployment using different tools... Root - lib - resources - src - events - models - modules - ui - org (used by the Rawr packaging system) > generate structure > ------------------ > > Key: BIOCAT-380 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-380 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 15 06:17:17 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:17:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-380) generate structure In-Reply-To: <32038048.5177.1276596135310.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3165825.5181.1276597037533.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-380?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-380. ------------------------------------ Resolution: Fixed > generate structure > ------------------ > > Key: BIOCAT-380 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-380 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 15 06:17:20 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:17:20 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-380) generate structure In-Reply-To: <32038048.5177.1276596135310.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12065804.5182.1276597040212.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-380?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15251#action_15251 ] Mannie Tagarira edited comment on BIOCAT-380 at 15/06/10 11:17: ---------------------------------------------------------------- Changed the application's structure to a more generic structure (this is to allow for easier packing and deployment using different tools... Root - lib - resources - src - src/events - src/models - src/modules - src/ui - src/org (used by the Rawr packaging system) was (Author: mannie): Changed the application's structure to a more generic structure (this is to allow for easier packing and deployment using different tools... Root - lib - resources - src - events - models - modules - ui - org (used by the Rawr packaging system) > generate structure > ------------------ > > Key: BIOCAT-380 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-380 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 15 06:22:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:22:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-379) decide on which graphics framework to use for the app In-Reply-To: <17105394.5175.1276595955405.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6065405.5183.1276597335342.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-379?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-379. ---------------------------------- The decision was to use JRuby as it takes advantage of the readability of Ruby at the same time taking advantage of Java's rich GUI APIs. > decide on which graphics framework to use for the app > ----------------------------------------------------- > > Key: BIOCAT-379 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-379 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 15 06:22:17 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:22:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-380) generate structure In-Reply-To: <32038048.5177.1276596135310.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12963609.5184.1276597337479.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-380?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-380. ---------------------------------- > generate structure > ------------------ > > Key: BIOCAT-380 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-380 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 15 06:29:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:29:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-381) Implement basic browsing functionality for the BioCatalogue services Message-ID: <17831261.5185.1276597755307.JavaMail.jira@rosalind.cs.man.ac.uk> Implement basic browsing functionality for the BioCatalogue services -------------------------------------------------------------------- Key: BIOCAT-381 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-381 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira The user needs a way of browsing and selecting the services which he/she would like to annotate; this has to be done within the app... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 06:33:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:33:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-381) Implement basic browsing functionality for the BioCatalogue services In-Reply-To: <17831261.5185.1276597755307.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14390027.5186.1276597995329.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-381?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-381. ------------------------------------ Resolution: Fixed Implemented a main window (which contains the paginated service browser) and a separate window showing which services are currently selected. > Implement basic browsing functionality for the BioCatalogue services > -------------------------------------------------------------------- > > Key: BIOCAT-381 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-381 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > The user needs a way of browsing and selecting the services which he/she would like to annotate; this has to be done within the app... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 06:33:18 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:33:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-381) Implement basic browsing functionality for the BioCatalogue services In-Reply-To: <17831261.5185.1276597755307.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11883430.5187.1276597998791.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-381?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-381. ---------------------------------- > Implement basic browsing functionality for the BioCatalogue services > -------------------------------------------------------------------- > > Key: BIOCAT-381 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-381 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > The user needs a way of browsing and selecting the services which he/she would like to annotate; this has to be done within the app... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 06:35:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:35:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-382) Disable Export button when no services have been selected Message-ID: <16545748.5188.1276598115345.JavaMail.jira@rosalind.cs.man.ac.uk> Disable Export button when no services have been selected --------------------------------------------------------- Key: BIOCAT-382 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-382 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira The Export button is clickable even when there is nothing to export. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 06:37:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:37:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-383) Implement searching of services Message-ID: <19965158.5189.1276598235436.JavaMail.jira@rosalind.cs.man.ac.uk> Implement searching of services ------------------------------- Key: BIOCAT-383 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-383 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira The user needs to be able to search for services from within the app. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 06:39:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:39:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-384) Implement generation of spreadsheet with the selected services Message-ID: <5586653.5211.1276598355307.JavaMail.jira@rosalind.cs.man.ac.uk> Implement generation of spreadsheet with the selected services -------------------------------------------------------------- Key: BIOCAT-384 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-384 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Jiten Bhagat Serialise the selected services into a spreadsheet file which can then be used by the user as a template. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 06:42:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:42:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-384) Implement generation of spreadsheet with the selected services In-Reply-To: <5586653.5211.1276598355307.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12805.5212.1276598535332.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-384?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira reassigned BIOCAT-384: -------------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Implement generation of spreadsheet with the selected services > -------------------------------------------------------------- > > Key: BIOCAT-384 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-384 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > Serialise the selected services into a spreadsheet file which can then be used by the user as a template. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 06:44:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:44:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-384) Implement generation of spreadsheet containing the selected services In-Reply-To: <5586653.5211.1276598355307.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8425541.5213.1276598655324.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-384?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-384: ----------------------------------- Summary: Implement generation of spreadsheet containing the selected services (was: Implement generation of spreadsheet with the selected services) > Implement generation of spreadsheet containing the selected services > -------------------------------------------------------------------- > > Key: BIOCAT-384 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-384 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > Serialise the selected services into a spreadsheet file which can then be used by the user as a template. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 06:44:17 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:44:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-384) Implement generation of spreadsheet containing the selected services In-Reply-To: <5586653.5211.1276598355307.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31218301.5214.1276598657352.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-384?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-384. ------------------------------------ Resolution: Fixed Used the spreadsheet gem to create Excel files. > Implement generation of spreadsheet containing the selected services > -------------------------------------------------------------------- > > Key: BIOCAT-384 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-384 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > Serialise the selected services into a spreadsheet file which can then be used by the user as a template. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 06:46:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:46:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-384) Implement generation of spreadsheet containing the selected services In-Reply-To: <5586653.5211.1276598355307.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23755443.5215.1276598775308.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-384?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-384. ---------------------------------- > Implement generation of spreadsheet containing the selected services > -------------------------------------------------------------------- > > Key: BIOCAT-384 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-384 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > Serialise the selected services into a spreadsheet file which can then be used by the user as a template. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 06:50:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:50:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-385) Implement annotation support for REST Services Message-ID: <29346203.5237.1276599015355.JavaMail.jira@rosalind.cs.man.ac.uk> Implement annotation support for REST Services ---------------------------------------------- Key: BIOCAT-385 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-385 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira Only the annotation of SOAP Services is currently supported; extend the app to allow for REST Services as well... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 15 06:52:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:52:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-386) Add support for extra annotation fields Message-ID: <31176879.5245.1276599135310.JavaMail.jira@rosalind.cs.man.ac.uk> Add support for extra annotation fields --------------------------------------- Key: BIOCAT-386 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-386 Project: BioCatalogue Issue Type: Sub-task Components: Curation Dashboard Reporter: Mannie Tagarira Assignee: Jiten Bhagat Only descriptions, example data, and tags can be annotated via the spreadsheet; allow for more annotation fields e.g. Categories -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 06:54:24 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:54:24 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-387) Allow the user to be able to deselect services via the Selected Services Window Message-ID: <8545676.5253.1276599264901.JavaMail.jira@rosalind.cs.man.ac.uk> Allow the user to be able to deselect services via the Selected Services Window ------------------------------------------------------------------------------- Key: BIOCAT-387 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-387 Project: BioCatalogue Issue Type: Sub-task Components: Curation Dashboard Reporter: Mannie Tagarira Assignee: Jiten Bhagat For whatever reason, the checkbox for services cannot be deselected from the Selected Services Window -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 06:56:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:56:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-388) Implement syncing of application caches Message-ID: <29588812.5282.1276599375381.JavaMail.jira@rosalind.cs.man.ac.uk> Implement syncing of application caches --------------------------------------- Key: BIOCAT-388 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-388 Project: BioCatalogue Issue Type: Sub-task Components: Curation Dashboard Reporter: Mannie Tagarira Assignee: Jiten Bhagat The panels in the caches and the services in the caches need updating everytime something happens, otherwise they will remain "stale" -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 06:56:25 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:56:25 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-387) Allow the user to be able to deselect services via the Selected Services Window In-Reply-To: <8545676.5253.1276599264901.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21743323.5290.1276599385370.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-387?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-387. ------------------------------------ Resolution: Fixed Implemented some syncing/updating of the service and listing caches. > Allow the user to be able to deselect services via the Selected Services Window > ------------------------------------------------------------------------------- > > Key: BIOCAT-387 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-387 > Project: BioCatalogue > Issue Type: Sub-task > Components: Curation Dashboard > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > > For whatever reason, the checkbox for services cannot be deselected from the Selected Services Window -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 06:58:45 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 11:58:45 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-381) Implement basic browsing functionality for the BioCatalogue services In-Reply-To: <17831261.5185.1276597755307.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32937000.5333.1276599525539.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-381?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15256#action_15256 ] Mannie Tagarira commented on BIOCAT-381: ---------------------------------------- I also added some caches to the browsing so that the app does not refetch data that is already available. > Implement basic browsing functionality for the BioCatalogue services > -------------------------------------------------------------------- > > Key: BIOCAT-381 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-381 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > The user needs a way of browsing and selecting the services which he/she would like to annotate; this has to be done within the app... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:00:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:00:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-378) Develop app for mass curation via spreadsheets In-Reply-To: <21283392.5166.1276592415369.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25077584.5355.1276599615450.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-378?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-378 started by Mannie Tagarira. > Develop app for mass curation via spreadsheets > ---------------------------------------------- > > Key: BIOCAT-378 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-378 > Project: BioCatalogue > Issue Type: New Feature > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Original Estimate: 3 weeks > Remaining Estimate: 3 weeks > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:00:28 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:00:28 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-388) Implement syncing of application caches In-Reply-To: <29588812.5282.1276599375381.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26252620.5363.1276599628811.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-388?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira reassigned BIOCAT-388: -------------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Implement syncing of application caches > --------------------------------------- > > Key: BIOCAT-388 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-388 > Project: BioCatalogue > Issue Type: Sub-task > Components: Curation Dashboard > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > The panels in the caches and the services in the caches need updating everytime something happens, otherwise they will remain "stale" -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:00:29 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:00:29 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-386) Add support for extra annotation fields In-Reply-To: <31176879.5245.1276599135310.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11516427.5364.1276599629780.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-386?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira reassigned BIOCAT-386: -------------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Add support for extra annotation fields > --------------------------------------- > > Key: BIOCAT-386 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-386 > Project: BioCatalogue > Issue Type: Sub-task > Components: Curation Dashboard > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > Only descriptions, example data, and tags can be annotated via the spreadsheet; allow for more annotation fields e.g. Categories -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:00:30 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:00:30 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-387) Allow the user to be able to deselect services via the Selected Services Window In-Reply-To: <8545676.5253.1276599264901.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4827782.5365.1276599630710.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-387?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira reassigned BIOCAT-387: -------------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Allow the user to be able to deselect services via the Selected Services Window > ------------------------------------------------------------------------------- > > Key: BIOCAT-387 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-387 > Project: BioCatalogue > Issue Type: Sub-task > Components: Curation Dashboard > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > For whatever reason, the checkbox for services cannot be deselected from the Selected Services Window -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:02:24 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:02:24 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-388) Implement syncing of application caches In-Reply-To: <29588812.5282.1276599375381.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <33498033.5380.1276599744953.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-388?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15257#action_15257 ] Mannie Tagarira commented on BIOCAT-388: ---------------------------------------- I implemented some level of cache updating. Only the local caches are updated based on what is in the main application cache; I still need to update the application cache as well based on some new data that may be present in the local caches > Implement syncing of application caches > --------------------------------------- > > Key: BIOCAT-388 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-388 > Project: BioCatalogue > Issue Type: Sub-task > Components: Curation Dashboard > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > The panels in the caches and the services in the caches need updating everytime something happens, otherwise they will remain "stale" -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:11:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:11:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-389) Parse a spreadsheet and POST the annotations to BioCatalogue Message-ID: <27516594.5409.1276600275368.JavaMail.jira@rosalind.cs.man.ac.uk> Parse a spreadsheet and POST the annotations to BioCatalogue ------------------------------------------------------------ Key: BIOCAT-389 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-389 Project: BioCatalogue Issue Type: Sub-task Components: Curation Dashboard Reporter: Mannie Tagarira Assignee: Mannie Tagarira Use the spreadsheet gem to extract the annotation data from the spreadsheet (supplied by the user via a file selection dialog) and POST the annotation data (in JSON): POST /annotations/bulk_create -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:11:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:11:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-389) Parse a spreadsheet and POST the annotations to BioCatalogue In-Reply-To: <27516594.5409.1276600275368.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19659036.5410.1276600276523.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-389?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-389. ------------------------------------ Resolution: Fixed > Parse a spreadsheet and POST the annotations to BioCatalogue > ------------------------------------------------------------ > > Key: BIOCAT-389 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-389 > Project: BioCatalogue > Issue Type: Sub-task > Components: Curation Dashboard > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > Use the spreadsheet gem to extract the annotation data from the spreadsheet (supplied by the user via a file selection dialog) and POST the annotation data (in JSON): > POST /annotations/bulk_create -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:15:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:15:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-390) POST only changed/new annotations Message-ID: <15090140.5411.1276600515325.JavaMail.jira@rosalind.cs.man.ac.uk> POST only changed/new annotations --------------------------------- Key: BIOCAT-390 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-390 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira The application currently POSTs all the annotations that are found in the spreadsheet, regardless of whether they have changed or not. Only the annotations that are new or have changed should be POSTed. Doing this may reduce the chances of errors occurring, and will definitely increase the POSTing efficiency. