From hamon at elda.org Fri Jan 7 13:34:57 2011 From: hamon at elda.org (Olivier Hamon) Date: Fri, 07 Jan 2011 19:34:57 +0100 Subject: [BioCatalogue-hackers] Fwd: Worker script issue In-Reply-To: <4D0A389C.8020209@ebi.ac.uk> References: <4D0650EC.6030701@cs.man.ac.uk> <4D09FB64.1010406@ebi.ac.uk> <4D0A1925.4000504@elda.org> <4D0A1BAA.9010904@ebi.ac.uk> <4D0A1E52.2090606@elda.org> <4D0A247E.7050605@ebi.ac.uk> <4D0A2D08.2040608@elda.org> <4D0A2ED0.3080408@ebi.ac.uk> <4D0A34AB.5060301@elda.org> <4D0A389C.8020209@ebi.ac.uk> Message-ID: <4D275CD1.8090900@elda.org> Dear Eric, Very best wishes for 2011 to you and the Biocatalogue team. I'm coming back with the same issue... fortunately, Father Christmas brought me another hint :) I realised the table "delayed_jobs has" a text field called "handler", and that this field may contain huge data. This data is, from time to time, cut because its size is up to 65 000 characters (the limitation of the text type). I first change the type to "longtext", but I guess that is only a way to postpone the outcome... So, in case this is a good hint, I would like to know if there is a way to make the data of this field smaller? I can see the data is composed of other data from tables "activity_logs" and/or "test_results": maybe the solution is to clean up those tables, but how, and is it not too risky? Furthermore, this "handler" data seems to contain only log information quite outdated for most of it... Thanks in advance for your help, Olivier On 16/12/2010 17:04, Eric Nzuobontane wrote: > Great! If you come across any other issues, please let us know. > > cheers, > Eric > > > On 16/12/2010 15:47, Olivier Hamon wrote: >> Great! I managed to run the migration. >> >> After restarting Biocatalogue, the worker and making a first update >> and check of urls, it seems to be working fine :) >> >> Now I don't have any jobs that stay in the delayed_jobs table. >> >> I will keep an eye on it, but it seems the issue is solved. >> >> Thank you very much! >> Olivier >> >> On 16/12/2010 16:22, Eric Nzuobontane wrote: >>> It looks like you are missing >>> >>> # Attribute identifier template to distinguish if terms come from a >>> controlled >>> # vocabulary or not. >>> # Note: Default value would work for most instances, so you probably >>> do not need >>> # to set this. >>> ANNOTATION_ATTRIBUTE_DEFAULT_IDENTIFIER_TEMPLATE= >>> "http://biocatalogue.org/attribute/%s" >>> >>> in your >>> config/initializers/biocat_local.rb >>> >>> file. You can just copy it and stick it to the end of your file. As >>> a rule for future updates, always check if >>> config/initializers/biocat_local.rb.pre >>> has changed. If it does change, then it means you need to update >>> your local file accordingly. >>> >>> Give it a go and let me know if there are any further problems. >>> >>> Eric >>> >>> >>> >>> On 16/12/2010 15:15, Olivier Hamon wrote: >>>> Hi, >>>> >>>> Sorry to bother you again... >>>> Using the command (after svn update): rake db:migrate >>>> RAILS_ENV=development >>>> I get the following error message: >>>> >>>> Running in development mode... >>>> Configuring the BioCatalogue application... >>>> Setting up caches... >>>> memcache-client version = 1.7.4 >>>> memcache_client servers: [>>> (NOT CONNECTED)>] >>>> rake aborted! >>>> uninitialized constant ANNOTATION_ATTRIBUTE_DEFAULT_IDENTIFIER_TEMPLATE >>>> >>>> I have a similar error when giving production environment. >>>> >>>> Olivier >>>> >>>> >>>> On 16/12/2010 15:38, Eric Nzuobontane wrote: >>>>> Hi Oliver, >>>>> >>>>> You are running on an older revision of the code. I think you >>>>> should update. Let me know if you have any problems. >>>>> >>>>> Eric >>>>> >>>>> >>>>> On 16/12/2010 14:12, Olivier Hamon wrote: >>>>>> Hi Eric, >>>>>> >>>>>> On 16/12/2010 15:01, Eric Nzuobontane wrote: >>>>>>> Hi Oliver, >>>>>>> >>>>>>> Thanks for the info. In fact what I need to know is if you are >>>>>>> running the current head code. If you run the command >>>>>>> >>>>>>> svn info >>>>>> Here is the result of the command: >>>>>> >>>>>> Path: . >>>>>> URL: http://biocatalogue.rubyforge.org/svn/trunk >>>>>> Repository Root: http://biocatalogue.rubyforge.org/svn >>>>>> Repository UUID: 1acaf488-1b9d-4964-8077-0a2fdb83ef00 >>>>>> Revision: 2277 >>>>>> Node Kind: directory >>>>>> Schedule: normal >>>>>> Last Changed Author: jits >>>>>> Last Changed Rev: 2277 >>>>>> Last Changed Date: 2010-10-18 13:44:26 +0200 (Mon, 18 Oct 2010) >>>>>> >>>>>> I guess this is the last version, isn't it? Otherwise, if you >>>>>> confirm to me, I will update the codebase. >>>>>> >>>>>> Best, >>>>>> Olivier >>>>>> >>>>>>> >>>>>>> from the application root and send me the output, I will be able >>>>>>> to see what revision of the code you are running. >>>>>>> >>>>>>> I guess you will need to do /svn update/ from your application >>>>>>> root to update the codebase. You might then need to run >>>>>>> migrations with >>>>>>> rake db:migrate RAILS_ENV= >>>>>>> >>>>>>> Eric >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 16/12/2010 13:50, Olivier Hamon wrote: >>>>>>>> Hi Eric, >>>>>>>> >>>>>>>> Thanks for your reply. On a Debian distribution, the gem env >>>>>>>> command gives me the following results >>>>>>>> >>>>>>>> RubyGems Environment: >>>>>>>> - RUBYGEMS VERSION: 1.3.7 >>>>>>>> - RUBY VERSION: 1.8.7 (2008-08-11 patchlevel 72) [i486-linux] >>>>>>>> - INSTALLATION DIRECTORY: /usr/lib/ruby/gems/1.8 >>>>>>>> - RUBY EXECUTABLE: /usr/bin/ruby1.8 >>>>>>>> - EXECUTABLE DIRECTORY: /usr/bin >>>>>>>> - RUBYGEMS PLATFORMS: >>>>>>>> - ruby >>>>>>>> - x86-linux >>>>>>>> - GEM PATHS: >>>>>>>> - /usr/lib/ruby/gems/1.8 >>>>>>>> - /home/carsten/.gem/ruby/1.8 >>>>>>>> - GEM CONFIGURATION: >>>>>>>> - :update_sources => true >>>>>>>> - :verbose => true >>>>>>>> - :benchmark => false >>>>>>>> - :backtrace => false >>>>>>>> - :bulk_threshold => 1000 >>>>>>>> - :sources => ["http://rubygems.org/", >>>>>>>> "http://gems.github.com"] >>>>>>>> - REMOTE SOURCES: >>>>>>>> - http://rubygems.org/ >>>>>>>> - http://gems.github.com >>>>>>>> >>>>>>>> I can certainly update, although I'm not very confident on the >>>>>>>> exact procedure to follow :) >>>>>>>> >>>>>>>> Best, >>>>>>>> Olivier >>>>>>>> >>>>>>>> On 16/12/2010 12:43, Eric Nzuobontane wrote: >>>>>>>>> Hi Oliver, >>>>>>>>> >>>>>>>>> Sorry about the problems. I believe this issue was solved some >>>>>>>>> time ago, but maybe not? I tried reproducing the problem but >>>>>>>>> could not. Could you please let me know the version of the >>>>>>>>> codebase you are running? Would you be able to update if you >>>>>>>>> are not running on head? >>>>>>>>> >>>>>>>>> regards, >>>>>>>>> >>>>>>>>> Eric >>>>>>>>> >>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -------- Original Message -------- >>>>>>>>>> Subject: [BioCatalogue-hackers] Worker script issue >>>>>>>>>> Date: Mon, 13 Dec 2010 12:46:59 +0100 >>>>>>>>>> From: Olivier Hamon >>>>>>>>>> To: biocatalogue-hackers at rubyforge.org >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Dear all, >>>>>>>>>> >>>>>>>>>> Working on a local Biocatalogue, I have some issues with the worker >>>>>>>>>> script. The script crashes and therefore, services cannot be registered >>>>>>>>>> and