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:15:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:15:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-390) POST only changed/new annotations In-Reply-To: <15090140.5411.1276600515325.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18391846.5412.1276600516217.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-390?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-390. ------------------------------------ Resolution: Fixed > POST only changed/new annotations > --------------------------------- > > Key: BIOCAT-390 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-390 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > The application currently POSTs all the annotations that are found in the spreadsheet, regardless of whether they have changed or not. Only the annotations that are new or have changed should be POSTed. Doing this may reduce the chances of errors occurring, and will definitely increase the POSTing efficiency. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:17:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:17:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-391) Add functionality to "Preview" a service Message-ID: <31129328.5414.1276600635346.JavaMail.jira@rosalind.cs.man.ac.uk> Add functionality to "Preview" a service ---------------------------------------- Key: BIOCAT-391 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-391 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira Implement a "preview browser" similar to the myExperiment plugin one to view service information -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:17:18 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:17:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-391) Add functionality to "Preview" a service In-Reply-To: <31129328.5414.1276600635346.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28667608.5415.1276600638911.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-391?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-391 started by Mannie Tagarira. > Add functionality to "Preview" a service > ---------------------------------------- > > Key: BIOCAT-391 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-391 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > Implement a "preview browser" similar to the myExperiment plugin one to view service information -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:21:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:21:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-391) Add functionality to "Preview" a service In-Reply-To: <31129328.5414.1276600635346.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8223919.5417.1276600876428.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-391?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-391. ---------------------------------- > Add functionality to "Preview" a service > ---------------------------------------- > > Key: BIOCAT-391 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-391 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > Implement a "preview browser" similar to the myExperiment plugin one to view service information -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:23:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:23:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-383) Implement searching of services In-Reply-To: <19965158.5189.1276598235436.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19103867.5418.1276600995313.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-383?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-383. ------------------------------------ Resolution: Fixed I implemented basic search functionality, limiting the search results to X (where X is a variable int) > Implement searching of services > ------------------------------- > > Key: BIOCAT-383 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-383 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > The user needs to be able to search for services from within the app. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:15:17 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:15:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-390) POST only changed/new annotations In-Reply-To: <15090140.5411.1276600515325.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12864917.5413.1276600517357.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-390?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-390. ---------------------------------- > POST only changed/new annotations > --------------------------------- > > Key: BIOCAT-390 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-390 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > The application currently POSTs all the annotations that are found in the spreadsheet, regardless of whether they have changed or not. Only the annotations that are new or have changed should be POSTed. Doing this may reduce the chances of errors occurring, and will definitely increase the POSTing efficiency. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:25:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:25:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-392) Show more search results Message-ID: <1507555.5419.1276601115303.JavaMail.jira@rosalind.cs.man.ac.uk> Show more search results ------------------------ Key: BIOCAT-392 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-392 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira The user requested the ability to view more search results via pagination similar to that used when browsing services in the main window. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:21:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:21:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-391) Add functionality to "Preview" a service In-Reply-To: <31129328.5414.1276600635346.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4402544.5416.1276600875321.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-391?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-391. ------------------------------------ Resolution: Fixed Due to time restriction, I have had to command the "Preview" button to open a web browser tab (or window depending on the browser's policy) showing the BioCatalogue entry for the service. > Add functionality to "Preview" a service > ---------------------------------------- > > Key: BIOCAT-391 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-391 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > Implement a "preview browser" similar to the myExperiment plugin one to view service information -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:29:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:29:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-393) Add colour codes to be able to differentiate between well annotated and poorly annotated services Message-ID: <25009088.5420.1276601355307.JavaMail.jira@rosalind.cs.man.ac.uk> Add colour codes to be able to differentiate between well annotated and poorly annotated services ------------------------------------------------------------------------------------------------- Key: BIOCAT-393 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-393 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira Users want to be able to tell which services have a greater need for annotations via the use of colour codes... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:31:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:31:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-394) Get rid of # signs in the generated spreadsheet Message-ID: <26591893.5421.1276601475301.JavaMail.jira@rosalind.cs.man.ac.uk> Get rid of # signs in the generated spreadsheet ----------------------------------------------- Key: BIOCAT-394 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-394 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira Some descriptions appear to have #s in the cell but when they are double clicked for editing, the # signs disappear. This is something to do with the cell's formatting. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:39:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:39:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-396) Fix panel conflict in the Selected Services Window Message-ID: <7420561.5423.1276601955395.JavaMail.jira@rosalind.cs.man.ac.uk> Fix panel conflict in the Selected Services Window -------------------------------------------------- Key: BIOCAT-396 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-396 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira After making selections and deselecting all those services, and then selecting another service, there is some panel overlap... Some panel has not been hidden or removed; this has to be handled properly. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:39:33 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:39:33 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-383) Implement searching of services In-Reply-To: <19965158.5189.1276598235436.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17027867.5432.1276601973439.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-383?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-383. ---------------------------------- > Implement searching of services > ------------------------------- > > Key: BIOCAT-383 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-383 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > The user needs to be able to search for services from within the app. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:39:34 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:39:34 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-387) Allow the user to be able to deselect services via the Selected Services Window In-Reply-To: <8545676.5253.1276599264901.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15247015.5433.1276601974828.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-387?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-387. ---------------------------------- > Allow the user to be able to deselect services via the Selected Services Window > ------------------------------------------------------------------------------- > > Key: BIOCAT-387 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-387 > Project: BioCatalogue > Issue Type: Sub-task > Components: Curation Dashboard > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > For whatever reason, the checkbox for services cannot be deselected from the Selected Services Window -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:39:37 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:39:37 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-382) Disable Export button when no services have been selected In-Reply-To: <16545748.5188.1276598115345.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17276584.5434.1276601977132.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-382?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-382. ---------------------------------- Resolution: Fixed > Disable Export button when no services have been selected > --------------------------------------------------------- > > Key: BIOCAT-382 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-382 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > The Export button is clickable even when there is nothing to export. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:35:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:35:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-395) Allow the user to change their Preferences Message-ID: <15547864.5422.1276601715309.JavaMail.jira@rosalind.cs.man.ac.uk> Allow the user to change their Preferences ------------------------------------------ Key: BIOCAT-395 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-395 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira Add a preference pane to allow the user to specify their own parameters e.g. how many services should be returned in a search, custom biocatalogue host, etc -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 15 07:41:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:41:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-392) Show more search results In-Reply-To: <1507555.5419.1276601115303.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27708273.5435.1276602075350.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-392?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-392 started by Mannie Tagarira. > Show more search results > ------------------------ > > Key: BIOCAT-392 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-392 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > The user requested the ability to view more search results via pagination similar to that used when browsing services in the main window. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:41:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:41:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-396) Fix panel conflict in the Selected Services Window In-Reply-To: <7420561.5423.1276601955395.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29437072.5436.1276602076198.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-396?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-396 started by Mannie Tagarira. > Fix panel conflict in the Selected Services Window > -------------------------------------------------- > > Key: BIOCAT-396 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-396 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > After making selections and deselecting all those services, and then selecting another service, there is some panel overlap... Some panel has not been hidden or removed; this has to be handled properly. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 15 07:39:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 15 Jun 2010 12:39:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-397) Update the application's main.rb file to take in custom arguments Message-ID: <30133966.5424.1276601956432.JavaMail.jira@rosalind.cs.man.ac.uk> Update the application's main.rb file to take in custom arguments ----------------------------------------------------------------- Key: BIOCAT-397 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-397 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 16 05:36:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 16 Jun 2010 10:36:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-395) Allow the user to change their Preferences In-Reply-To: <15547864.5422.1276601715309.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26776803.6208.1276680975420.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-395?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-395 started by Mannie Tagarira. > Allow the user to change their Preferences > ------------------------------------------ > > Key: BIOCAT-395 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-395 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > Add a preference pane to allow the user to specify their own parameters e.g. how many services should be returned in a search, custom biocatalogue host, etc -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 16 05:36:26 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 16 Jun 2010 10:36:26 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-395) Allow the user to change their Preferences In-Reply-To: <15547864.5422.1276601715309.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6603414.6209.1276680986234.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-395?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-395 stopped by Mannie Tagarira. > Allow the user to change their Preferences > ------------------------------------------ > > Key: BIOCAT-395 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-395 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > Add a preference pane to allow the user to specify their own parameters e.g. how many services should be returned in a search, custom biocatalogue host, etc -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 16 05:38:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 16 Jun 2010 10:38:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-397) Update the application's main.rb file to take in custom arguments In-Reply-To: <30133966.5424.1276601956432.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30650794.6210.1276681095360.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-397?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-397. ------------------------------------ Resolution: Fixed > Update the application's main.rb file to take in custom arguments > ----------------------------------------------------------------- > > Key: BIOCAT-397 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-397 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 16 05:38:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 16 Jun 2010 10:38:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-397) Update the application's main.rb file to take in custom arguments In-Reply-To: <30133966.5424.1276601956432.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6786688.6211.1276681096468.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-397?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-397. ---------------------------------- > Update the application's main.rb file to take in custom arguments > ----------------------------------------------------------------- > > Key: BIOCAT-397 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-397 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 16 08:13:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 16 Jun 2010 13:13:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-398) Update /soap_operations/{id}/annotations.json endpoint to show the inputs and the outputs for the SOAP operation Message-ID: <4137965.6232.1276690395403.JavaMail.jira@rosalind.cs.man.ac.uk> Update /soap_operations/{id}/annotations.json endpoint to show the inputs and the outputs for the SOAP operation ---------------------------------------------------------------------------------------------------------------- Key: BIOCAT-398 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-398 Project: BioCatalogue Issue Type: New Feature Components: REST API, SOAP Services Support Reporter: Mannie Tagarira Assignee: Jiten Bhagat GET /soap_operations/{id}/annotations.json?also=inputs,outputs and GET /soap_operations/{id}/annotations.xml?also=inputs,outputs should return (roughly) the same content in different formats. The JSON alternative currently behaves as thought no query parameters were provided, i.e. behaves just like GET /soap_operations/{id}/annotations.json would behave... -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 16 13:26:16 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 16 Jun 2010 18:26:16 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: [Biocatalogue-support] BioCatalogue feedback from Martijn van Iersel (martijn.vaniersel@bigcat.unimaas.nl)] Message-ID: <4C190938.60904@cs.man.ac.uk> Eric, Please see the email below... Can you please activate Martijn's account (the one with the email address) and delete any other accounts he may have inadvertently created. Please also investigate why he was having so much trouble signing up!! I didn't see any error emails about this, which is worrying.... Jits -------- Original Message -------- Subject: Re: [Biocatalogue-support] BioCatalogue feedback from Martijn van Iersel (martijn.vaniersel at bigcat.unimaas.nl) Date: Wed, 16 Jun 2010 18:24:22 +0100 From: Jiten Bhagat To: martijn.vaniersel at bigcat.unimaas.nl CC: contact at biocatalogue.org References: <4c19067885b17_315b1573bf7567d01f3 at pweb-4a.ebi.ac.uk.tmail> Hello Martijn, Sorry to hear about your troubles signing up. I have forwarded this on to the team that manages the system and we will investigate this further to ensure it doesn't happen again. In the meantime, it looks like you are registered but not activated, so we will manually activate your account first thing tomorrow morning (UK time) and get back to you. Have a good evening. Jiten Bhagat contact at biocatalogue.org wrote: > BioCatalogue feedback from: Martijn van Iersel (martijn.vaniersel at bigcat.unimaas.nl) > > Subject: Lot's of trouble signing up > > Message: > I had lots of trouble signing up. > I tried to fill in the sign up form twice, each time it responded with an error message that my email address was incorrect. > Later on two activation emails showed up in my inbox anyway. I clicked on the activation link in both, both led to a page saying that the activation code was incorrect. > > I also tried to sign up using one of my openid accounts, that didn't work either. > _______________________________________________ > Biocatalogue-support mailing list > Biocatalogue-support at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-support > From jits at cs.man.ac.uk Thu Jun 17 00:32:57 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 17 Jun 2010 05:32:57 +0100 Subject: [BioCatalogue-developers] [Fwd: [Production ERROR] annotations#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56741"] Message-ID: <4C19A579.7030305@cs.man.ac.uk> We're getting at a stage where these errors are becoming a MAJOR ISSUE. Trish has been trying to annotate her REST services but can't because of errors like this. What's going on? Jits -------- Original Message -------- Subject: [Production ERROR] annotations#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56741" Date: Wed, 16 Jun 2010 23:44:06 +0100 From: BioCatalogue Errors To: ericnzuo at ebi.ac.uk, jits at cs.man.ac.uk A ActiveRecord::StatementInvalid occurred in annotations#destroy: Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56741 [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' ------------------------------- Request: ------------------------------- * URL : http://www.biocatalogue.org/annotations/54101 * Method : DELETE * IP address: 171.65.32.69 * Parameters: {"action"=>"destroy", "_method"=>"delete", "authenticity_token"=>"UcDYXr0rd6CeAHuHqsKiMALW+9H+rtRzW/pJFxWU/vo=", "id"=>"54101", "controller"=>"annotations"} * Rails root: /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue ------------------------------- Session: ------------------------------- * session id: nil * data: nil ------------------------------- Environment: ------------------------------- * CONTENT_LENGTH : 88 * CONTENT_TYPE : application/x-www-form-urlencoded * 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 : en-us,en;q=0.5 * HTTP_CONNECTION : keep-alive * HTTP_CONTENT_TYPE : application/x-www-form-urlencoded * HTTP_COOKIE : _session_id=41519df5efd6f215e077a8912a5591ad; __utma=15951013.828308017.1276727401.1276727401.1276727401.1; __utmb=15951013.15.10.1276727401; __utmc=15951013; __utmz=15951013.1276727401.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none) * HTTP_HOST : www.biocatalogue.org * HTTP_KEEP_ALIVE : 300 * HTTP_REFERER : http://www.biocatalogue.org/rest_methods/91 * HTTP_USER_AGENT : Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.1.6) Gecko/20091201 Firefox/3.5.6 * HTTP_X_CLUSTER_CLIENT_IP : 171.65.32.69 * PATH_INFO : /annotations/54101 * QUERY_STRING : * REMOTE_ADDR : 171.65.32.69 * REMOTE_PORT : 41048 * REQUEST_METHOD : DELETE * REQUEST_URI : /annotations/54101 * SCRIPT_NAME : * SERVER_ADDR : 172.18.1.109 * SERVER_ADMIN : root at localhost * SERVER_NAME : www.biocatalogue.org * SERVER_PORT : 80 * SERVER_PROTOCOL : HTTP/1.1 * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) * _ : _ * action_controller.request.query_parameters : * action_controller.request.request_parameters: authenticity_tokenUcDYXr0rd6CeAHuHqsKiMALW+9H+rtRzW/pJFxWU/vo=_methoddelete * action_controller.rescue.request : # * action_controller.rescue.response : # * rack.errors : # * rack.input : # * rack.methodoverride.original_method : POST * rack.multiprocess : true * rack.multithread : false * rack.request : # * rack.request.cookie_hash : __utma15951013.828308017.1276727401.1276727401.1276727401.1__utmb15951013.15.10.1276727401_session_id41519df5efd6f215e077a8912a5591ad__utmc15951013__utmz15951013.1276727401.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none) * rack.request.cookie_string : _session_id=41519df5efd6f215e077a8912a5591ad; __utma=15951013.828308017.1276727401.1276727401.1276727401.1; __utmb=15951013.15.10.1276727401; __utmc=15951013; __utmz=15951013.1276727401.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none) * rack.request.form_hash : authenticity_tokenUcDYXr0rd6CeAHuHqsKiMALW+9H+rtRzW/pJFxWU/vo=_methoddelete * rack.request.form_input : # * rack.request.form_vars : _method=delete&authenticity_token=UcDYXr0rd6CeAHuHqsKiMALW%2B9H%2BrtRzW%2FpJFxWU%2Fvo%3D * rack.request.query_hash : * rack.request.query_string : * rack.routing_args : actiondestroyid54101controllerannotations * rack.run_once : false * rack.session : user_id110previous_url/annotations/54101_csrf_tokenUcDYXr0rd6CeAHuHqsKiMALW+9H+rtRzW/pJFxWU/vo=services_index_listing_typedetaileduse_tab_cookietrueflash * rack.session.options : securefalseexpire_afterkey_session_idid41519df5efd6f215e077a8912a5591adhttponlytruedomaincookie_onlytruepath/ * rack.session.record : # * rack.url_scheme : http * rack.version : 10 * Process: 31581 * Server : pweb-4a * request.format: text/html ------------------------------- Backtrace: ------------------------------- [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:320:in `execute' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:265:in `update_sql' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:335:in `update_sql' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:270:in `delete_sql' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:54:in `delete_without_query_dirty' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:18:in `delete' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:2578:in `destroy_without_lock' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/locking/optimistic.rb:113:in `destroy_without_callbacks' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:337:in `destroy_without_transactions' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `send' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `with_transaction_returning_status' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in `with_transaction_returning_status' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in `destroy' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_versions' [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `each' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `send' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in `method_missing' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in `method_missing_without_paginate' [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in `method_missing' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in `has_many_dependent_destroy_for_versions' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `send' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `evaluate_method' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in `call' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in `run' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `each' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `send' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in `run' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in `run_callbacks' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in `callback' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in `destroy_without_transactions' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `send' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in `with_transaction_returning_status' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in `with_transaction_returning_status' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in `destroy_without_trash' [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in `destroy' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in `transaction' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in `transaction' [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in `destroy' [RAILS_ROOT]/vendor/plugins/annotations/lib/app/controllers/annotations_controller.rb:121:in `destroy' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in `send' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in `perform_action_without_filters' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:617:in `call_filters' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:610:in `perform_action_without_benchmark' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in `ms' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:10:in `realtime' [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in `ms' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rescue.rb:160:in `perform_action_without_flash' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb:141:in `perform_action' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in `send' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in `process_without_filters' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:606:in `process' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:391:in `process' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:386:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/route_set.rb:433:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:88:in `dispatch' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:111:in `_call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:82:in `initialize' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/methodoverride.rb:24:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/params_parser.rb:15:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rewindable_input.rb:25:in `call' [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in `call' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in `call' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in `cache' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in `cache' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in `call' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `synchronize' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in `call' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in `safe_fork' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in `start' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in `start' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 From ericnzuo at ebi.ac.uk Thu Jun 17 02:28:29 2010 From: ericnzuo at ebi.ac.uk (ericnzuo at ebi.ac.uk) Date: Thu, 17 Jun 2010 07:28:29 +0100 (BST) Subject: [BioCatalogue-developers] [Fwd: [Production ERROR] annotations#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `annotation_versions` WHERE `id` = 56741"] In-Reply-To: <4C19A579.7030305@cs.man.ac.uk> References: <4C19A579.7030305@cs.man.ac.uk> Message-ID: <56003.86.1.40.156.1276756109.squirrel@webmail.ebi.ac.uk> > We're getting at a stage where these errors are becoming a MAJOR ISSUE. Yes, it is a show stopper and needs to be solved immediately. I will check the timing as I suspect there may have been a collision with the backup of the database. This database server host is a shared machine and one thing I want to find out today is if there is any correlation with other mysql instances that have experienced problems recently. I know that there has been an overun backup process that has caused problems for at least one database. > > Trish has been trying to annotate her REST services but can't because of > errors like this. I saw the error messages this morning and it is a locking between the annotations and annotation versions tables. I do not have access to the logs so will have to ask the admins when I get back to the office if there is detection of any deadlocks. > > What's going on? I am puzzled by this and as it is only happening in production, it is a bit hard to solve. > > Jits > > > -------- Original Message -------- > Subject: [Production ERROR] annotations#destroy > (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout > exceeded; try restarting transaction: DELETE FROM `annotation_versions` > WHERE `id` = 56741" > Date: Wed, 16 Jun 2010 23:44:06 +0100 > From: BioCatalogue Errors > To: ericnzuo at ebi.ac.uk, jits at cs.man.ac.uk > > > > A ActiveRecord::StatementInvalid occurred in annotations#destroy: > > Mysql::Error: Lock wait timeout exceeded; try restarting transaction: > DELETE FROM `annotation_versions` WHERE `id` = 56741 > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in > `log' > > ------------------------------- > Request: > ------------------------------- > > * URL : http://www.biocatalogue.org/annotations/54101 > * Method : DELETE > * IP address: 171.65.32.69 > * Parameters: {"action"=>"destroy", "_method"=>"delete", > "authenticity_token"=>"UcDYXr0rd6CeAHuHqsKiMALW+9H+rtRzW/pJFxWU/vo=", > "id"=>"54101", "controller"=>"annotations"} > * Rails root: > /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue > > ------------------------------- > Session: > ------------------------------- > > * session id: nil > * data: nil > > ------------------------------- > Environment: > ------------------------------- > > * CONTENT_LENGTH : 88 > * CONTENT_TYPE : > application/x-www-form-urlencoded > * 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 : en-us,en;q=0.5 > * HTTP_CONNECTION : keep-alive > * HTTP_CONTENT_TYPE : > application/x-www-form-urlencoded > * HTTP_COOKIE : > _session_id=41519df5efd6f215e077a8912a5591ad; > __utma=15951013.828308017.1276727401.1276727401.1276727401.1; > __utmb=15951013.15.10.1276727401; __utmc=15951013; > __utmz=15951013.1276727401.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none) > * HTTP_HOST : www.biocatalogue.org > * HTTP_KEEP_ALIVE : 300 > * HTTP_REFERER : > http://www.biocatalogue.org/rest_methods/91 > * HTTP_USER_AGENT : Mozilla/5.0 (Macintosh; > U; Intel Mac OS X 10.5; en-US; rv:1.9.1.6) Gecko/20091201 Firefox/3.5.6 > * HTTP_X_CLUSTER_CLIENT_IP : 171.65.32.69 > * PATH_INFO : /annotations/54101 > * QUERY_STRING : > * REMOTE_ADDR : 171.65.32.69 > * REMOTE_PORT : 41048 > * REQUEST_METHOD : DELETE > * REQUEST_URI : /annotations/54101 > * SCRIPT_NAME : > * SERVER_ADDR : 172.18.1.109 > * SERVER_ADMIN : root at localhost > * SERVER_NAME : www.biocatalogue.org > * SERVER_PORT : 80 > * SERVER_PROTOCOL : HTTP/1.1 > * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) > * _ : _ > * action_controller.request.query_parameters : > * action_controller.request.request_parameters: > authenticity_tokenUcDYXr0rd6CeAHuHqsKiMALW+9H+rtRzW/pJFxWU/vo=_methoddelete > * action_controller.rescue.request : > # > * action_controller.rescue.response : > # > * rack.errors : # > * rack.input : > # > * rack.methodoverride.original_method : POST > * rack.multiprocess : true > * rack.multithread : false > * rack.request : > # > * rack.request.cookie_hash : > __utma15951013.828308017.1276727401.1276727401.1276727401.1__utmb15951013.15.10.1276727401_session_id41519df5efd6f215e077a8912a5591ad__utmc15951013__utmz15951013.1276727401.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none) > * rack.request.cookie_string : > _session_id=41519df5efd6f215e077a8912a5591ad; > __utma=15951013.828308017.1276727401.1276727401.1276727401.1; > __utmb=15951013.15.10.1276727401; __utmc=15951013; > __utmz=15951013.1276727401.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none) > * rack.request.form_hash : > authenticity_tokenUcDYXr0rd6CeAHuHqsKiMALW+9H+rtRzW/pJFxWU/vo=_methoddelete > * rack.request.form_input : > # > * rack.request.form_vars : > _method=delete&authenticity_token=UcDYXr0rd6CeAHuHqsKiMALW%2B9H%2BrtRzW%2FpJFxWU%2Fvo%3D > * rack.request.query_hash : > * rack.request.query_string : > * rack.routing_args : > actiondestroyid54101controllerannotations > * rack.run_once : false > * rack.session : > user_id110previous_url/annotations/54101_csrf_tokenUcDYXr0rd6CeAHuHqsKiMALW+9H+rtRzW/pJFxWU/vo=services_index_listing_typedetaileduse_tab_cookietrueflash > * rack.session.options : > securefalseexpire_afterkey_session_idid41519df5efd6f215e077a8912a5591adhttponlytruedomaincookie_onlytruepath/ > * rack.session.record : > # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 31581 > * Server : pweb-4a > > * request.format: text/html > > ------------------------------- > Backtrace: > ------------------------------- > > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in > `log' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:320:in > `execute' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:265:in > `update_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/mysql_adapter.rb:335:in > `update_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:270:in > `delete_sql' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:54:in > `delete_without_query_dirty' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:18:in > `delete' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:2578:in > `destroy_without_lock' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/locking/optimistic.rb:113:in > `destroy_without_callbacks' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:337:in > `destroy_without_transactions' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in > `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in > `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in > `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in > `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in > `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in > `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in > `has_many_dependent_destroy_for_versions' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in > `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in > `method_missing_without_paginate' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in > `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in > `each' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in > `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_proxy.rb:219:in > `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations/association_collection.rb:364:in > `method_missing_without_paginate' > [RAILS_ROOT]/vendor/plugins/will_paginate/lib/will_paginate/finder.rb:168:in > `method_missing' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/associations.rb:1364:in > `has_many_dependent_destroy_for_versions' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in > `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in > `evaluate_method' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in > `call' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:93:in > `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in > `each' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in > `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:92:in > `run' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:276:in > `run_callbacks' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:344:in > `callback' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/callbacks.rb:336:in > `destroy_without_transactions' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in > `send' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:229:in > `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in > `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in > `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:228:in > `with_transaction_returning_status' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:192:in > `destroy_without_trash' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:41:in > `destroy' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:136:in > `transaction' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/transactions.rb:182:in > `transaction' > [RAILS_ROOT]/vendor/plugins/acts_as_trashable/lib/acts_as_trashable.rb:38:in > `destroy' > [RAILS_ROOT]/vendor/plugins/annotations/lib/app/controllers/annotations_controller.rb:121:in > `destroy' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in > `send' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:1322:in > `perform_action_without_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:617:in > `call_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:610:in > `perform_action_without_benchmark' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in > `perform_action_without_rescue' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in > `ms' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:10:in > `realtime' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in > `ms' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in > `perform_action_without_rescue' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rescue.rb:160:in > `perform_action_without_flash' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb:141:in > `perform_action' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in > `send' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in > `process_without_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:606:in > `process' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:391:in > `process' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:386:in > `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/route_set.rb:433:in > `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:88:in > `dispatch' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:111:in > `_call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:82:in > `initialize' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in > `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in > `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/methodoverride.rb:24:in > `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/params_parser.rb:15:in > `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rewindable_input.rb:25:in > `call' > [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in > `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in > `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in > `cache' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in > `cache' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in > `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in > `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in > `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in > `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in > `synchronize' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in > `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in > `call' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in > `process_request' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in > `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in > `start_request_handler' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in > `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in > `safe_fork' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in > `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in > `__send__' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in > `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in > `start_synchronously' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in > `start' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in > `start' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in > `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in > `lookup_or_add' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in > `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in > `synchronize' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in > `synchronize' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in > `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in > `spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in > `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in > `__send__' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in > `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in > `start_synchronously' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 > > > From ericnzuo at ebi.ac.uk Thu Jun 17 05:13:11 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 17 Jun 2010 10:13:11 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: [Biocatalogue-support] BioCatalogue feedback from Martijn van Iersel (martijn.vaniersel@bigcat.unimaas.nl)] In-Reply-To: <4C190938.60904@cs.man.ac.uk> References: <4C190938.60904@cs.man.ac.uk> Message-ID: <4C19E727.2080700@ebi.ac.uk> Jiten Bhagat wrote: > Eric, > > Please see the email below... > > Can you please activate Martijn's account (the one with the email > address) and delete any other accounts he may have inadvertently created. > He created two accounts and both have the email address. I will delete the latest one and activated the one that was created before that. > Please also investigate why he was having so much trouble signing up!! I > didn't see any error emails about this, which is worrying.... > I did not receive any failure mails either. The current state of the live application does not seem to be very healthy especially with all these database errors. I have delegated the database problems to the systems people. They manage the databases anyway. However, I want to take steps towards making sure there is nothing in terms of deployment, that affects live adversely. So I will be spending the day today looking at the live deployment and searching for any configurations that could potentially affect the application. > Jits > > > -------- Original Message -------- > Subject: Re: [Biocatalogue-support] BioCatalogue feedback from Martijn > van Iersel (martijn.vaniersel at bigcat.unimaas.nl) > Date: Wed, 16 Jun 2010 18:24:22 +0100 > From: Jiten Bhagat > To: martijn.vaniersel at bigcat.unimaas.nl > CC: contact at biocatalogue.org > References: <4c19067885b17_315b1573bf7567d01f3 at pweb-4a.ebi.ac.uk.tmail> > > > > Hello Martijn, > > Sorry to hear about your troubles signing up. > > I have forwarded this on to the team that manages the system and we will > investigate this further to ensure it doesn't happen again. > > In the meantime, it looks like you are registered but not activated, so > we will manually activate your account first thing tomorrow morning (UK > time) and get back to you. > > Have a good evening. > > Jiten Bhagat > > > contact at biocatalogue.org wrote: > >> BioCatalogue feedback from: Martijn van Iersel (martijn.vaniersel at bigcat.unimaas.nl) >> >> Subject: Lot's of trouble signing up >> >> Message: >> I had lots of trouble signing up. >> I tried to fill in the sign up form twice, each time it responded with an error message that my email address was incorrect. >> Later on two activation emails showed up in my inbox anyway. I clicked on the activation link in both, both led to a page saying that the activation code was incorrect. >> >> I also tried to sign up using one of my openid accounts, that didn't work either. >> _______________________________________________ >> 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 ericnzuo at ebi.ac.uk Thu Jun 17 05:46:13 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 17 Jun 2010 10:46:13 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: [Biocatalogue-support] BioCatalogue feedback from Martijn van Iersel (martijn.vaniersel@bigcat.unimaas.nl)] In-Reply-To: <4C190938.60904@cs.man.ac.uk> References: <4C190938.60904@cs.man.ac.uk> Message-ID: <4C19EEE5.4080903@ebi.ac.uk> show innodb status ---TRANSACTION 0 342318416, not started, process no 5339, OS thread id 1161120096 MySQL thread id 26747, query id 352492272 pweb-3b.ebi.ac.uk 172.18.1.108 admin ---TRANSACTION 0 342320194, not started, process no 5339, OS thread id 1160321376 MySQL thread id 26739, query id 352494130 pweb-4a.ebi.ac.uk 172.18.1.109 admin ---TRANSACTION 0 342322274, not started, process no 5339, OS thread id 1162451296 MySQL thread id 25052, query id 352496251 pweb-3b.ebi.ac.uk 172.18.1.108 admin ---TRANSACTION 0 342320684, ACTIVE 44 sec, process no 5339, OS thread id 1159522656 3 lock struct(s), heap size 368, undo log entries 2 MySQL thread id 26750, query id 352494634 pweb-3b.ebi.ac.uk 172.18.1.108 admin Trx read view will not see trx with id >= 0 342320685, sees < 0 342316486 TABLE LOCK table `biocatalogue_production/trash_records` trx id 0 342320684 lock mode IX TABLE LOCK table `biocatalogue_production/users` trx id 0 342320684 lock mode IX RECORD LOCKS space id 0 page no 48168 n bits 144 index `PRIMARY` of table `biocatalogue_production/users` trx id 0 342320684 lock_mode X locks rec but not gap Record lock, heap no 77 PHYSICAL RECORD: n_fields 19; compact format; info bits 32 0: len 4; hex 8000023a; asc :;; 1: len 6; hex 00001467662c; asc gf,;; 2: len 7; hex 000000c82e0c3b; asc . ;;; 3: len 30; hex 6d617274696a6e2e76616e69657273656c406269676361742e756e696d61; asc martijn.vaniersel at bigcat.unima;...(truncated); 4: len 30; hex 636232663161323865373730346265303663303432643635343862333934; asc cb2f1a28e7704be06c042d6548b394;...(truncated); 5: len 30; hex 656364653634336538636635656439663534306561373633396530653264; asc ecde643e8cf5ed9f540ea7639e0e2d;...(truncated); 6: SQL NULL; 7: len 30; hex 303138363264363633636135633762643039376664313061656165323361; asc 01862d663ca5c7bd097fd10aeae23a;...(truncated); 8: len 18; hex 4d617274696a6e2076616e2049657273656c; asc Martijn van Iersel;; 9: SQL NULL; 10: SQL NULL; 11: len 21; hex 4d61617374726963687420556e6976657273697479; asc Maastricht University;; 12: len 11; hex 4e65746865726c616e6473; asc Netherlands;; 13: len 8; hex 800012480a162c06; asc H , ;; 14: len 8; hex 800012480a162c06; asc H , ;; 15: len 0; hex ; asc ;; 16: len 1; hex 80; asc ;; 17: SQL NULL; 18: SQL NULL; I think I have been looking at the problems for this locking and timouts at the database level. Actually, I am now convinced it is the application that needs to be investigated thoroughly. While trying to delete a user record for user with no activity, I get the following transactions. That does not look good at all. It took at least 3 minutes from the console to finally delete the user. I believe that the trashing of the records has a considerable adverse effect on the performance of the db and also since this table is basically a write table, it is locked when writes occur. Is there a way of turning trashing off? Eric ---TRANSACTION 0 342316486, ACTIVE 142 sec, process no 5339, OS thread id 1163782496 5 lock struct(s), heap size 1216, undo log entries 3 MySQL thread id 26752, query id 352490227 pweb-4a.ebi.ac.uk 172.18.1.109 admin Trx read view will not see trx with id >= 0 342316487, sees < 0 342316487 TABLE LOCK table `biocatalogue_production/trash_records` trx id 0 342316486 lock mode IX TABLE LOCK table `biocatalogue_production/annotation_versions` trx id 0 342316486 lock mode IX RECORD LOCKS space id 0 page no 42317 n bits 112 index `PRIMARY` of table `biocatalogue_production/annotation_versions` trx id 0 342316486 lock_mode X locks rec but not gap Record lock, heap no 25 PHYSICAL RECORD: n_fields 15; compact format; info bits 32 0: len 4; hex 8000ddae; asc ;; 1: len 6; hex 0000146755c6; asc gU ;; 2: len 7; hex 000000c82d1f8f; asc - ;; 3: len 4; hex 8000d35e; asc ^;; 4: len 4; hex 80000001; asc ;; 5: SQL NULL; 6: len 4; hex 55736572; asc User;; 7: len 4; hex 8000001b; asc ;; 8: len 13; hex 536f61704f7065726174696f6e; asc SoapOperation;; 9: len 4; hex 8000000c; asc ;; 10: len 4; hex 80000002; asc ;; 11: len 7; hex 626c61626c6168; asc blablah;; 12: len 6; hex 537472696e67; asc String;; 13: len 8; hex 800012480a243906; asc H $9 ;; 14: len 8; hex 800012480a243906; asc H $9 ;; TABLE LOCK table `biocatalogue_production/annotations` trx id 0 342316486 lock mode IX RECORD LOCKS space id 0 page no 60250 n bits 96 index `PRIMARY` of table `biocatalogue_production/annotations` trx id 0 342316486 lock_mode X locks rec but not gap Record lock, heap no 8 PHYSICAL RECORD: n_fields 14; compact format; info bits 32 0: len 4; hex 8000d35e; asc ^;; 1: len 6; hex 0000146755c6; asc gU ;; 2: len 7; hex 000000c82d1fb8; asc - ;; 3: len 4; hex 55736572; asc User;; 4: len 4; hex 8000001b; asc ;; 5: len 13; hex 536f61704f7065726174696f6e; asc SoapOperation;; 6: len 4; hex 8000000c; asc ;; 7: len 4; hex 80000002; asc ;; 8: len 7; hex 626c61626c6168; asc blablah;; 9: len 6; hex 537472696e67; asc String;; 10: len 8; hex 800012480a243906; asc H $9 ;; 11: len 8; hex 800012480a243906; asc H $9 ;; 12: len 4; hex 80000001; asc ;; 13: SQL NULL; Jiten Bhagat wrote: > Eric, > > Please see the email below... > > Can you please activate Martijn's account (the one with the email > address) and delete any other accounts he may have inadvertently created. > > Please also investigate why he was having so much trouble signing up!! I > didn't see any error emails about this, which is worrying.... > > Jits > > > -------- Original Message -------- > Subject: Re: [Biocatalogue-support] BioCatalogue feedback from Martijn > van Iersel (martijn.vaniersel at bigcat.unimaas.nl) > Date: Wed, 16 Jun 2010 18:24:22 +0100 > From: Jiten Bhagat > To: martijn.vaniersel at bigcat.unimaas.nl > CC: contact at biocatalogue.org > References: <4c19067885b17_315b1573bf7567d01f3 at pweb-4a.ebi.ac.uk.tmail> > > > > Hello Martijn, > > Sorry to hear about your troubles signing up. > > I have forwarded this on to the team that manages the system and we will > investigate this further to ensure it doesn't happen again. > > In the meantime, it looks like you are registered but not activated, so > we will manually activate your account first thing tomorrow morning (UK > time) and get back to you. > > Have a good evening. > > Jiten Bhagat > > > contact at biocatalogue.org wrote: > >> BioCatalogue feedback from: Martijn van Iersel (martijn.vaniersel at bigcat.unimaas.nl) >> >> Subject: Lot's of trouble signing up >> >> Message: >> I had lots of trouble signing up. >> I tried to fill in the sign up form twice, each time it responded with an error message that my email address was incorrect. >> Later on two activation emails showed up in my inbox anyway. I clicked on the activation link in both, both led to a page saying that the activation code was incorrect. >> >> I also tried to sign up using one of my openid accounts, that didn't work either. >> _______________________________________________ >> 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 ericnzuo at ebi.ac.uk Thu Jun 17 06:05:42 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 17 Jun 2010 11:05:42 +0100 Subject: [BioCatalogue-developers] trashing & annotation versions? Message-ID: <4C19F376.7050302@ebi.ac.uk> This happens every time there is a delete of an annotation and consequently any further attempts to delete will fail and cause the time out problem. So trashing and annotation versions need to further examination. 5 lock struct(s), heap size 1216, undo log entries 3 MySQL thread id 26771, query id 352521420 pweb-4a.ebi.ac.uk 172.18.1.109 admin Trx read view will not see trx with id >= 0 342346175, sees < 0 342346175 TABLE LOCK table `biocatalogue_production/trash_records` trx id 0 342346174 lock mode IX TABLE LOCK table `biocatalogue_production/annotation_versions` trx id 0 342346174 lock mode IX RECORD LOCKS space id 0 page no 42316 n bits 184 index `PRIMARY` of table `biocatalogue_production/annotation_versions` trx id 0 342346174 lock_mode X locks rec but not gap Record lock, heap no 48 PHYSICAL RECORD: n_fields 15; compact format; info bits 32 0: len 4; hex 8000dd4e; asc N;; 1: len 6; hex 00001467c9be; asc g ;; 2: len 7; hex 000000c8300dd7; asc 0 ;; 3: len 4; hex 8000d2fe; asc ;; 4: len 4; hex 80000001; asc ;; 5: SQL NULL; 6: len 4; hex 55736572; asc User;; 7: len 4; hex 8000001b; asc ;; 8: len 13; hex 536f61704f7065726174696f6e; asc SoapOperation;; 9: len 4; hex 80000023; asc #;; 10: len 4; hex 80000001; asc ;; 11: len 30; hex 52657472697665732061206c697374206f6620454c4d7320746861742068; asc Retrives a list of ELMs that h;...(truncated); 12: len 6; hex 537472696e67; asc String;; 13: len 8; hex 800012480a16190a; asc H ;; 14: len 8; hex 800012480a16190a; asc H ;; TABLE LOCK table `biocatalogue_production/annotations` trx id 0 342346174 lock mode IX RECORD LOCKS space id 0 page no 60249 n bits 200 index `PRIMARY` of table `biocatalogue_production/annotations` trx id 0 342346174 lock_mode X locks rec but not gap Record lock, heap no 44 PHYSICAL RECORD: n_fields 14; compact format; info bits 32 0: len 4; hex 8000d2fe; asc ;; 1: len 6; hex 00001467c9be; asc g ;; 2: len 7; hex 000000c8300e00; asc 0 ;; 3: len 4; hex 55736572; asc User;; 4: len 4; hex 8000001b; asc ;; 5: len 13; hex 536f61704f7065726174696f6e; asc SoapOperation;; 6: len 4; hex 80000023; asc #;; 7: len 4; hex 80000001; asc ;; 8: len 30; hex 52657472697665732061206c697374206f6620454c4d7320746861742068; asc Retrives a list of ELMs that h;...(truncated); 9: len 6; hex 537472696e67; asc String;; 10: len 8; hex 800012480a16190a; asc H ;; 11: len 8; hex 800012480a16190a; asc H ;; 12: len 4; hex 80000001; asc ;; 13: SQL NULL; -- 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 Jun 17 06:21:23 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 17 Jun 2010 11:21:23 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: [Biocatalogue-support] BioCatalogue feedback from Martijn van Iersel (martijn.vaniersel@bigcat.unimaas.nl)] In-Reply-To: <4C19EEE5.4080903@ebi.ac.uk> References: <4C190938.60904@cs.man.ac.uk> <4C19EEE5.4080903@ebi.ac.uk> Message-ID: <4C19F723.8080604@cs.man.ac.uk> At the moment the only way to turn off trashing is by removing the acts_as_trashable, BUT let me change this to use a config option, like we have for ENABLE_SEARCH etc. I will do this now and commit it. With regards to below... why is this problem not present on the test, sandbox and other dev environments?? Database transactions and high throughput is exactly what things like MySQL are designed for. If there was something seriously wrong in the application then we would at least see this happening in other environments. Still, it's good to check all layers. Jits Eric Nzuobontane wrote: > > > show innodb status > ---TRANSACTION 0 342318416, not started, process no 5339, OS thread id > 1161120096 > MySQL thread id 26747, query id 352492272 pweb-3b.ebi.ac.uk > 172.18.1.108 admin > ---TRANSACTION 0 342320194, not started, process no 5339, OS thread id > 1160321376 > MySQL thread id 26739, query id 352494130 pweb-4a.ebi.ac.uk > 172.18.1.109 admin > ---TRANSACTION 0 342322274, not started, process no 5339, OS thread id > 1162451296 > MySQL thread id 25052, query id 352496251 pweb-3b.ebi.ac.uk > 172.18.1.108 admin > ---TRANSACTION 0 342320684, ACTIVE 44 sec, process no 5339, OS thread > id 1159522656 > 3 lock struct(s), heap size 368, undo log entries 2 > MySQL thread id 26750, query id 352494634 pweb-3b.ebi.ac.uk > 172.18.1.108 admin > Trx read view will not see trx with id >= 0 342320685, sees < 0 342316486 > TABLE LOCK table `biocatalogue_production/trash_records` trx id 0 > 342320684 lock mode IX > TABLE LOCK table `biocatalogue_production/users` trx id 0 342320684 > lock mode IX > RECORD LOCKS space id 0 page no 48168 n bits 144 index `PRIMARY` of > table `biocatalogue_production/users` trx id 0 342320684 lock_mode X > locks rec but not gap > Record lock, heap no 77 PHYSICAL RECORD: n_fields 19; compact format; > info bits 32 > 0: len 4; hex 8000023a; asc :;; 1: len 6; hex 00001467662c; asc > gf,;; 2: len 7; hex 000000c82e0c3b; asc . ;;; 3: len 30; hex > 6d617274696a6e2e76616e69657273656c406269676361742e756e696d61; asc > martijn.vaniersel at bigcat.unima;...(truncated); 4: len 30; hex > 636232663161323865373730346265303663303432643635343862333934; asc > cb2f1a28e7704be06c042d6548b394;...(truncated); 5: len 30; hex > 656364653634336538636635656439663534306561373633396530653264; asc > ecde643e8cf5ed9f540ea7639e0e2d;...(truncated); 6: SQL NULL; 7: len 30; > hex 303138363264363633636135633762643039376664313061656165323361; asc > 01862d663ca5c7bd097fd10aeae23a;...(truncated); 8: len 18; hex > 4d617274696a6e2076616e2049657273656c; asc Martijn van Iersel;; 9: SQL > NULL; 10: SQL NULL; 11: len 21; hex > 4d61617374726963687420556e6976657273697479; asc Maastricht > University;; 12: len 11; hex 4e65746865726c616e6473; asc Netherlands;; > 13: len 8; hex 800012480a162c06; asc H , ;; 14: len 8; hex > 800012480a162c06; asc H , ;; 15: len 0; hex ; asc ;; 16: len 1; > hex 80; asc ;; 17: SQL NULL; 18: SQL NULL; > > I think I have been looking at the problems for this locking and > timouts at the database level. Actually, I am now convinced it is the > application that needs to be investigated thoroughly. While trying to > delete a user record for user with no activity, I get the following > transactions. That does not look good at all. It took at least 3 > minutes from the console to finally delete the user. I believe that > the trashing of the records has a considerable adverse effect on the > performance of the db and also since this table is basically a write > table, it is locked when writes occur. Is there a way of turning > trashing off? > > Eric > > > > ---TRANSACTION 0 342316486, ACTIVE 142 sec, process no 5339, OS thread > id 1163782496 > 5 lock struct(s), heap size 1216, undo log entries 3 > MySQL thread id 26752, query id 352490227 pweb-4a.ebi.ac.uk > 172.18.1.109 admin > Trx read view will not see trx with id >= 0 342316487, sees < 0 342316487 > TABLE LOCK table `biocatalogue_production/trash_records` trx id 0 > 342316486 lock mode IX > TABLE LOCK table `biocatalogue_production/annotation_versions` trx id > 0 342316486 lock mode IX > RECORD LOCKS space id 0 page no 42317 n bits 112 index `PRIMARY` of > table `biocatalogue_production/annotation_versions` trx id 0 342316486 > lock_mode X locks rec but not gap > Record lock, heap no 25 PHYSICAL RECORD: n_fields 15; compact format; > info bits 32 > 0: len 4; hex 8000ddae; asc ;; 1: len 6; hex 0000146755c6; asc > gU ;; 2: len 7; hex 000000c82d1f8f; asc - ;; 3: len 4; hex > 8000d35e; asc ^;; 4: len 4; hex 80000001; asc ;; 5: SQL NULL; > 6: len 4; hex 55736572; asc User;; 7: len 4; hex 8000001b; asc ;; > 8: len 13; hex 536f61704f7065726174696f6e; asc SoapOperation;; 9: len > 4; hex 8000000c; asc ;; 10: len 4; hex 80000002; asc ;; 11: > len 7; hex 626c61626c6168; asc blablah;; 12: len 6; hex 537472696e67; > asc String;; 13: len 8; hex 800012480a243906; asc H $9 ;; 14: len > 8; hex 800012480a243906; asc H $9 ;; > > TABLE LOCK table `biocatalogue_production/annotations` trx id 0 > 342316486 lock mode IX > RECORD LOCKS space id 0 page no 60250 n bits 96 index `PRIMARY` of > table `biocatalogue_production/annotations` trx id 0 342316486 > lock_mode X locks rec but not gap > Record lock, heap no 8 PHYSICAL RECORD: n_fields 14; compact format; > info bits 32 > 0: len 4; hex 8000d35e; asc ^;; 1: len 6; hex 0000146755c6; asc > gU ;; 2: len 7; hex 000000c82d1fb8; asc - ;; 3: len 4; hex > 55736572; asc User;; 4: len 4; hex 8000001b; asc ;; 5: len 13; hex > 536f61704f7065726174696f6e; asc SoapOperation;; 6: len 4; hex > 8000000c; asc ;; 7: len 4; hex 80000002; asc ;; 8: len 7; hex > 626c61626c6168; asc blablah;; 9: len 6; hex 537472696e67; asc String;; > 10: len 8; hex 800012480a243906; asc H $9 ;; 11: len 8; hex > 800012480a243906; asc H $9 ;; 12: len 4; hex 80000001; asc ;; > 13: SQL NULL; > > > > > Jiten Bhagat wrote: >> Eric, >> >> Please see the email below... >> >> Can you please activate Martijn's account (the one with the email >> address) and delete any other accounts he may have inadvertently >> created. >> >> Please also investigate why he was having so much trouble signing up!! I >> didn't see any error emails about this, which is worrying.... >> >> Jits >> >> >> -------- Original Message -------- >> Subject: Re: [Biocatalogue-support] BioCatalogue feedback from >> Martijn >> van Iersel (martijn.vaniersel at bigcat.unimaas.nl) >> Date: Wed, 16 Jun 2010 18:24:22 +0100 >> From: Jiten Bhagat >> To: martijn.vaniersel at bigcat.unimaas.nl >> CC: contact at biocatalogue.org >> References: >> <4c19067885b17_315b1573bf7567d01f3 at pweb-4a.ebi.ac.uk.tmail> >> >> >> >> Hello Martijn, >> >> Sorry to hear about your troubles signing up. >> >> I have forwarded this on to the team that manages the system and we will >> investigate this further to ensure it doesn't happen again. >> >> In the meantime, it looks like you are registered but not activated, so >> we will manually activate your account first thing tomorrow morning (UK >> time) and get back to you. >> >> Have a good evening. >> >> Jiten Bhagat >> >> >> contact at biocatalogue.org wrote: >> >>> BioCatalogue feedback from: Martijn van Iersel >>> (martijn.vaniersel at bigcat.unimaas.nl) >>> >>> Subject: Lot's of trouble signing up >>> >>> Message: >>> I had lots of trouble signing up. I tried to fill in the sign up >>> form twice, each time it responded with an error message that my >>> email address was incorrect. >>> Later on two activation emails showed up in my inbox anyway. I >>> clicked on the activation link in both, both led to a page saying >>> that the activation code was incorrect. >>> >>> I also tried to sign up using one of my openid accounts, that didn't >>> work either. >>> _______________________________________________ >>> Biocatalogue-support mailing list >>> Biocatalogue-support at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-support >>> >> >> >> > > From ericnzuo at ebi.ac.uk Thu Jun 17 06:32:33 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 17 Jun 2010 11:32:33 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: [Fwd: [Production ERROR] annotations#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE (SYS#59995)] Message-ID: <4C19F9C1.5060501@ebi.ac.uk> I have just received this from the systems guys. 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: Radoslaw Ryckowski Subject: Re: [Fwd: [Production ERROR] annotations#destroy (ActiveRecord::StatementInvalid) "Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE (SYS#59995) Date: Thu, 17 Jun 2010 11:22:38 +0100 Size: 22578 URL: From jits at cs.man.ac.uk Thu Jun 17 06:44:20 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 17 Jun 2010 11:44:20 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: [Biocatalogue-support] BioCatalogue feedback from Martijn van Iersel (martijn.vaniersel@bigcat.unimaas.nl)] In-Reply-To: <4C19F723.8080604@cs.man.ac.uk> References: <4C190938.60904@cs.man.ac.uk> <4C19EEE5.4080903@ebi.ac.uk> <4C19F723.8080604@cs.man.ac.uk> Message-ID: <4C19FC84.5020108@cs.man.ac.uk> Another thing... this transaction timeout issue is happening during UPDATEs too. Not just DELETEs. The acts_as_trashable only takes effect on deletes. Jits Jiten Bhagat wrote: > At the moment the only way to turn off trashing is by removing the > acts_as_trashable, BUT let me change this to use a config option, like > we have for ENABLE_SEARCH etc. > > I will do this now and commit it. > > With regards to below... why is this problem not present on the test, > sandbox and other dev environments?? Database transactions and high > throughput is exactly what things like MySQL are designed for. If there > was something seriously wrong in the application then we would at least > see this happening in other environments. Still, it's good to check all > layers. > > Jits > > > Eric Nzuobontane wrote: > >> show innodb status >> ---TRANSACTION 0 342318416, not started, process no 5339, OS thread id >> 1161120096 >> MySQL thread id 26747, query id 352492272 pweb-3b.ebi.ac.uk >> 172.18.1.108 admin >> ---TRANSACTION 0 342320194, not started, process no 5339, OS thread id >> 1160321376 >> MySQL thread id 26739, query id 352494130 pweb-4a.ebi.ac.uk >> 172.18.1.109 admin >> ---TRANSACTION 0 342322274, not started, process no 5339, OS thread id >> 1162451296 >> MySQL thread id 25052, query id 352496251 pweb-3b.ebi.ac.uk >> 172.18.1.108 admin >> ---TRANSACTION 0 342320684, ACTIVE 44 sec, process no 5339, OS thread >> id 1159522656 >> 3 lock struct(s), heap size 368, undo log entries 2 >> MySQL thread id 26750, query id 352494634 pweb-3b.ebi.ac.uk >> 172.18.1.108 admin >> Trx read view will not see trx with id >= 0 342320685, sees < 0 342316486 >> TABLE LOCK table `biocatalogue_production/trash_records` trx id 0 >> 342320684 lock mode IX >> TABLE LOCK table `biocatalogue_production/users` trx id 0 342320684 >> lock mode IX >> RECORD LOCKS space id 0 page no 48168 n bits 144 index `PRIMARY` of >> table `biocatalogue_production/users` trx id 0 342320684 lock_mode X >> locks rec but not gap >> Record lock, heap no 77 PHYSICAL RECORD: n_fields 19; compact format; >> info bits 32 >> 0: len 4; hex 8000023a; asc :;; 1: len 6; hex 00001467662c; asc >> gf,;; 2: len 7; hex 000000c82e0c3b; asc . ;;; 3: len 30; hex >> 6d617274696a6e2e76616e69657273656c406269676361742e756e696d61; asc >> martijn.vaniersel at bigcat.unima;...(truncated); 4: len 30; hex >> 636232663161323865373730346265303663303432643635343862333934; asc >> cb2f1a28e7704be06c042d6548b394;...(truncated); 5: len 30; hex >> 656364653634336538636635656439663534306561373633396530653264; asc >> ecde643e8cf5ed9f540ea7639e0e2d;...(truncated); 6: SQL NULL; 7: len 30; >> hex 303138363264363633636135633762643039376664313061656165323361; asc >> 01862d663ca5c7bd097fd10aeae23a;...(truncated); 8: len 18; hex >> 4d617274696a6e2076616e2049657273656c; asc Martijn van Iersel;; 9: SQL >> NULL; 10: SQL NULL; 11: len 21; hex >> 4d61617374726963687420556e6976657273697479; asc Maastricht >> University;; 12: len 11; hex 4e65746865726c616e6473; asc Netherlands;; >> 13: len 8; hex 800012480a162c06; asc H , ;; 14: len 8; hex >> 800012480a162c06; asc H , ;; 15: len 0; hex ; asc ;; 16: len 1; >> hex 80; asc ;; 17: SQL NULL; 18: SQL NULL; >> >> I think I have been looking at the problems for this locking and >> timouts at the database level. Actually, I am now convinced it is the >> application that needs to be investigated thoroughly. While trying to >> delete a user record for user with no activity, I get the following >> transactions. That does not look good at all. It took at least 3 >> minutes from the console to finally delete the user. I believe that >> the trashing of the records has a considerable adverse effect on the >> performance of the db and also since this table is basically a write >> table, it is locked when writes occur. Is there a way of turning >> trashing off? >> >> Eric >> >> >> >> ---TRANSACTION 0 342316486, ACTIVE 142 sec, process no 5339, OS thread >> id 1163782496 >> 5 lock struct(s), heap size 1216, undo log entries 3 >> MySQL thread id 26752, query id 352490227 pweb-4a.ebi.ac.uk >> 172.18.1.109 admin >> Trx read view will not see trx with id >= 0 342316487, sees < 0 342316487 >> TABLE LOCK table `biocatalogue_production/trash_records` trx id 0 >> 342316486 lock mode IX >> TABLE LOCK table `biocatalogue_production/annotation_versions` trx id >> 0 342316486 lock mode IX >> RECORD LOCKS space id 0 page no 42317 n bits 112 index `PRIMARY` of >> table `biocatalogue_production/annotation_versions` trx id 0 342316486 >> lock_mode X locks rec but not gap >> Record lock, heap no 25 PHYSICAL RECORD: n_fields 15; compact format; >> info bits 32 >> 0: len 4; hex 8000ddae; asc ;; 1: len 6; hex 0000146755c6; asc >> gU ;; 2: len 7; hex 000000c82d1f8f; asc - ;; 3: len 4; hex >> 8000d35e; asc ^;; 4: len 4; hex 80000001; asc ;; 5: SQL NULL; >> 6: len 4; hex 55736572; asc User;; 7: len 4; hex 8000001b; asc ;; >> 8: len 13; hex 536f61704f7065726174696f6e; asc SoapOperation;; 9: len >> 4; hex 8000000c; asc ;; 10: len 4; hex 80000002; asc ;; 11: >> len 7; hex 626c61626c6168; asc blablah;; 12: len 6; hex 537472696e67; >> asc String;; 13: len 8; hex 800012480a243906; asc H $9 ;; 14: len >> 8; hex 800012480a243906; asc H $9 ;; >> >> TABLE LOCK table `biocatalogue_production/annotations` trx id 0 >> 342316486 lock mode IX >> RECORD LOCKS space id 0 page no 60250 n bits 96 index `PRIMARY` of >> table `biocatalogue_production/annotations` trx id 0 342316486 >> lock_mode X locks rec but not gap >> Record lock, heap no 8 PHYSICAL RECORD: n_fields 14; compact format; >> info bits 32 >> 0: len 4; hex 8000d35e; asc ^;; 1: len 6; hex 0000146755c6; asc >> gU ;; 2: len 7; hex 000000c82d1fb8; asc - ;; 3: len 4; hex >> 55736572; asc User;; 4: len 4; hex 8000001b; asc ;; 5: len 13; hex >> 536f61704f7065726174696f6e; asc SoapOperation;; 6: len 4; hex >> 8000000c; asc ;; 7: len 4; hex 80000002; asc ;; 8: len 7; hex >> 626c61626c6168; asc blablah;; 9: len 6; hex 537472696e67; asc String;; >> 10: len 8; hex 800012480a243906; asc H $9 ;; 11: len 8; hex >> 800012480a243906; asc H $9 ;; 12: len 4; hex 80000001; asc ;; >> 13: SQL NULL; >> >> >> >> >> Jiten Bhagat wrote: >> >>> Eric, >>> >>> Please see the email below... >>> >>> Can you please activate Martijn's account (the one with the email >>> address) and delete any other accounts he may have inadvertently >>> created. >>> >>> Please also investigate why he was having so much trouble signing up!! I >>> didn't see any error emails about this, which is worrying.... >>> >>> Jits >>> >>> >>> -------- Original Message -------- >>> Subject: Re: [Biocatalogue-support] BioCatalogue feedback from >>> Martijn >>> van Iersel (martijn.vaniersel at bigcat.unimaas.nl) >>> Date: Wed, 16 Jun 2010 18:24:22 +0100 >>> From: Jiten Bhagat >>> To: martijn.vaniersel at bigcat.unimaas.nl >>> CC: contact at biocatalogue.org >>> References: >>> <4c19067885b17_315b1573bf7567d01f3 at pweb-4a.ebi.ac.uk.tmail> >>> >>> >>> >>> Hello Martijn, >>> >>> Sorry to hear about your troubles signing up. >>> >>> I have forwarded this on to the team that manages the system and we will >>> investigate this further to ensure it doesn't happen again. >>> >>> In the meantime, it looks like you are registered but not activated, so >>> we will manually activate your account first thing tomorrow morning (UK >>> time) and get back to you. >>> >>> Have a good evening. >>> >>> Jiten Bhagat >>> >>> >>> contact at biocatalogue.org wrote: >>> >>> >>>> BioCatalogue feedback from: Martijn van Iersel >>>> (martijn.vaniersel at bigcat.unimaas.nl) >>>> >>>> Subject: Lot's of trouble signing up >>>> >>>> Message: >>>> I had lots of trouble signing up. I tried to fill in the sign up >>>> form twice, each time it responded with an error message that my >>>> email address was incorrect. >>>> Later on two activation emails showed up in my inbox anyway. I >>>> clicked on the activation link in both, both led to a page saying >>>> that the activation code was incorrect. >>>> >>>> I also tried to sign up using one of my openid accounts, that didn't >>>> work either. >>>> _______________________________________________ >>>> Biocatalogue-support mailing list >>>> Biocatalogue-support at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-support >>>> >>>> >>> >>> >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From noreply at rubyforge.org Thu Jun 17 07:04:57 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 17 Jun 2010 07:04:57 -0400 (EDT) Subject: [BioCatalogue-developers] [2098] trunk: Work for trashing, in particular making it configurable. Message-ID: <20100617110457.ED3E21858368@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Jun 17 07:31:53 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 17 Jun 2010 07:31:53 -0400 (EDT) Subject: [BioCatalogue-developers] [2099] trunk/vendor/plugins/annotations/lib/annotations_version_fu.rb: Local modification to the Annotation plugin - annotation_version records are not deleted anymore when their parents are deleted . Message-ID: <20100617113153.19F1918583AA@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu Jun 17 08:10:52 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 17 Jun 2010 13:10:52 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: Biocatalogue and registration of parameterized REST Web services] Message-ID: <4C1A10CC.1070900@cs.man.ac.uk> FYI (see thread below) Their API doc wiki page is: http://www.bioontology.org/wiki/index.php/NCBO_REST_services. Jits -------- Original Message -------- Subject: Re: Biocatalogue and registration of parameterized REST Web services Date: Thu, 17 Jun 2010 13:09:28 +0100 From: Jiten Bhagat To: Trish Whetzel References: <4a5a32f326c49_5ca415cdb689f7d0187 at pweb-3b.ebi.ac.uk.tmail> <4A5AF36D.8070902 at ebi.ac.uk> <4A5B11B5.9010303 at cs.man.ac.uk> <1241B5A6-956F-46F0-B26E-CEE213A7EF51 at stanford.edu> <4A5B58FF.5060103 at ebi.ac.uk> <00d101ca04f7$3a3f7170$aebe5450$@edu> <4A5DA235.9000408 at cs.man.ac.uk> <5AF544CA-E9F2-4716-B110-9DB12893BA7A at stanford.edu> <4ADEE566.1000804 at cs.man.ac.uk> <03650A44-0293-4F87-B20A-481EF18BE23E at stanford.edu> <4BF39F36.4000001 at cs.man.ac.uk> Hello again Trish, Firstly, it's great to see the NCBO/BioPortal services in the BioCatalogue :-) It looks like they are composed of a number of high level groups of functionality (Ontologies, Search, Hierarchies, etc), which then have specific tasks / API calls within them (eg: "Get parents/children of a given concept in a specific ontology version"). Is this correct? Also, is it safe to assume that all these API calls are made to one "base URL" - http://rest.bioontology.org/bioportal/ ? If so, maybe we can treat everything as one REST service in the BioCatalogue and then add individual endpoints for each specific API call you have listed on the wiki page? So for example: REST Service: NCBO/BioPortal Endpoint 1: List all the latest version of ontologies Endpoint 2: Get a specific ontology based on a version id ... Endpoint 15: Search BioPortal ... Thereby collecting all the calls into one single location in the BioCatalogue. Then what we can do for you, in the near future, is implement some simple grouping mechanism so you are able to group these endpoints they way they are grouped on the wiki page. How does this sound to you? Note that the notion of an "endpoint" for REST services in the BioCatalogue is a very flexible one. You can either have a highly generic one, eg: /{parameters} ... and then describe all the possible parameters and outputs within it. Or, you can choose to have specific, "pre cooked" endpoints, like: /search/{query}[?{optional args}]&email={email_address} ... which correspond to the individual API calls / tasks in your case. Then we can go through and translate information like below into the parameters, representation and annotations required to document these endpoints: Signature: ./virtual/[parents|children]/{ontlogyId}/{conceptId}[?email={email_address}&{optional args}] Example: http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?email=example at example.org Example: http://rest.bioontology.org/bioportal/virtual/children/1032/Melanoma?email=example at example.org Optional arguments: level= - limits results to a given level in the hierarchy offset= ? results offset (used for pagination) limit= ? limits the number of results Example: http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?level=1&offset=1&limit=3&email=example at example.org Description: The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology. Do you have this information in a structured form? We might be able to write a script for you that automatically generates all this in the catalogue (and assign you the credit for annotations etc). Let me know what you think. It might be best to carry this conversation on Skype chat? Thanks, Jits Trish Whetzel wrote: > Can you help me sort out what information to add to the different > fields for the REST endpoints for the Web service documented > at: http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Hierarchy_Services. > Perhaps we can set-up a Skype session to review. > > Thanks! > Trish > > > On May 19, 2010, at 1:20 AM, Jiten Bhagat wrote: > >> Hi Trish, >> >> Yes it does now. My apologies for not informing you of this earlier! >> This was released a few weeks back and we've been testing it out to make >> sure it all works. >> >> For your REST services you should now see an "Endpoints" tab. For >> example, here: http://www.biocatalogue.org/services/2052#endpoints. >> >> Here you can specify the different endpoints (or calls) in your REST >> service and define the exact parameters and representations each >> endpoint has. These endpoints can be the parameterised calls that can be >> made to your service. >> >> The REST service itself has a base URL that all the endpoints build on, >> which can be edited to your liking. >> >> And in the next release (next week) the service monitoring will be fixed >> to use any "example" URLs that have been added to these endpoints. For >> example, the URL in the "Example Endpoint(s)" section here: >> http://www.biocatalogue.org/rest_methods/78 will be used in the >> monitoring of the service. This way you can define a specific URL that >> you know should work and we will use that to test the monitoring. >> >> We hope this is useful to you. Let us know if we can assist you in any >> way. And please feel free to give us any feedback/suggestions etc. >> >> Many thanks, >> Jits >> >> >> >> Trish Whetzel wrote: >>> Hi Jits, >>> >>> Does Biocatalogue support registration of parameterized REST Web >>> services? >>> >>> Trish >> > > Trish Whetzel, PhD > Outreach Coordinator > The National Center for Biomedical Ontology > Ph: 650-721-2378 > whetzel at stanford.edu > http://www.bioontology.org > > > From jits at cs.man.ac.uk Thu Jun 17 08:21:19 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 17 Jun 2010 13:21:19 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: Biocatalogue and registration of parameterized REST Web services] Message-ID: <4C1A133F.2000600@cs.man.ac.uk> Mannie, Have a look below. We need to revisit the documentation of adding endpoints etc. See also my previous email. Can you start a public wiki page on the help section of the wiki to document REST services please? Cheers, Jits -------- Original Message -------- Subject: Re: Biocatalogue and registration of parameterized REST Web services Date: Thu, 17 Jun 2010 13:19:20 +0100 From: Jiten Bhagat To: Trish Whetzel References: <4a5a32f326c49_5ca415cdb689f7d0187 at pweb-3b.ebi.ac.uk.tmail> <4A5AF36D.8070902 at ebi.ac.uk> <4A5B11B5.9010303 at cs.man.ac.uk> <1241B5A6-956F-46F0-B26E-CEE213A7EF51 at stanford.edu> <4A5B58FF.5060103 at ebi.ac.uk> <00d101ca04f7$3a3f7170$aebe5450$@edu> <4A5DA235.9000408 at cs.man.ac.uk> <5AF544CA-E9F2-4716-B110-9DB12893BA7A at stanford.edu> <4ADEE566.1000804 at cs.man.ac.uk> <03650A44-0293-4F87-B20A-481EF18BE23E at stanford.edu> <4BF39F36.4000001 at cs.man.ac.uk> <4C19A6AB.4000608 at cs.man.ac.uk> Hi Trish, When adding endpoints, you can specify the parameters as part of the string you use for the endpoint and the system picks these out and makes them required parameters. You can then individually add annotations etc for each of these parameters that were picked up, as well as add new (and optional) parameters. So adding this as an endpoint: /{nodeType}/{ontlogyVersionId}/{conceptId}?email={email_address} ... will create: Endpoint: /{nodeType}/{ontlogyVersionId}/{conceptId} Parameter 1: nodeType Parameter 2: ontlogyVersionId Parameter 3: conceptId Parameter 4: email_address We'll improve our documentation to explain this better :-) Jits Trish Whetzel wrote: > Thanks! For the parameters, our service is set-up as > /[parents|children]/{ontlogyVersionId}/{conceptId}[?email={email_address}&{optional > args}] and I was not sure if each parameter is entered separately on > the form or as one entry. > > Trish > > > On Jun 16, 2010, at 9:38 PM, Jiten Bhagat wrote: > >> Hi Trish, >> >> Certainly. I'll check out what you have so far, and the page you >> mentioned, and I'll send a separate email with some pointers / advice. >> >> My skype ID is j.bhagat. Feel free to add me on and we can set up a >> Skype session to go through things. >> >> As a side note, we've been having some issues with the site recently; >> have you had any trouble adding or deleting information? If so, very >> sorry about that. Were looking into this and will fix asap. >> >> Thanks, >> Jits >> >> >> >> Trish Whetzel wrote: >>> Can you help me sort out what information to add to the different >>> fields for the REST endpoints for the Web service documented >>> at: >>> http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Hierarchy_Services. >>> >>> Perhaps we can set-up a Skype session to review. >>> >>> Thanks! >>> Trish >>> >>> >>> On May 19, 2010, at 1:20 AM, Jiten Bhagat wrote: >>> >>>> Hi Trish, >>>> >>>> Yes it does now. My apologies for not informing you of this earlier! >>>> This was released a few weeks back and we've been testing it out to >>>> make >>>> sure it all works. >>>> >>>> For your REST services you should now see an "Endpoints" tab. For >>>> example, here: http://www.biocatalogue.org/services/2052#endpoints. >>>> >>>> Here you can specify the different endpoints (or calls) in your REST >>>> service and define the exact parameters and representations each >>>> endpoint has. These endpoints can be the parameterised calls that >>>> can be >>>> made to your service. >>>> >>>> The REST service itself has a base URL that all the endpoints build >>>> on, >>>> which can be edited to your liking. >>>> >>>> And in the next release (next week) the service monitoring will be >>>> fixed >>>> to use any "example" URLs that have been added to these endpoints. >>>> For >>>> example, the URL in the "Example Endpoint(s)" section here: >>>> http://www.biocatalogue.org/rest_methods/78 will be used in the >>>> monitoring of the service. This way you can define a specific URL that >>>> you know should work and we will use that to test the monitoring. >>>> >>>> We hope this is useful to you. Let us know if we can assist you in any >>>> way. And please feel free to give us any feedback/suggestions etc. >>>> >>>> Many thanks, >>>> Jits >>>> >>>> >>>> >>>> Trish Whetzel wrote: >>>>> Hi Jits, >>>>> >>>>> Does Biocatalogue support registration of parameterized REST Web >>>>> services? >>>>> >>>>> Trish >>>> >>> >>> Trish Whetzel, PhD >>> Outreach Coordinator >>> The National Center for Biomedical Ontology >>> Ph: 650-721-2378 >>> whetzel at stanford.edu >>> http://www.bioontology.org >>> >>> >>> >> > From ericnzuo at ebi.ac.uk Thu Jun 17 09:02:47 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 17 Jun 2010 14:02:47 +0100 Subject: [BioCatalogue-developers] [Fwd: Re: Biocatalogue and registration of parameterized REST Web services] In-Reply-To: <4C1A10CC.1070900@cs.man.ac.uk> References: <4C1A10CC.1070900@cs.man.ac.uk> Message-ID: <4C1A1CF7.4090409@ebi.ac.uk> > Note that the notion of an "endpoint" for REST services in the > BioCatalogue is a very flexible one. You can either have a highly > generic one, eg: > I am just wondering whether what we now call example endpoints are not really example resources? It seems that maybe changing the terminology would make notion of endpoint less ambiguous. Eric > /{parameters} > > ... and then describe all the possible parameters and outputs within it. > > Or, you can choose to have specific, "pre cooked" endpoints, like: > > /search/{query}[?{optional args}]&email={email_address} > > ... which correspond to the individual API calls / tasks in your case. > > Then we can go through and translate information like below into the > parameters, representation and annotations required to document these > endpoints: > > Signature: > ./virtual/[parents|children]/{ontlogyId}/{conceptId}[?email={email_address}&{optional > args}] > Example: > http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?email=example at example.org > Example: > http://rest.bioontology.org/bioportal/virtual/children/1032/Melanoma?email=example at example.org > Optional arguments: > level= - limits results to a given level in the hierarchy > offset= ? results offset (used for pagination) > limit= ? limits the number of results > Example: > http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?level=1&offset=1&limit=3&email=example at example.org > Description: The same as the previous services, but takes an ontology id > and returns parents from the latest version of that ontology. > > Do you have this information in a structured form? We might be able to > write a script for you that automatically generates all this in the > catalogue (and assign you the credit for annotations etc). > > Let me know what you think. It might be best to carry this conversation > on Skype chat? > > Thanks, > Jits > > > Trish Whetzel wrote: > >> Can you help me sort out what information to add to the different >> fields for the REST endpoints for the Web service documented >> at: http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Hierarchy_Services. >> Perhaps we can set-up a Skype session to review. >> >> Thanks! >> Trish >> >> >> On May 19, 2010, at 1:20 AM, Jiten Bhagat wrote: >> >> >>> Hi Trish, >>> >>> Yes it does now. My apologies for not informing you of this earlier! >>> This was released a few weeks back and we've been testing it out to make >>> sure it all works. >>> >>> For your REST services you should now see an "Endpoints" tab. For >>> example, here: http://www.biocatalogue.org/services/2052#endpoints. >>> >>> Here you can specify the different endpoints (or calls) in your REST >>> service and define the exact parameters and representations each >>> endpoint has. These endpoints can be the parameterised calls that can be >>> made to your service. >>> >>> The REST service itself has a base URL that all the endpoints build on, >>> which can be edited to your liking. >>> >>> And in the next release (next week) the service monitoring will be fixed >>> to use any "example" URLs that have been added to these endpoints. For >>> example, the URL in the "Example Endpoint(s)" section here: >>> http://www.biocatalogue.org/rest_methods/78 will be used in the >>> monitoring of the service. This way you can define a specific URL that >>> you know should work and we will use that to test the monitoring. >>> >>> We hope this is useful to you. Let us know if we can assist you in any >>> way. And please feel free to give us any feedback/suggestions etc. >>> >>> Many thanks, >>> Jits >>> >>> >>> >>> Trish Whetzel wrote: >>> >>>> Hi Jits, >>>> >>>> Does Biocatalogue support registration of parameterized REST Web >>>> services? >>>> >>>> Trish >>>> >> Trish Whetzel, PhD >> Outreach Coordinator >> The National Center for Biomedical Ontology >> Ph: 650-721-2378 >> whetzel at stanford.edu >> http://www.bioontology.org >> >> >> >> > > > _______________________________________________ > 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 issues at mygrid.org.uk Thu Jun 17 09:44:18 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 17 Jun 2010 14:44:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-399) Allow the user to be post to biocatalogue using stored credentials In-Reply-To: <5030519.6299.1276782255457.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24882724.6300.1276782258724.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-399?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-399. ------------------------------------ Resolution: Fixed > Allow the user to be post to biocatalogue using stored credentials > ------------------------------------------------------------------ > > Key: BIOCAT-399 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-399 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 17 09:44:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 17 Jun 2010 14:44:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-399) Allow the user to be post to biocatalogue using stored credentials Message-ID: <5030519.6299.1276782255457.JavaMail.jira@rosalind.cs.man.ac.uk> Allow the user to be post to biocatalogue using stored credentials ------------------------------------------------------------------ Key: BIOCAT-399 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-399 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 17 09:44:19 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 17 Jun 2010 14:44:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-399) Allow the user to be post to biocatalogue using stored credentials In-Reply-To: <5030519.6299.1276782255457.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32537990.6301.1276782259884.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-399?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-399. ---------------------------------- > Allow the user to be post to biocatalogue using stored credentials > ------------------------------------------------------------------ > > Key: BIOCAT-399 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-399 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Thu Jun 17 12:00:20 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 17 Jun 2010 17:00:20 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromAminoAcidSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromAminoAcidSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1000 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Jun 17 14:03:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 17 Jun 2010 19:03:06 +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 utopia at cs.man.ac.uk Thu Jun 17 22:55:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 18 Jun 2010 03:55:33 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'CLUSTAL W multiple alignment (CNRS IBCP)' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'CLUSTAL W multiple alignment (CNRS IBCP)' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/91 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jun 18 00:16:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 18 Jun 2010 05:16:33 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:solvateStructureWithLigandsFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:solvateStructureWithLigandsFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1180 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 Jun 18 05:17:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 18 Jun 2010 10:17:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-400) some example endpoints do not resolve to valid URI Message-ID: <31506485.6312.1276852635419.JavaMail.jira@rosalind.cs.man.ac.uk> some example endpoints do not resolve to valid URI --------------------------------------------------- Key: BIOCAT-400 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-400 Project: BioCatalogue Issue Type: Bug Components: REST Services Support Reporter: Eric Nzuobontane Assignee: Jiten Bhagat Some example endpoints seem to be displayed as relative to the base end point. This affects monitoring such endpoints as they would resolve to invalid URI. Example is http://www.biocatalogue.org/services/2705#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 Fri Jun 18 05:17:18 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 18 Jun 2010 10:17:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-400) some example endpoints do not resolve to valid URI In-Reply-To: <31506485.6312.1276852635419.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21220240.6313.1276852638832.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-400?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-400: --------------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > some example endpoints do not resolve to valid URI > --------------------------------------------------- > > Key: BIOCAT-400 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-400 > Project: BioCatalogue > Issue Type: Bug > Components: REST Services Support > Reporter: Eric Nzuobontane > Assignee: Mannie Tagarira > > Some example endpoints seem to be displayed as relative to the base end point. This affects monitoring such endpoints as they would resolve to invalid URI. Example is http://www.biocatalogue.org/services/2705#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 Fri Jun 18 05:24:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 18 Jun 2010 10:24:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-400) some example endpoints do not resolve to valid URI In-Reply-To: <31506485.6312.1276852635419.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10264705.6314.1276853055337.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-400?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15283#action_15283 ] Jiten Bhagat commented on BIOCAT-400: ------------------------------------- I am working with Trish to resolve this (ie: update the annotations to be absolute examples). We can't go about changing annotation values so I don't see that we can do much on our end. > some example endpoints do not resolve to valid URI > --------------------------------------------------- > > Key: BIOCAT-400 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-400 > Project: BioCatalogue > Issue Type: Bug > Components: REST Services Support > Reporter: Eric Nzuobontane > Assignee: Mannie Tagarira > > Some example endpoints seem to be displayed as relative to the base end point. This affects monitoring such endpoints as they would resolve to invalid URI. Example is http://www.biocatalogue.org/services/2705#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 ericnzuo at ebi.ac.uk Fri Jun 18 05:07:59 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 18 Jun 2010 10:07:59 +0100 Subject: [BioCatalogue-developers] re-indexing the live site Message-ID: <4C1B376F.1060907@ebi.ac.uk> Hi Guys, Unfortunately the re-indexing of the live site failed last night. So I have restarted the process this morning and it is progressing normally. When this is done, I will work with Franck to make sure the timing issues are no longer observable. In the longer term, it will be necessary to examine and possibly optimize the connections between the search server and the CRUD operations on the database. 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 issues at mygrid.org.uk Fri Jun 18 05:28:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 18 Jun 2010 10:28:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-401) Start a wiki page to document REST Services Message-ID: <25813643.6315.1276853295310.JavaMail.jira@rosalind.cs.man.ac.uk> Start a wiki page to document REST Services ------------------------------------------- Key: BIOCAT-401 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-401 Project: BioCatalogue Issue Type: New Feature Components: Wiki Reporter: Mannie Tagarira Assignee: Mannie Tagarira -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 18 05:31:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 18 Jun 2010 10:31:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-402) Make the exported spreadsheet show all "description" (and possibly "example_data") annotations Message-ID: <9446032.6316.1276853475352.JavaMail.jira@rosalind.cs.man.ac.uk> Make the exported spreadsheet show all "description" (and possibly "example_data") annotations ---------------------------------------------------------------------------------------------- Key: BIOCAT-402 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-402 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 18 05:31:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 18 Jun 2010 10:31:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-402) Make the exported spreadsheet show all "description" (and possibly "example_data") annotations In-Reply-To: <9446032.6316.1276853475352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <62171.6317.1276853476489.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-402?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-402 started by Mannie Tagarira. > Make the exported spreadsheet show all "description" (and possibly "example_data") annotations > ---------------------------------------------------------------------------------------------- > > Key: BIOCAT-402 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-402 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Fri Jun 18 05:32:08 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 18 Jun 2010 10:32:08 +0100 Subject: [BioCatalogue-developers] re-indexing the live site In-Reply-To: <4C1B376F.1060907@ebi.ac.uk> References: <4C1B376F.1060907@ebi.ac.uk> Message-ID: <4C1B3D18.3090705@cs.man.ac.uk> Eric, OK, cool. > [...] examine and possibly optimize the connections between the search > server and the CRUD operations on the database. It doesn't sound to me like this is the major issue; I think it's the search server itself that needs a closer look and "optimising", and is sometimes being problematic and a blocker. Jits Eric Nzuobontane wrote: > Hi Guys, > > Unfortunately the re-indexing of the live site failed last night. So I > have restarted the process this morning and it is progressing > normally. When this is done, I will work with Franck to make sure the > timing issues are no longer observable. In the longer term, it will be > necessary to examine and possibly optimize the connections between the > search server and the CRUD operations on the database. > > Eric > From issues at mygrid.org.uk Fri Jun 18 05:33:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 18 Jun 2010 10:33:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-403) In the exported spreadsheet, differentiate between existing annotations and new annotations Message-ID: <32711689.6318.1276853595313.JavaMail.jira@rosalind.cs.man.ac.uk> In the exported spreadsheet, differentiate between existing annotations and new annotations ------------------------------------------------------------------------------------------- Key: BIOCAT-403 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-403 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 18 05:33:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 18 Jun 2010 10:33:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-404) The exported spreadsheet should have an extra worksheet for "Help" Message-ID: <11257636.6319.1276853596321.JavaMail.jira@rosalind.cs.man.ac.uk> The exported spreadsheet should have an extra worksheet for "Help" ------------------------------------------------------------------ Key: BIOCAT-404 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-404 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 18 05:37:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 18 Jun 2010 10:37:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-405) Create 2 wiki pages for curation app: one to serve as a "front page" and the other for developers Message-ID: <17552405.6320.1276853835309.JavaMail.jira@rosalind.cs.man.ac.uk> Create 2 wiki pages for curation app: one to serve as a "front page" and the other for developers ------------------------------------------------------------------------------------------------- Key: BIOCAT-405 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-405 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition, Wiki Reporter: Mannie Tagarira Assignee: Mannie Tagarira -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ytanoh at cs.man.ac.uk Fri Jun 18 05:47:35 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 18 Jun 2010 10:47:35 +0100 Subject: [BioCatalogue-developers] re-indexing the live site In-Reply-To: <4C1B376F.1060907@ebi.ac.uk> References: <4C1B376F.1060907@ebi.ac.uk> Message-ID: <122BC4A1-D369-4402-B80F-7C84F41C7FE0@cs.man.ac.uk> A lot of EBI services failed last night as well... something to do with you guys being kicked out at 5.30pm. Most of them are back on track. Franck On 18 Jun 2010, at 10:07, Eric Nzuobontane wrote: > Hi Guys, > > Unfortunately the re-indexing of the live site failed last night. So > I have restarted the process this morning and it is progressing > normally. When this is done, I will work with Franck to make sure > the timing issues are no longer observable. In the longer term, it > will be necessary to examine and possibly optimize the connections > between the search server and the CRUD operations on the database. > > 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 Fri Jun 18 06:00:47 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 18 Jun 2010 11:00:47 +0100 Subject: [BioCatalogue-developers] re-indexing the live site In-Reply-To: <122BC4A1-D369-4402-B80F-7C84F41C7FE0@cs.man.ac.uk> References: <4C1B376F.1060907@ebi.ac.uk> <122BC4A1-D369-4402-B80F-7C84F41C7FE0@cs.man.ac.uk> Message-ID: <4C1B43CF.4030503@ebi.ac.uk> Franck Tanoh wrote: > A lot of EBI services failed last night as well... something to do > with you guys being kicked out at 5.30pm. > Most of them are back on track. Well there was a problem with the server hosting those services. I believe the problem is rectified now. It is good to see that the BioCatalogue is picking up these things. Eric > > Franck > > On 18 Jun 2010, at 10:07, Eric Nzuobontane wrote: > >> Hi Guys, >> >> Unfortunately the re-indexing of the live site failed last night. So >> I have restarted the process this morning and it is progressing >> normally. When this is done, I will work with Franck to make sure the >> timing issues are no longer observable. In the longer term, it will >> be necessary to examine and possibly optimize the connections between >> the search server and the CRUD operations on the database. >> >> 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 noreply at rubyforge.org Fri Jun 18 09:32:35 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 18 Jun 2010 09:32:35 -0400 (EDT) Subject: [BioCatalogue-developers] [2100] trunk: disable monitoring for archived services Message-ID: <20100618133235.60F0D1858384@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 18 09:46:18 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 18 Jun 2010 14:46:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-303) Investigate database timout errors when deleting entries Message-ID: <18337052.6324.1276868778740.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-303?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-303. ------------------------------------- Original Estimate: 1 day Remaining Estimate: 1 day Resolution: Fixed > Investigate database timout errors when deleting entries > -------------------------------------------------------- > > Key: BIOCAT-303 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-303 > Project: BioCatalogue > Issue Type: Bug > Components: Server Management > Environment: MySQL datatabase, RoR activerecord > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > When deleting some errors the following timeout error occurs > Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `service_versions` WHERE `id` = 609 > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 18 09:50:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 18 Jun 2010 14:50:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-324) Archived services should not be monitored anymore In-Reply-To: <5845695.58.1273658296994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12177600.6325.1276869015346.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-324?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15285#action_15285 ] Eric Nzuobontane commented on BIOCAT-324: ----------------------------------------- Monitoring for archived services is disabled by disabling all service tests. > 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 Fri Jun 18 09:46:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 18 Jun 2010 14:46:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-303) Investigate database timout errors when deleting entries Message-ID: <15769673.6323.1276868775422.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-303?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15284#action_15284 ] Eric Nzuobontane commented on BIOCAT-303: ----------------------------------------- Apparently the connection to search server was taking too long making updates and inserts to the database to time out. Trashing disabled and index cleared improved the performance. > Investigate database timout errors when deleting entries > -------------------------------------------------------- > > Key: BIOCAT-303 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-303 > Project: BioCatalogue > Issue Type: Bug > Components: Server Management > Environment: MySQL datatabase, RoR activerecord > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > When deleting some errors the following timeout error occurs > Mysql::Error: Lock wait timeout exceeded; try restarting transaction: DELETE FROM `service_versions` WHERE `id` = 609 > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 18 09:50:20 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 18 Jun 2010 14:50:20 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-324) Archived services should not be monitored anymore In-Reply-To: <5845695.58.1273658296994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16185779.6326.1276869020248.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-324?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-324. ------------------------------------- Original Estimate: 1 day Remaining Estimate: 1 day Resolution: Fixed > 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 > Original Estimate: 1 day > Remaining Estimate: 1 day > > 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 noreply at rubyforge.org Fri Jun 18 10:05:10 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 18 Jun 2010 10:05:10 -0400 (EDT) Subject: [BioCatalogue-developers] [2101] trunk/lib/bio_catalogue/monitoring.rb: use archived? instead of archived_at Message-ID: <20100618140510.71EFB185835E@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jun 21 05:35:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 21 Jun 2010 05:35:09 -0400 (EDT) Subject: [BioCatalogue-developers] [2102] trunk/script/biocatalogue/monitoring_report.rb: order failing service by descending duration of failure Message-ID: <20100621093509.C90F7185834E@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Mon Jun 21 06:25:56 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 21 Jun 2010 11:25:56 +0100 Subject: [BioCatalogue-developers] Monitoring report in drop box Message-ID: <4C1F3E34.7040703@ebi.ac.uk> Hi Franck, I have put a monitoring report in dropbox. It is not the most pretty report just an html table with the listing of the failing services. Thing now is that they are ordered according to how long they have been failing, with longest duration at the top. You may want to have a look at this to see which services need a follow up, archiving... 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 issues at mygrid.org.uk Mon Jun 21 06:29:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 21 Jun 2010 11:29:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-355) recreate the search index(by running solr reindex) In-Reply-To: <4344127.1657.1274908276998.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24329796.6340.1277116155439.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-355?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-355. ------------------------------------- Resolution: Fixed > 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 > 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 Mon Jun 21 06:29:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 21 Jun 2010 11:29:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-359) Cleanup pre-release notes and move them to the release notes section In-Reply-To: <33157500.1664.1274955616998.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6930588.6341.1277116156639.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-359?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-359. ------------------------------------- Resolution: Fixed Done > 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 > Original Estimate: 1 hour > Remaining Estimate: 1 hour > > 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 ytanoh at cs.man.ac.uk Mon Jun 21 06:30:36 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 21 Jun 2010 11:30:36 +0100 Subject: [BioCatalogue-developers] BioMoby failing Message-ID: Hi guys, All the BioMoby we imported from seekda are failing (WSDL not accessible) and some from the INB guys as well. http://www.biocatalogue.org/service_providers/37#services http://www.biocatalogue.org/service_providers/141#services http://www.biocatalogue.org/service_providers/306#services http://www.biocatalogue.org/service_providers/132#services http://www.biocatalogue.org/service_providers/32#services http://www.biocatalogue.org/service_providers/134#services http://www.biocatalogue.org/service_providers/10#services http://www.biocatalogue.org/service_providers/119#services If by tomorrow they are not back I'll ask the BioMoby guys. Franck, -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jun 21 06:33:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 21 Jun 2010 11:33:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (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: <6471788.6343.1277116397703.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 resolved BIOCAT-354. ------------------------------------- Resolution: Fixed Release deployed. > 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 Mon Jun 21 06:33:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 21 Jun 2010 11:33:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (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: <21253295.6342.1277116395336.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-356?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-356. ------------------------------------- Resolution: Fixed Failed test were due stricter rule that responses to empty soap messages in must be valid soap faults only. Rule now relaxed to any xml response > 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 ericnzuo at ebi.ac.uk Mon Jun 21 06:43:51 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 21 Jun 2010 11:43:51 +0100 Subject: [BioCatalogue-developers] monitoring status for http://www.biocatalogue.org/services/2705 Message-ID: <4C1F4267.4020507@ebi.ac.uk> Hi, Currently we have an amber sign on the service indicating that there may be a problem. I am not very comfortable with this as it is the first service in the listing and it might actually be working fine. Just that the given endpoint does not resolve to a valid url (does not point to any resource). http://www.biocatalogue.org/services/2705 We could disable this test until the point when we know we can monitor it properly. What do you think? -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ytanoh at cs.man.ac.uk Mon Jun 21 06:46:03 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 21 Jun 2010 11:46:03 +0100 Subject: [BioCatalogue-developers] Monitoring report in drop box In-Reply-To: <4C1F3E34.7040703@ebi.ac.uk> References: <4C1F3E34.7040703@ebi.ac.uk> Message-ID: Hi Eric, That's a really good start Cheers, Franck On 21 June 2010 11:25, Eric Nzuobontane wrote: > > Hi Franck, > > I have put a monitoring report in dropbox. It is not the most pretty report > just an html table with the listing of the failing services. Thing now is > that they are ordered according to how long they have been failing, with > longest duration at the top. You may want to have a look at this to see > which services need a follow up, archiving... > > 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 > ================================== > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jun 21 06:48:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 21 Jun 2010 11:48:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-334) Monitor example endpoints for REST services In-Reply-To: <13728321.108.1273826057119.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28823811.6345.1277117295355.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 ] Eric Nzuobontane resolved BIOCAT-334. ------------------------------------- Resolution: Fixed > 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 Mon Jun 21 07:04:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 21 Jun 2010 12:04:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-392) Paginate search results In-Reply-To: <1507555.5419.1276601115303.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4879449.6352.1277118255328.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-392?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-392: ----------------------------------- Summary: Paginate search results (was: Show more search results) Priority: Blocker (was: Major) > Paginate search results > ----------------------- > > Key: BIOCAT-392 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-392 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > > The user requested the ability to view more search results via pagination similar to that used when browsing services in the main window. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 21 07:06:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 21 Jun 2010 12:06:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-395) Allow the user to change their Preferences In-Reply-To: <15547864.5422.1276601715309.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3252185.6353.1277118375366.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-395?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-395. ------------------------------------ Resolution: Responded I implemented the support to read and write a config file... > Allow the user to change their Preferences > ------------------------------------------ > > Key: BIOCAT-395 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-395 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > Add a preference pane to allow the user to specify their own parameters e.g. how many services should be returned in a search, custom biocatalogue host, etc -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ytanoh at cs.man.ac.uk Mon Jun 21 07:07:57 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 21 Jun 2010 12:07:57 +0100 Subject: [BioCatalogue-developers] monitoring status for http://www.biocatalogue.org/services/2705 In-Reply-To: <4C1F4267.4020507@ebi.ac.uk> References: <4C1F4267.4020507@ebi.ac.uk> Message-ID: That's the same issue with the DDBJ service ... and I'm happy with that either. >We could disable this test until the point when we know we can monitor it properly. That will be my view too but i think we need to check with others. Also if you can come up with a better way to monitor then that will be good too. Franck On 21 June 2010 11:43, Eric Nzuobontane wrote: > Hi, > > Currently we have an amber sign on the service indicating that there may be > a problem. I am not very comfortable with this as it is the first service in > the listing and it might actually be working fine. Just that the given > endpoint does not resolve to a valid url (does not point to any resource). > > http://www.biocatalogue.org/services/2705 > > > We could disable this test until the point when we know we can monitor it > properly. > > > What do you think? > > > -- > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jun 21 07:08:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 21 Jun 2010 12:08:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-403) In the exported spreadsheet, differentiate between existing annotations and new annotations In-Reply-To: <32711689.6318.1276853595313.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <86407.6354.1277118496073.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-403?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira reassigned BIOCAT-403: -------------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > In the exported spreadsheet, differentiate between existing annotations and new annotations > ------------------------------------------------------------------------------------------- > > Key: BIOCAT-403 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-403 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jun 21 07:08:19 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 21 Jun 2010 12:08:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-403) In the exported spreadsheet, differentiate between existing annotations and new annotations In-Reply-To: <32711689.6318.1276853595313.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4351858.6355.1277118499260.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-403?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-403 started by Mannie Tagarira. > In the exported spreadsheet, differentiate between existing annotations and new annotations > ------------------------------------------------------------------------------------------- > > Key: BIOCAT-403 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-403 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jun 21 07:08:20 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 21 Jun 2010 12:08:20 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-403) In the exported spreadsheet, differentiate between existing annotations and new annotations In-Reply-To: <32711689.6318.1276853595313.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26365575.6356.1277118500111.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-403?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15296#action_15296 ] Mannie Tagarira commented on BIOCAT-403: ---------------------------------------- Implemented support for descriptions... Cell borders need to be implemented... > In the exported spreadsheet, differentiate between existing annotations and new annotations > ------------------------------------------------------------------------------------------- > > Key: BIOCAT-403 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-403 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jun 21 07:10:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 21 Jun 2010 12:10:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-402) Make the exported spreadsheet show all "description" (and possibly "example_data") annotations In-Reply-To: <9446032.6316.1276853475352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32986878.6357.1277118615471.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-402?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-402 stopped by Mannie Tagarira. > Make the exported spreadsheet show all "description" (and possibly "example_data") annotations > ---------------------------------------------------------------------------------------------- > > Key: BIOCAT-402 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-402 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jun 21 07:10:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 21 Jun 2010 12:10:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-402) Make the exported spreadsheet show all "description" (and possibly "example_data") annotations In-Reply-To: <9446032.6316.1276853475352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23706926.6358.1277118616780.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-402?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15297#action_15297 ] Mannie Tagarira commented on BIOCAT-402: ---------------------------------------- Implemented support to show all description annotations... > Make the exported spreadsheet show all "description" (and possibly "example_data") annotations > ---------------------------------------------------------------------------------------------- > > Key: BIOCAT-402 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-402 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jun 21 07:12:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 21 Jun 2010 12:12:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-396) Fix panel conflict in the Selected Services Window In-Reply-To: <7420561.5423.1276601955395.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10628048.6359.1277118735306.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-396?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15298#action_15298 ] Mannie Tagarira commented on BIOCAT-396: ---------------------------------------- It turns out that the error only occurs when a users rapidly deselects the selected services (sequentially) via the Selected Services window. This could be something to do with Threads clashing and not hiding/showing panels properly. > Fix panel conflict in the Selected Services Window > -------------------------------------------------- > > Key: BIOCAT-396 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-396 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > After making selections and deselecting all those services, and then selecting another service, there is some panel overlap... Some panel has not been hidden or removed; this has to be handled properly. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 21 07:14:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 21 Jun 2010 12:14:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-406) Test app in other OSs apart from Mac OS X 10.5 Message-ID: <31264361.6361.1277118856217.JavaMail.jira@rosalind.cs.man.ac.uk> Test app in other OSs apart from Mac OS X 10.5 ---------------------------------------------- Key: BIOCAT-406 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-406 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira Priority: Blocker The app was developed on Mac OS X 10.5, and the main user (the same user who was testing the app) uses the same operating system. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 21 08:53:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 21 Jun 2010 13:53:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-407) Add BioCatalogue NAR reference to homepage Message-ID: <21597958.6378.1277124795309.JavaMail.jira@rosalind.cs.man.ac.uk> Add BioCatalogue NAR reference to homepage ------------------------------------------ Key: BIOCAT-407 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-407 Project: BioCatalogue Issue Type: New Feature Components: Web Interface Reporter: Jiten Bhagat Assignee: Jiten Bhagat ... so people know what to use to cite the 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 utopia at cs.man.ac.uk Tue Jun 22 00:38:41 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 22 Jun 2010 05:38:41 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMetaAlignmentGFF' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMetaAlignmentGFF' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/781 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Tue Jun 22 04:29:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 22 Jun 2010 09:29:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-408) Write addiction endpoint checking tests where basic test fails Message-ID: <23193000.6462.1277195355409.JavaMail.jira@rosalind.cs.man.ac.uk> Write addiction endpoint checking tests where basic test fails -------------------------------------------------------------- Key: BIOCAT-408 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-408 Project: BioCatalogue Issue Type: Task Components: Service Monitoring Environment: RoR Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Add supplementary tests for the service where basic checks fails. For the endpoint of soap services, try connecting to 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 Jun 22 04:29:17 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 22 Jun 2010 09:29:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-408) Write addiction endpoint checking tests where basic test fails In-Reply-To: <23193000.6462.1277195355409.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1382028.6463.1277195357882.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-408?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-408 started by Eric Nzuobontane. > Write addiction endpoint checking tests where basic test fails > -------------------------------------------------------------- > > Key: BIOCAT-408 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-408 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Environment: RoR > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > Add supplementary tests for the service where basic checks fails. For the endpoint of soap services, try connecting to 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 noreply at rubyforge.org Tue Jun 22 04:53:06 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 22 Jun 2010 04:53:06 -0400 (EDT) Subject: [BioCatalogue-developers] [2103] trunk/app/models/soap_service.rb: added test to connect to services to check end point availability Message-ID: <20100622085307.C69BC1858363@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Jun 22 04:53:45 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 22 Jun 2010 04:53:45 -0400 (EDT) Subject: [BioCatalogue-developers] [2104] trunk/lib/bio_catalogue/monitoring.rb: additional check for end point availability Message-ID: <20100622085345.E626C1858370@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Tue Jun 22 07:21:51 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 22 Jun 2010 12:21:51 +0100 Subject: [BioCatalogue-developers] BioMoby failing In-Reply-To: References: Message-ID: They're up again ... Franck On 21 June 2010 11:30, Franck Tanoh wrote: > Hi guys, > > All the BioMoby we imported from seekda are failing (WSDL not accessible) > and some from the INB guys as well. > http://www.biocatalogue.org/service_providers/37#services > http://www.biocatalogue.org/service_providers/141#services > http://www.biocatalogue.org/service_providers/306#services > http://www.biocatalogue.org/service_providers/132#services > http://www.biocatalogue.org/service_providers/32#services > http://www.biocatalogue.org/service_providers/134#services > http://www.biocatalogue.org/service_providers/10#services > http://www.biocatalogue.org/service_providers/119#services > > If by tomorrow they are not back I'll ask the BioMoby guys. > > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue Jun 22 07:40:10 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 22 Jun 2010 12:40:10 +0100 Subject: [BioCatalogue-developers] BioMoby failing In-Reply-To: References: Message-ID: <4C20A11A.6050601@ebi.ac.uk> possibly a server went down. Franck Tanoh wrote: > They're up again ... > > Franck > > On 21 June 2010 11:30, Franck Tanoh > wrote: > > Hi guys, > > All the BioMoby we imported from seekda are failing (WSDL not > accessible) and some from the INB guys as well. > http://www.biocatalogue.org/service_providers/37#services > http://www.biocatalogue.org/service_providers/141#services > http://www.biocatalogue.org/service_providers/306#services > http://www.biocatalogue.org/service_providers/132#services > http://www.biocatalogue.org/service_providers/32#services > http://www.biocatalogue.org/service_providers/134#services > http://www.biocatalogue.org/service_providers/10#services > http://www.biocatalogue.org/service_providers/119#services > > If by tomorrow they are not back I'll ask the BioMoby guys. > > 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 ytanoh at cs.man.ac.uk Tue Jun 22 09:53:35 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 22 Jun 2010 14:53:35 +0100 Subject: [BioCatalogue-developers] wiki is down.. Message-ID: http://www.biocatalogue.org/wiki/ Servers updates at the EBI? or something to do with our wiki? ...it's been off for about 1h Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Jun 22 10:08:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 22 Jun 2010 15:08:33 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getPubMed' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getPubMed' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1090 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ytanoh at cs.man.ac.uk Tue Jun 22 10:47:26 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 22 Jun 2010 15:47:26 +0100 Subject: [BioCatalogue-developers] wiki is down.. In-Reply-To: References: Message-ID: it's back now .... On 22 Jun 2010, at 14:53, Franck Tanoh wrote: > http://www.biocatalogue.org/wiki/ > > Servers updates at the EBI? or something to do with our > wiki? ...it's been off for about 1h > > Franck > > -- > "Science knows no country, because knowledge belongs to humanity, > and is the torch which illuminates the world." - Louis Pasteur > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue Jun 22 10:55:41 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 22 Jun 2010 15:55:41 +0100 Subject: [BioCatalogue-developers] wiki is down.. In-Reply-To: References: Message-ID: <4C20CEED.1060905@ebi.ac.uk> We had a power outage a short while ago. So all services may not be up. I am going through to see if all services are restarted properly. Eric Franck Tanoh wrote: > http://www.biocatalogue.org/wiki/ > > Servers updates at the EBI? or something to do with our wiki? ...it's > been off for about 1h > > Franck > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- 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 Jun 22 11:38:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 22 Jun 2010 16:38:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-402) Make the exported spreadsheet show all "description" (and possibly "example_data") annotations In-Reply-To: <9446032.6316.1276853475352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16793099.6509.1277221096311.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-402?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-402. ------------------------------------ Resolution: Fixed > Make the exported spreadsheet show all "description" (and possibly "example_data") annotations > ---------------------------------------------------------------------------------------------- > > Key: BIOCAT-402 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-402 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 22 11:38:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 22 Jun 2010 16:38:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-409) Implement cache for all performed searched Message-ID: <7774214.6508.1277221095333.JavaMail.jira@rosalind.cs.man.ac.uk> Implement cache for all performed searched ------------------------------------------ Key: BIOCAT-409 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-409 Project: BioCatalogue Issue Type: Sub-task Components: Content Acquisition Reporter: Mannie Tagarira Assignee: Mannie Tagarira 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 Jun 22 12:10:29 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 22 Jun 2010 17:10:29 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-392) Paginate search results In-Reply-To: <1507555.5419.1276601115303.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4845086.6522.1277223029791.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-392?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-392. ------------------------------------ Resolution: Fixed > Paginate search results > ----------------------- > > Key: BIOCAT-392 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-392 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > > The user requested the ability to view more search results via pagination similar to that used when browsing services in the main window. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 22 12:10:30 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 22 Jun 2010 17:10:30 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-392) Paginate search results In-Reply-To: <1507555.5419.1276601115303.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30188367.6523.1277223030651.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-392?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-392. ---------------------------------- > Paginate search results > ----------------------- > > Key: BIOCAT-392 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-392 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > > The user requested the ability to view more search results via pagination similar to that used when browsing services in the main window. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 22 12:10:28 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 22 Jun 2010 17:10:28 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-392) Paginate search results In-Reply-To: <1507555.5419.1276601115303.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24061180.6521.1277223028883.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-392?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-392 stopped by Mannie Tagarira. > Paginate search results > ----------------------- > > Key: BIOCAT-392 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-392 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > > The user requested the ability to view more search results via pagination similar to that used when browsing services in the main window. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 22 13:02:51 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 22 Jun 2010 13:02:51 -0400 (EDT) Subject: [BioCatalogue-developers] [2105] trunk/config/routes.rb: REST API work: allow HTTP POST calls on the /search.:format endpoint. Message-ID: <20100622170251.2B4C3185834E@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Jun 22 13:28:04 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 22 Jun 2010 13:28:04 -0400 (EDT) Subject: [BioCatalogue-developers] [2106] trunk: Fix for handling of Mime Types, provided by Tod Jackson from Emory University. Message-ID: <20100622172804.F12EB1858317@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jun 23 08:27:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 23 Jun 2010 13:27:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-410) Unable to submit feedback from IE8 Message-ID: <24362963.6567.1277296035304.JavaMail.jira@rosalind.cs.man.ac.uk> Unable to submit feedback from IE8 ---------------------------------- Key: BIOCAT-410 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-410 Project: BioCatalogue Issue Type: Bug Components: Web Interface Environment: Internet Explorer 8 Reporter: Sergejs Aleksejevs Assignee: Jiten Bhagat The contact form (on /contact) is broken on IE8 due to the Security Number checking method. This is due to the inconsistencies in the way browsers treat the String#split method (which is what is used under the hood). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 23 08:29:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 23 Jun 2010 13:29:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-410) Unable to submit feedback from IE8 In-Reply-To: <24362963.6567.1277296035304.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13270983.6569.1277296156277.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-410?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15324#action_15324 ] Jiten Bhagat commented on BIOCAT-410: ------------------------------------- The above mentioned solution has been packaged into this toolkit: http://xregexp.com/ > Unable to submit feedback from IE8 > ---------------------------------- > > Key: BIOCAT-410 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-410 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Environment: Internet Explorer 8 > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Remaining Estimate: 2 hours > > The contact form (on /contact) is broken on IE8 due to the Security Number checking method. > This is due to the inconsistencies in the way browsers treat the String#split method (which is what is used under the hood). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 23 08:37:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 23 Jun 2010 13:37:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-367) Fix issue with breadcrumbs still being generated even on error pages In-Reply-To: <28275846.1959.1275558137646.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17228183.6570.1277296635337.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-367?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-367. ------------------------------- > Fix issue with breadcrumbs still being generated even on error pages > -------------------------------------------------------------------- > > Key: BIOCAT-367 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-367 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 1 hour, 30 minutes > Remaining Estimate: 30 minutes > > Currently, if an error page is rendered the system will still try to build the breadcrumbs bar. This is not good because further errors are then generated if objects are not accessible within the _breadcrumbs partial. > This is causing lots of error emails to be sent for the /soap_operations and /rest_methods endpoints. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 23 08:46:55 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 23 Jun 2010 08:46:55 -0400 (EDT) Subject: [BioCatalogue-developers] [2107] trunk: [BIOCAT-410] Bugfixes for the contact form ( to do with Javascript issues across browsers). Message-ID: <20100623124655.955EC1858374@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jun 23 08:48:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 23 Jun 2010 13:48:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-410) Unable to submit feedback from IE8 In-Reply-To: <24362963.6567.1277296035304.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23925367.6572.1277297295325.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-410?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-410. --------------------------------- Resolution: Fixed Done in revision 2107 > Unable to submit feedback from IE8 > ---------------------------------- > > Key: BIOCAT-410 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-410 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Environment: Internet Explorer 8 > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Remaining Estimate: 2 hours > > The contact form (on /contact) is broken on IE8 due to the Security Number checking method. > This is due to the inconsistencies in the way browsers treat the String#split method (which is what is used under the hood). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 23 08:51:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 23 Jun 2010 13:51:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-411) Broken layout for operations view of KEGG service (/services/11#operations) in IE8 Message-ID: <18208170.6573.1277297475353.JavaMail.jira@rosalind.cs.man.ac.uk> Broken layout for operations view of KEGG service (/services/11#operations) in IE8 ---------------------------------------------------------------------------------- Key: BIOCAT-411 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-411 Project: BioCatalogue Issue Type: Bug Components: Web Interface Environment: Internet Explorer 8 Reporter: Sergejs Aleksejevs Assignee: Jiten Bhagat >From Sergey: {quote} I've just noticed that the layout of the page is broken in Internet Explorer 8 (works fine in Firefox). After "Quick Browse" section two operations are diplayed correctly in the list, but all of the following ones appear to be outside of the "Operations" tab. This way the next 3 operations are a little less indented on the left-hand side; then there's a gap; then next 4 operations are even less indented. Finally, all of the remaining operations are not indented at all and the rest of the contents of the page are not indented either (thus, they appear directly on the left edge of the page). {quote} -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 23 08:51:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 23 Jun 2010 13:51:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-410) Unable to submit feedback from IE8 In-Reply-To: <24362963.6567.1277296035304.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24842202.6574.1277297476322.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-410?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10411 ] Jiten Bhagat logged work on BIOCAT-410: --------------------------------------- Author: Jiten Bhagat Created on: 2010-06-23 13:50 Start Date: 2010-06-23 11:00 Worklog Time Spent: 1 hour, 30 minutes Issue Time Tracking ------------------- Remaining Estimate: 30 minutes (was: 2 hours) Time Spent: 1 hour, 30 minutes > Unable to submit feedback from IE8 > ---------------------------------- > > Key: BIOCAT-410 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-410 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Environment: Internet Explorer 8 > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 1 hour, 30 minutes > Remaining Estimate: 30 minutes > > The contact form (on /contact) is broken on IE8 due to the Security Number checking method. > This is due to the inconsistencies in the way browsers treat the String#split method (which is what is used under the hood). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 23 08:51:18 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 23 Jun 2010 13:51:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-411) Broken layout for operations view of KEGG service (/services/11#operations) in IE8 In-Reply-To: <18208170.6573.1277297475353.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18694628.6575.1277297478792.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-411?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-411: -------------------------------- Original Estimate: 2 hours (was: 3 hours) Remaining Estimate: 2 hours (was: 3 hours) > Broken layout for operations view of KEGG service (/services/11#operations) in IE8 > ---------------------------------------------------------------------------------- > > Key: BIOCAT-411 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-411 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Environment: Internet Explorer 8 > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Remaining Estimate: 2 hours > > From Sergey: > {quote} > I've just noticed that the layout of the page is broken in Internet Explorer 8 (works fine in Firefox). > After "Quick Browse" section two operations are diplayed correctly in the list, but all of the following ones appear to be outside of the "Operations" tab. This way the next 3 operations are a little less indented on the left-hand side; then there's a gap; then next 4 operations are even less indented. Finally, all of the remaining operations are not indented at all and the rest of the contents of the page are not indented either (thus, they appear directly on the left edge of the page). > {quote} -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 23 08:29:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 23 Jun 2010 13:29:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-410) Unable to submit feedback from IE8 In-Reply-To: <24362963.6567.1277296035304.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10074134.6568.1277296155344.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-410?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15323#action_15323 ] Jiten Bhagat commented on BIOCAT-410: ------------------------------------- More details on the problem, and a proposed solution: http://blog.stevenlevithan.com/archives/cross-browser-split > Unable to submit feedback from IE8 > ---------------------------------- > > Key: BIOCAT-410 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-410 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Environment: Internet Explorer 8 > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Remaining Estimate: 2 hours > > The contact form (on /contact) is broken on IE8 due to the Security Number checking method. > This is due to the inconsistencies in the way browsers treat the String#split method (which is what is used under the hood). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 23 09:10:34 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 23 Jun 2010 09:10:34 -0400 (EDT) Subject: [BioCatalogue-developers] [2108] trunk/app/views/soap_operations/_listing.html.erb: [BIOCAT-411] Fixes for broken layout in IE. Message-ID: <20100623131034.B09ED185835E@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jun 23 09:12:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 23 Jun 2010 14:12:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-411) Broken layout for operations view of KEGG service (/services/11#operations) in IE8 In-Reply-To: <18208170.6573.1277297475353.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <719454.6578.1277298735344.