the monitoring fails. >>>>>>>>>> >>>>>>>>>> This seems to occur when getting specific job(s) in the delayed_job >>>>>>>>>> table, generally a service update such as (in the handler field of the >>>>>>>>>> table): >>>>>>>>>> >>>>>>>>>> --- !ruby/struct:BioCatalogue::Jobs::UpdateServiceTestSuccessRate >>>>>>>>>> test_result:&id002 !ruby/object:TestResult >>>>>>>>>> attributes: >>>>>>>>>> result: 0 >>>>>>>>>> created_at:&id001 2010-12-10 15:33:41.875030 Z >>>>>>>>>> updated_at: *id001 >>>>>>>>>> action: http_head >>>>>>>>>> id: 8834 >>>>>>>>>> message: | >>>>>>>>>> HTTP/1.1 200 OK >>>>>>>>>> Server: Apache-Coyote/1.1 >>>>>>>>>> Content-Type: text/xml >>>>>>>>>> Transfer-Encoding: chunked >>>>>>>>>> Date: Fri, 10 Dec 2010 15:33:41 GMT >>>>>>>>>> >>>>>>>>>> [...] - the rest of the message in the field is very long. >>>>>>>>>> >>>>>>>>>> When restarting the worker script, either many jobs are added while only >>>>>>>>>> one or two jobs are deleted from the table, or the script crashes after >>>>>>>>>> deleting one or two jobs (rarely the first one in the table). Added jobs >>>>>>>>>> are always "UpdateServiceTestSuccessRate" with one of the following >>>>>>>>>> actions: http_head, soap_fault or soap_client. >>>>>>>>>> >>>>>>>>>> In the meantime, I found the following error message in >>>>>>>>>> tmp/pids/biocatalogue_worker.log: >>>>>>>>>> >>>>>>>>>> *** below you find all exception objects found in memory, some of them >>>>>>>>>> may have been thrown in your application, others may just be in memory >>>>>>>>>> because they are standard exceptions *** >>>>>>>>>> # >>>>>>>>>> # >>>>>>>>>> # >>>>>>>>>> # >>>>>>>>>> # >>>>>>>>>> #>>>>>>>>> '> >>>>>>>>>> #>>>>>>>>> BioCatalogue::Jobs::UpdateServiceTestSuccessRate> >>>>>>>>>> # >>>>>>>>>> # >>>>>>>>>> >>>>>>>>>> I don't know whether the two problems are related or not. >>>>>>>>>> >>>>>>>>>> Thanks a lot in advance for your help, >>>>>>>>>> Olivier Hamon >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> BioCatalogue-hackers mailing list >>>>>>>>>> BioCatalogue-hackers at rubyforge.org >>>>>>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-hackers >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> 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 >>>>>>>>> ================================== >>>>>>>> >>>>>>>> -- >>>>>>>> --------------------------------------------------------------------------------------------------- >>>>>>>> Olivier HAMONhamon at elda.org >>>>>>>> ELDA - Evaluations and Language resources Distribution Agency >>>>>>>> 55-57, rue Brillat Savarin Tel : +33 1 43 13 33 43 >>>>>>>> 75013 Paris - France Fax : +33 1 43 13 33 30 >>>>>>>> http://www.elda.org http://www.lrec-conf.org >>>>>>>> http://catalog.elra.info http://www.hlt-evaluation.org >>>>>>>> --------------------------------------------------------------------------------------------------- >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> 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 >>>>>>> ================================== >>>>>> >>>>>> -- >>>>>> --------------------------------------------------------------------------------------------------- >>>>>> Olivier HAMONhamon at elda.org >>>>>> ELDA - Evaluations and Language resources Distribution Agency >>>>>> 55-57, rue Brillat Savarin Tel : +33 1 43 13 33 43 >>>>>> 75013 Paris - France Fax : +33 1 43 13 33 30 >>>>>> http://www.elda.org http://www.lrec-conf.org >>>>>> http://catalog.elra.info http://www.hlt-evaluation.org >>>>>> --------------------------------------------------------------------------------------------------- >>>>>> >>>>> >>>>> >>>>> -- >>>>> 