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-411?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10412 ] Jiten Bhagat logged work on BIOCAT-411: --------------------------------------- Author: Jiten Bhagat Created on: 2010-06-23 14:11 Start Date: 2010-06-23 13:11 Worklog Time Spent: 1 hour Issue Time Tracking ------------------- Remaining Estimate: 1 hour (was: 2 hours) Time Spent: 1 hour > Broken layout for operations view of KEGG service (/services/11#operations) in IE8 > ---------------------------------------------------------------------------------- > > Key: BIOCAT-411 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-411 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Environment: Internet Explorer 8 > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 1 hour > Remaining Estimate: 1 hour > > From Sergey: > {quote} > I've just noticed that the layout of the page is broken in Internet Explorer 8 (works fine in Firefox). > After "Quick Browse" section two operations are diplayed correctly in the list, but all of the following ones appear to be outside of the "Operations" tab. This way the next 3 operations are a little less indented on the left-hand side; then there's a gap; then next 4 operations are even less indented. Finally, all of the remaining operations are not indented at all and the rest of the contents of the page are not indented either (thus, they appear directly on the left edge of the page). > {quote} -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 23 09:12:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 23 Jun 2010 14:12:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-411) Broken layout for operations view of KEGG service (/services/11#operations) in IE8 In-Reply-To: <18208170.6573.1277297475353.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22285176.6579.1277298737859.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-411?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-411. --------------------------------- Resolution: Fixed In revision 2108. > Broken layout for operations view of KEGG service (/services/11#operations) in IE8 > ---------------------------------------------------------------------------------- > > Key: BIOCAT-411 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-411 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Environment: Internet Explorer 8 > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 1 hour > Remaining Estimate: 1 hour > > From Sergey: > {quote} > I've just noticed that the layout of the page is broken in Internet Explorer 8 (works fine in Firefox). > After "Quick Browse" section two operations are diplayed correctly in the list, but all of the following ones appear to be outside of the "Operations" tab. This way the next 3 operations are a little less indented on the left-hand side; then there's a gap; then next 4 operations are even less indented. Finally, all of the remaining operations are not indented at all and the rest of the contents of the page are not indented either (thus, they appear directly on the left edge of the page). > {quote} -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 23 09:14:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 23 Jun 2010 14:14:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-412) News tab for services does not load in IE8 Message-ID: <3167445.6580.1277298855313.JavaMail.jira@rosalind.cs.man.ac.uk> News tab for services does not load in IE8 ------------------------------------------ Key: BIOCAT-412 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-412 Project: BioCatalogue Issue Type: Bug Components: Web Interface Environment: Internet Explorer 8 Reporter: Jiten Bhagat Assignee: Jiten Bhagat The news tab never successfully loads. Look into the AJAX call that is set up to run on page load and ensure it works. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 23 11:20:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 23 Jun 2010 16:20:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-57) Soaplab badge is not clickable Message-ID: <17162870.6594.1277306415340.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-57?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-57: -------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > Soaplab badge is not clickable > ------------------------------ > > Key: BIOCAT-57 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-57 > Project: BioCatalogue > Issue Type: Improvement > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > > Soaplab badge not clickable... need to get to a filtered list. This relates to the "service families" work. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 24 05:01:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 24 Jun 2010 10:01:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-57) Soaplab badge is not clickable - build a services filter for this Message-ID: <16009390.6603.1277370076593.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-57?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat reassigned BIOCAT-57: ---------------------------------- Assignee: Jiten Bhagat (was: Eric Nzuobontane) > Soaplab badge is not clickable - build a services filter for this > ----------------------------------------------------------------- > > Key: BIOCAT-57 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-57 > Project: BioCatalogue > Issue Type: Improvement > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Original Estimate: 1 day > Remaining Estimate: 1 day > > Soaplab badge not clickable... need to get to a filtered list. This relates to the "service families" work. > Note: this is about service filtering; we need to ensure the same consistent experience as when you click on the "SOAP" or "REST" badges. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 24 05:01:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 24 Jun 2010 10:01:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-57) Soaplab badge is not clickable - build a services filter for this Message-ID: <22670613.6602.1277370075363.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-57?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-57: ------------------------------- Summary: Soaplab badge is not clickable - build a services filter for this (was: Soaplab badge is not clickable) Original Estimate: 1 day Remaining Estimate: 1 day Description: Soaplab badge not clickable... need to get to a filtered list. This relates to the "service families" work. Note: this is about service filtering; we need to ensure the same consistent experience as when you click on the "SOAP" or "REST" badges. was:Soaplab badge not clickable... need to get to a filtered list. This relates to the "service families" work. > Soaplab badge is not clickable - build a services filter for this > ----------------------------------------------------------------- > > Key: BIOCAT-57 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-57 > Project: BioCatalogue > Issue Type: Improvement > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > Soaplab badge not clickable... need to get to a filtered list. This relates to the "service families" work. > Note: this is about service filtering; we need to ensure the same consistent experience as when you click on the "SOAP" or "REST" badges. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 24 05:03:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 24 Jun 2010 10:03:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-57) Soaplab badge is not clickable - build a services filter for this Message-ID: <19071276.6604.1277370195305.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-57?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-57: ------------------------------- Component/s: Search / Filtering / Browsing Web Interface > Soaplab badge is not clickable - build a services filter for this > ----------------------------------------------------------------- > > Key: BIOCAT-57 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-57 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing, Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Original Estimate: 1 day > Remaining Estimate: 1 day > > Soaplab badge not clickable... need to get to a filtered list. This relates to the "service families" work. > Note: this is about service filtering; we need to ensure the same consistent experience as when you click on the "SOAP" or "REST" badges. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 24 05:17:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 24 Jun 2010 10:17:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-413) Some urls in annotation fields are not formed properly Message-ID: <30372087.6609.1277371035302.JavaMail.jira@rosalind.cs.man.ac.uk> Some urls in annotation fields are not formed properly ------------------------------------------------------ Key: BIOCAT-413 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-413 Project: BioCatalogue Issue Type: Bug Components: Misc Codebase Reporter: Mannie Tagarira Assignee: Jiten Bhagat For example, "support at genouest.org" does not link to that email address, it links to "genouest.org" ("support@" is shown as is). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 24 05:19:15 2010 From: issues at mygrid.org.uk (Sergejs Aleksejevs (JIRA)) Date: Thu, 24 Jun 2010 10:19:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-414) SOAP Service Views - Grouping of operations by port Message-ID: <25888115.6610.1277371155310.JavaMail.jira@rosalind.cs.man.ac.uk> SOAP Service Views - Grouping of operations by port --------------------------------------------------- Key: BIOCAT-414 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-414 Project: BioCatalogue Issue Type: Improvement Components: SOAP Services Support Reporter: Sergejs Aleksejevs Assignee: Jiten Bhagat Service like http://www.biocatalogue.org/services/2160 have identical operations available at different ports. The UI would be much clearer if the operations were grouped by ports, thus eliminating duplicates in the overall list of operations as it happens now. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 24 05:22:15 2010 From: issues at mygrid.org.uk (Sergejs Aleksejevs (JIRA)) Date: Thu, 24 Jun 2010 10:22:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-415) Item lookup via API - for SOAP services may need to add ports as another checking criteria Message-ID: <5200307.6611.1277371335311.JavaMail.jira@rosalind.cs.man.ac.uk> Item lookup via API - for SOAP services may need to add ports as another checking criteria ------------------------------------------------------------------------------------------ Key: BIOCAT-415 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-415 Project: BioCatalogue Issue Type: Task Components: REST API Reporter: Sergejs Aleksejevs Assignee: Jiten Bhagat Currently only WSDL location and the operation name determine the SOAP operation. In case there are identical operations on different SOAP ports, the one on the first known port is always returned by the lookup. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 24 05:26:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 24 Jun 2010 10:26:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-413) Some urls in annotation fields are not formed properly In-Reply-To: <30372087.6609.1277371035302.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16493023.6614.1277371575317.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-413?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-413: -------------------------------- Reporter: Sergejs Aleksejevs (was: Mannie Tagarira) > Some urls in annotation fields are not formed properly > ------------------------------------------------------ > > Key: BIOCAT-413 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-413 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > > For example, "support at genouest.org" does not link to that email address, it links to "genouest.org" ("support@" is shown as is). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 24 05:26:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 24 Jun 2010 10:26:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-413) Some urls in annotation fields are not formed properly In-Reply-To: <30372087.6609.1277371035302.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3293325.6615.1277371576294.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-413?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-413: -------------------------------- Component/s: Web Interface (was: Misc Codebase) > Some urls in annotation fields are not formed properly > ------------------------------------------------------ > > Key: BIOCAT-413 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-413 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > > For example, "support at genouest.org" does not link to that email address, it links to "genouest.org" ("support@" is shown as is). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 24 05:29:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 24 Jun 2010 10:29:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-413) Some urls in annotation fields are not formed properly In-Reply-To: <30372087.6609.1277371035302.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2973049.6616.1277371755325.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-413?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat reassigned BIOCAT-413: ----------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) Possible regression after previous fixes to the auto_link method. > Some urls in annotation fields are not formed properly > ------------------------------------------------------ > > Key: BIOCAT-413 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-413 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Sergejs Aleksejevs > Assignee: Mannie Tagarira > > For example, "support at genouest.org" does not link to that email address, it links to "genouest.org" ("support@" is shown as is). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 24 05:29:26 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 24 Jun 2010 10:29:26 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-413) Some urls in annotation fields are not formed properly In-Reply-To: <30372087.6609.1277371035302.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21506226.6617.1277371766672.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-413?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-413: -------------------------------- Priority: Critical (was: Major) > Some urls in annotation fields are not formed properly > ------------------------------------------------------ > > Key: BIOCAT-413 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-413 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Sergejs Aleksejevs > Assignee: Mannie Tagarira > Priority: Critical > > For example, "support at genouest.org" does not link to that email address, it links to "genouest.org" ("support@" is shown as is). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 24 05:35:15 2010 From: issues at mygrid.org.uk (Sergejs Aleksejevs (JIRA)) Date: Thu, 24 Jun 2010 10:35:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-243) Make important pages HTTPS Message-ID: <29474433.6618.1277372115318.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sergejs Aleksejevs updated BIOCAT-243: -------------------------------------- Priority: Blocker (was: Critical) > Make important pages HTTPS > -------------------------- > > Key: BIOCAT-243 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > > ... like log in, register etc etc -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Jun 24 09:23:18 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 24 Jun 2010 09:23:18 -0400 (EDT) Subject: [BioCatalogue-developers] [2109] trunk/app/views/services: [BiOCAT-412] Fixed loading of the "News" tab in IE8. Message-ID: <20100624132318.6DCF1185836D@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Jun 24 09:26:41 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 24 Jun 2010 09:26:41 -0400 (EDT) Subject: [BioCatalogue-developers] [2110] trunk/public/javascripts/application.js: Minor javascript fix. Message-ID: <20100624132641.2DC96185836D@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jun 24 09:31:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 24 Jun 2010 14:31:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-412) News tab for services does not load in IE8 In-Reply-To: <3167445.6580.1277298855313.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <33382302.6626.1277386276508.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-412?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-412. --------------------------------- Resolution: Fixed In revision 2109 > News tab for services does not load in IE8 > ------------------------------------------ > > Key: BIOCAT-412 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-412 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Environment: Internet Explorer 8 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 2 hours > Remaining Estimate: 0 minutes > > The news tab never successfully loads. Look into the AJAX call that is set up to run on page load and ensure it works. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 24 09:31:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 24 Jun 2010 14:31:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-412) News tab for services does not load in IE8 In-Reply-To: <3167445.6580.1277298855313.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12015238.6625.1277386275376.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-412?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#action_10414 ] Jiten Bhagat logged work on BIOCAT-412: --------------------------------------- Author: Jiten Bhagat Created on: 2010-06-24 14:28 Start Date: 2010-06-24 10:00 Worklog Time Spent: 2 hours Issue Time Tracking ------------------- Remaining Estimate: 0 minutes (was: 2 hours) Time Spent: 2 hours > News tab for services does not load in IE8 > ------------------------------------------ > > Key: BIOCAT-412 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-412 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Environment: Internet Explorer 8 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 2 hours > Remaining Estimate: 0 minutes > > The news tab never successfully loads. Look into the AJAX call that is set up to run on page load and ensure it works. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 24 10:03:15 2010 From: issues at mygrid.org.uk (Sergejs Aleksejevs (JIRA)) Date: Thu, 24 Jun 2010 15:03:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-416) Dynamically-generated search suggestions drop-down menu is in the wrong place in IE8 Message-ID: <3147156.6627.1277388195335.JavaMail.jira@rosalind.cs.man.ac.uk> Dynamically-generated search suggestions drop-down menu is in the wrong place in IE8 ------------------------------------------------------------------------------------ Key: BIOCAT-416 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-416 Project: BioCatalogue Issue Type: Bug Components: Web Interface Reporter: Sergejs Aleksejevs Assignee: Jiten Bhagat Priority: Minor The drop-down menu appears in the wrong place - some 3cm below and 2cm to the right from the edge of the search box. Screenshot attached. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the 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 Jun 24 10:07:15 2010 From: issues at mygrid.org.uk (Sergejs Aleksejevs (JIRA)) Date: Thu, 24 Jun 2010 15:07:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-416) Dynamically-generated search suggestions drop-down menu is in the wrong place in IE8 In-Reply-To: <3147156.6627.1277388195335.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18060569.6628.1277388435327.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-416?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sergejs Aleksejevs updated BIOCAT-416: -------------------------------------- Attachment: screenshot-1.jpg > Dynamically-generated search suggestions drop-down menu is in the wrong place in IE8 > ------------------------------------------------------------------------------------ > > Key: BIOCAT-416 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-416 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > Priority: Minor > Attachments: screenshot-1.jpg > > > The drop-down menu appears in the wrong place - some 3cm below and 2cm to the right from the edge of the search box. Screenshot attached. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Thu Jun 24 11:33:31 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 24 Jun 2010 16:33:31 +0100 Subject: [BioCatalogue-developers] Draft announcement... In-Reply-To: <4C0F8EA5.4010808@cs.man.ac.uk> References: <4C0F8475.1020501@cs.man.ac.uk> <4C0F897D.3040503@ebi.ac.uk> <4C0F8EA5.4010808@cs.man.ac.uk> Message-ID: <4C237ACB.50205@cs.man.ac.uk> Latest draft for announcement, below: Jits ... Title/Subject: Latest updates - service responsibility, monitoring status changes, service activity, service update checker and many more. Message: Hello all, We have updated the BioCatalogue (http://www.biocatalogue.org) with a number of new features and improvements in the last six weeks. Below we highlight and describe some of these: - Service responsibility request mechanism - Monitoring test changes feed - New activity feeds for individual services - Service update checker (WSDL updates for now) - Archiving services - REST endpoints in search - Service provider curation - Various service monitoring updates - New API features - Harvesting details from Soaplab services Service responsibility request mechanism Previously, the submitter of a service was the only one (together with site curators and admins) who had finer control on a service entry in the catalogue. They could delete the service or delete individual annotations on the service, and so on. But now, other members can request responsibility for a service in the catalogue. Thereby allowing more than one person to maintain a service entry. Requests can then be approved or denied by the submitter. * To request responsibility for a service: - You need to log in first - Browse to the service's profile page - Select the 'Take Responsibility' option from the 'Actions' drop down menu (the blue button on the left hand side next to the title of the service) - Follow the instructions on the subsequent page(s) * Note: in cases where no action has been taken on these requests, a site curator or admin can step in and take action. Monitoring test changes feed Service monitoring is a key feature offered by the BioCatalogue. Now you have the ability to see the latest monitoring status changes that have been logged for the individual service tests we carry out. This allows providers and consumers to easily keep track of monitoring changes across the catalogue. A short list can be seen on the homepage, towards the bottom list. With a more detailed list here: http://www.biocatalogue.org/latest#monitoring You can also subscribe to the ATOM feed for this: http://www.biocatalogue.org/status_changes.atom New activity feeds for individual services The 'Latest Activity' lists are a nice way of seeing what is happening in the catalogue. And now, as part of a new "News" tab on each service's profile page, we have introduced an activity list for each individual service. Here you can see the latest annotations, monitoring status changes, favourites, updates and so on. You can also subscribe to the ATOM feed, allowing you get instant notifications of new activity on any services that you are interested in. For example, for the EBI DBFetch service: http://www.biocatalogue.org/services/4#news (ATOM feed is: http://www.biocatalogue.org/services/4/activity.atom) Service update checker (WSDL updates for now) The interface for SOAP services - WSDL files - may often be updated by service providers. These updates can range from metadata changes/additions to substantial structural changes in the service and it's operations. The BioCatalogue now has the ability to pick up these changes and update service entries automatically. Any removed operations, inputs or outputs are still kept, but are marked as "archived". All changes are logged and shown under the new "News" tab on a service's profile page. See for example: http://www.biocatalogue.org/services/8#updates_from_wsdl_5. This allows service consumers to see a changelog of a service over time. Archiving services Services can now be marked as archived/deprecated by anyone who has responsibility for it in the catalogue.