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 >>>>> ================================== >>>> >>>> -- >>>> --------------------------------------------------------------------------------------------------- >>>> Olivier HAMONhamon at elda.org >>>> ELDA - Evaluations and Language resources Distribution Agency >>>> 55-57, rue Brillat Savarin Tel : +33 1 43 13 33 43 >>>> 75013 Paris - France Fax : +33 1 43 13 33 30 >>>> http://www.elda.org http://www.lrec-conf.org >>>> http://catalog.elra.info http://www.hlt-evaluation.org >>>> --------------------------------------------------------------------------------------------------- >>>> >>> >>> >>> -- >>> 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 >>> ================================== >> >> -- >> --------------------------------------------------------------------------------------------------- >> Olivier HAMONhamon at elda.org >> ELDA - Evaluations and Language resources Distribution Agency >> 55-57, rue Brillat Savarin Tel : +33 1 43 13 33 43 >> 75013 Paris - France Fax : +33 1 43 13 33 30 >> http://www.elda.org http://www.lrec-conf.org >> http://catalog.elra.info http://www.hlt-evaluation.org >> --------------------------------------------------------------------------------------------------- >> > > > -- > 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 > ================================== -- --------------------------------------------------------------------------------------------------- Olivier HAMON hamon at elda.org ELDA - Evaluations and Language resources Distribution Agency 55-57, rue Brillat Savarin Tel : +33 1 43 13 33 43 75013 Paris - France Fax : +33 1 43 13 33 30 http://www.elda.org http://www.lrec-conf.org http://catalog.elra.info http://www.hlt-evaluation.org --------------------------------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Mon Jan 10 11:19:33 2011 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 10 Jan 2011 16:19:33 +0000 Subject: [BioCatalogue-hackers] BioCatalogue users survey final reminder Message-ID: Hello everyone, Happy New Year 2011! May I remind you once again to consider completing the BioCatalogue users' survey (https://www.surveymonkey.com/s/FN5RXLC) if you have not done it yet, please. It will take you 5min. Your responses will provide us with valuable feedback and aid in ongoing improvement of the BioCatalogue and its content. Please note that the survey will be closed this week Friday (14/01). Thank you to all of you who have completed it so far Regards, Franck On 24 November 2010 10:36, Franck Tanoh wrote: > Dear all, > > The BioCatalogue team would like to invite you to take part in a > survey, https://www.surveymonkey.com/s/FN5RXLC, which we are > conducting for the BioCatalogue project > (http://www.biocatalogue.org/). > Its aim is to gather feedback about your views of the BioCatalogue. > The purpose is to investigate how the BioCatalogue is being used, who > uses it and how we can improve it. Your responses will provide us with > valuable feedback and aid in ongoing improvement of the BioCatalogue > and its content. > > Every participant will also be entered into a draw for a ?20 Amazon voucher. > > All information provided will be treated as confidential and no > personal data will be disclosed to anyone outside of the project team. > > On behalf of the BioCatalogue project team, we thank you in advance > for your cooperation. > > Regards, > > BioCatalogue team > > -- > ?"Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur > -- ?"Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur