From noreply at rubyforge.org Mon Oct 1 15:29:46 2012 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 1 Oct 2012 15:29:46 +0000 (UTC) Subject: [BioCatalogue-developers] [2546] trunk/lib/tasks/eb-eye_dump.rake: Fixed annotation issue in ebeye dump Message-ID: <20121001152946.D64192E06C@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Oct 3 14:58:36 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:58:36 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-22) Broken links in the feta imports Message-ID: <583546524.485.1349276316034.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-22?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-22: -------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Broken links in the feta imports > -------------------------------- > > Key: BIOCAT-22 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-22 > Project: BioCatalogue > Issue Type: Bug > Components: Content Acquisition, Data > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > Revisit links from the feta import. Some (example workflows listed in the other annotation in biocat) don't work anymore: > http://www.mygrid.org.uk/feta/mygrid/example_workflow/DDBJ/blast/extractPosition_workflow.xml (blast should be capital BLAST) > http://www.mygrid.org.uk/feta/mygrid/example_workflow/DDBJ/blast/getSupportDatabaseList_workflow.xml (doesn't exist) -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:58:38 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:58:38 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-59) Secure delete actions Message-ID: <112408547.486.1349276318376.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-59?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-59: -------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Secure delete actions > --------------------- > > Key: BIOCAT-59 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-59 > Project: BioCatalogue > Issue Type: Improvement > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > Need to secure/disable all delete actions on resources -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:58:40 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:58:40 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-106) Allow the submitter to select a display name for a service Message-ID: <2066772394.487.1349276320353.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-106?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-106: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Allow the submitter to select a display name for a service > ---------------------------------------------------------- > > Key: BIOCAT-106 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-106 > Project: BioCatalogue > Issue Type: New Feature > Components: Annotations (in App), Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Robert Haines > Fix For: 1.1.1 > > > "I have a suggestion -- you allow people to add name aliases for services, but it would be really useful if you could tag one as the primary display name. > I wouldn't be surprised if quite a lot of the services out there have fairly unfriendly names in the WSDLs. > The EMBRACE Registry lets you enter a title for the service, which is what comes up in the human-readable web page, rather than the computer-readable name from the WSDL." > Posted by Andrew on the Biocat support list -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:58:45 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:58:45 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-200) Need to import the Soaplab services metadata from Feta Message-ID: <962848712.489.1349276325052.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-200?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-200: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Need to import the Soaplab services metadata from Feta > ------------------------------------------------------ > > Key: BIOCAT-200 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-200 > Project: BioCatalogue > Issue Type: Task > Components: Content Acquisition, Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > ... as these could not be imported in the first instance. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:58:54 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:58:54 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-224) Add caching to filters in filtering sidebar Message-ID: <1224095216.493.1349276334728.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-224?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-224: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Add caching to filters in filtering sidebar > ------------------------------------------- > > Key: BIOCAT-224 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-224 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > Currently the filtering sidebar is generated on each request. This is not scalable. Some caching work is required. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:58:59 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:58:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-243) Make ALL routes/pages HTTPS (SSL) Message-ID: <547043044.495.1349276339049.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-243: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Make ALL routes/pages HTTPS (SSL) > --------------------------------- > > Key: BIOCAT-243 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.1.1 > > > The decision now is to make the WHOLE site run on HTTPS. This simplifies things greatly. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:08 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:08 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-288) Reimplement the service filtering method for conditions/joining Message-ID: <970988867.499.1349276348489.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-288?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-288: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Reimplement the service filtering method for conditions/joining > --------------------------------------------------------------- > > Key: BIOCAT-288 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-288 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.1.1 > > > A new way of doing it was done for BioCatalogue::Filtering::Annotations::generate_conditions_and_joins_from_filters > Possibly reimplement the services one to do it this way. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:16 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-303) Investigate database timout errors when deleting entries Message-ID: <158138155.502.1349276356413.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-303?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-303: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > 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: Jiten Bhagat > Priority: Critical > Fix For: 1.1.1 > > 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. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:18 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-345) Update the annotation counts mechanism to take into account new fields In-Reply-To: <32597963.524.1274181737002.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1004925604.503.1349276358570.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-345?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-345: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Update the annotation counts mechanism to take into account new fields > ---------------------------------------------------------------------- > > Key: BIOCAT-345 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-345 > Project: BioCatalogue > Issue Type: Refinement > Components: Annotations (in App) > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > Update the annotation counts mechanism to take into account new fields (like soaplab_description and namespace) -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:20 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:20 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-709) JSON service summary is broken In-Reply-To: <1062644913.483.1349276192420.JavaMail.jira@proteus> Message-ID: <1339762759.504.1349276360655.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-709?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines resolved BIOCAT-709. ---------------------------------- Resolution: Fixed Simple fix. Think it was just a mistyped variable name! > JSON service summary is broken > ------------------------------ > > Key: BIOCAT-709 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-709 > Project: BioCatalogue > Issue Type: Bug > Components: REST API > Affects Versions: 1.1.0 > Reporter: Robert Haines > Assignee: Robert Haines > Priority: Critical > Original Estimate: 2 hours > Time Spent: 2 hours > Remaining Estimate: 0 minutes > > Getting data from, e.g., http://www.biocatalogue.org/services/4/summary.json causes a complete breakage. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:22 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:22 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-423) Fix Service Provider name autocomplete to show escaped names In-Reply-To: <29360194.6732.1277733735420.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1852082735.505.1349276362653.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-423?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-423: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Fix Service Provider name autocomplete to show escaped names > ------------------------------------------------------------ > > Key: BIOCAT-423 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-423 > Project: BioCatalogue > Issue Type: Bug > Components: Service Provider Management > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.1.1 > > > When a Service Provider has a name like "my provider ", it is shown as "my provider" in the autocomplete. When it has been selected, it will fill in the text box with "my provider alert("warning...");". > The autocomplete should show the name as is... -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:27 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:27 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-475) Rendering problem in safari when rendering search results In-Reply-To: <32851103.9736.1285188315321.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1043615936.507.1349276367817.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-475?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-475: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Rendering problem in safari when rendering search results > --------------------------------------------------------- > > Key: BIOCAT-475 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-475 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > Attachments: screenshot-1.jpg > > > buttons and listing are misaligned in safari when search results are returned. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:30 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:30 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-487) Exception generated by linked_data handler In-Reply-To: <18811203.9902.1285777575311.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27308132.508.1349276370065.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-487?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-487: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Exception generated by linked_data handler > ------------------------------------------ > > Key: BIOCAT-487 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-487 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.1.1 > > > LinkedDataHandler metal app... > Intial URL: /services/10 > undefined method `to_sym' for nil:NilClass > /rails/biocatalogue/app/metal/linked_data_handler.rb:86:in `call' > rails/biocatalogue/app/metal/linked_data_handler.rb:43:in `call' > lib/ruby/1.8/benchmark.rb:293:in `measure' -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:32 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:32 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-490) Need a mechanism for activating the first user in the system in new deployments In-Reply-To: <29633402.9917.1285951395303.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1970771031.509.1349276372165.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-490?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-490: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Need a mechanism for activating the first user in the system in new deployments > ------------------------------------------------------------------------------- > > Key: BIOCAT-490 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-490 > Project: BioCatalogue > Issue Type: Improvement > Components: User Management > Reporter: Jiten Bhagat > Assignee: Robert Haines > Fix For: 1.1.1 > > > When someone sets up a fresh instance of the BioCatalogue software they usually create a new user and then run into the issue of how to activate that user (in cases where a mail server wasn't set up). > Need a way of solving this issue. One potential solution is to always activate the first user in a system (and maybe automatically make them an admin too?) > OR when the app is first run have a "set up" wizard in which one of the tasks is to create an admin user. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:34 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:34 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-499) Create a new VM for the BioCatalogue system In-Reply-To: <13641006.9964.1286463075344.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <296721767.510.1349276374282.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-499?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-499: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Create a new VM for the BioCatalogue system > ------------------------------------------- > > Key: BIOCAT-499 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-499 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.1 > > > There is an old Fedora 11 VM that was used previously to allow people to easily set up their own BioCatalogue instance. This is now badly out of date. > So create a new VM (preferably Ubuntu based) with all the latest stuff. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:41 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:41 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-535) After release, update API docs and data model diagram In-Reply-To: <24641103.566.1289922271996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1044369440.513.1349276381928.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-535?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-535: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > After release, update API docs and data model diagram > ----------------------------------------------------- > > Key: BIOCAT-535 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-535 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > After the release has been carried out and before announcing, update the API docs and data model diagram using the material provided by Mannie (as a starting point). -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:47 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:47 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-542) After deleting an annotation from the service overview, it is not deterministic which of the tabs is shown to the user In-Reply-To: <20071148.102.1290181372807.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1287504412.515.1349276387155.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-542?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-542: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > After deleting an annotation from the service overview, it is not deterministic which of the tabs is shown to the user > ---------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-542 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-542 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:49 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:49 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-548) Investigate why there is a huge number of search entries in the activity logs with empty search terms In-Reply-To: <9364871.312.1291218472813.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1514251688.516.1349276389385.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-548?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-548: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Investigate why there is a huge number of search entries in the activity logs with empty search terms > ----------------------------------------------------------------------------------------------------- > > Key: BIOCAT-548 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-548 > Project: BioCatalogue > Issue Type: Task > Components: Data > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > It appears that the activity logs indicate a high number of searches. However, the majority of these search are not associated with any search term. This needs to be investigated. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:51 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:51 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-561) Update the public facing BioCatalogue Roadmap In-Reply-To: <5092817.172.1296128110712.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1022737140.517.1349276391485.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-561?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-561: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Update the public facing BioCatalogue Roadmap > --------------------------------------------- > > Key: BIOCAT-561 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-561 > Project: BioCatalogue > Issue Type: Task > Components: Wiki > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.1 > > > The BioCatalogue Roadmap needs to be updated with the 2011 plans. Current roadmap is for 2010! -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:53 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:53 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-568) Double rendering problem when ssl is switched on! In-Reply-To: <27513129.446.1297168809437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1997261068.518.1349276393652.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-568: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Double rendering problem when ssl is switched on! > ------------------------------------------------- > > Key: BIOCAT-568 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568 > Project: BioCatalogue > Issue Type: Bug > Reporter: Eric Nzuobontane > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.1.1 > > > Application issues a double rendering error when ssl is switched on. This has a major impact on all secure pages like loggin -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:56 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:56 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-574) Review the terms in the query suggestions file In-Reply-To: <33436805.622.1297849569376.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21031309.519.1349276396061.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-574?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-574: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Review the terms in the query suggestions file > ---------------------------------------------- > > Key: BIOCAT-574 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-574 > Project: BioCatalogue > Issue Type: Improvement > Affects Versions: 1.0.0 > Environment: RoR, Search > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > Original Estimate: 2 days > Remaining Estimate: 2 days > > The terms in the query suggestions file are generated from search terms by users, tags, categories and synonyms. For the search terms, they are automatically added from the activity logs without the data being screened. This make it possible for rubbish search terms to get listed as suggestions. There should be a process of screening the query suggestions txt file to make the suggestions more sensible( if not precise). -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:15 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-619) Get Solr upgraded to 1.4.1 on the EBI servers In-Reply-To: <20785327.1359.1307718355434.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1186841657.527.1349276415623.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-619?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-619: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Get Solr upgraded to 1.4.1 on the EBI servers > --------------------------------------------- > > Key: BIOCAT-619 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-619 > Project: BioCatalogue > Issue Type: Task > Components: Search / Filtering / Browsing, Server Management > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > The servers at the EBI are currently running Solr 1.3 which isn't available for download any more and has been superseded by Solr 1.4.1. > Look to upgrading Solr to 1.4.1. > Ensure that this is all checked locally first (especially on the staging server VM image) and remember to do a full reindex and (possibly) upgrade the schema file. All steps will need to be recorded to ensure that full instructions are sent to the EBI. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:22 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:22 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-623) Update API docs and changelog to mention this important (but not breaking) change to the API In-Reply-To: <10261285.1408.1308058675347.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <372609644.530.1349276422658.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-623?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-623: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Update API docs and changelog to mention this important (but not breaking) change to the API > -------------------------------------------------------------------------------------------- > > Key: BIOCAT-623 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-623 > Project: BioCatalogue > Issue Type: Sub-task > Components: Documentation > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:25 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:25 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-629) Upgrade to Solr 1.4.1 locally In-Reply-To: <32648861.1442.1308150955351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2038519435.531.1349276425453.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-629?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-629: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Upgrade to Solr 1.4.1 locally > ----------------------------- > > Key: BIOCAT-629 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-629 > Project: BioCatalogue > Issue Type: Sub-task > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > Before upgrading Solr on the live servers (at the EBI), we need to first do this locally and on the staging environment and learn the lessons and document the steps first. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:27 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:27 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-632) Improve the performance of API calls now that return more details In-Reply-To: <31372983.1470.1308220615376.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2121449131.532.1349276427605.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-632?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-632: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Improve the performance of API calls now that return more details > ----------------------------------------------------------------------------- > > Key: BIOCAT-632 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-632 > Project: BioCatalogue > Issue Type: Improvement > Components: Performance / Optimisations, REST API > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.1 > > > Due to the changes introduced in http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-662, the performance of API calls to resources has slowed down considerably. This is largely to do with the large amount of partial rendering. > Improve this! -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:31 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:31 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-641) Find a better way to differentiate (at a glance) between services or soap operations with the same name In-Reply-To: <14314667.1654.1308650284956.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1695693940.534.1349276431911.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-641?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-641: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Find a better way to differentiate (at a glance) between services or soap operations with the same name > ------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-641 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-641 > Project: BioCatalogue > Issue Type: Improvement > Components: SOAP Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.1.1 > > Attachments: -service_providers-240#services.jpg, fix for simple listings.jpg, grid view.jpg, soap operations.jpg > > > There is a long list of services (of type Soaplab) within the BioCatalogue which have the name "Analysis" but are differentiated by the WSDL location. > A similar case exists for soap operations whose name is the same but differ by, for example, the input and output sets. > At a glance, some of these subtleties are not obvious. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:34 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:34 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-642) Failing to parse WSDL: http://www.cbs.dtu.dk/ws/NetCTL/NetCTL_1_2_ws0.wsdl In-Reply-To: <22897105.1684.1308666115355.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1805870314.535.1349276434079.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-642?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-642: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Failing to parse WSDL: http://www.cbs.dtu.dk/ws/NetCTL/NetCTL_1_2_ws0.wsdl > -------------------------------------------------------------------------- > > Key: BIOCAT-642 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-642 > Project: BioCatalogue > Issue Type: Bug > Components: SOAP Services Support > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.1 > > > The following WSDL: > {code} > http://www.cbs.dtu.dk/ws/NetCTL/NetCTL_1_2_ws0.wsdl > {code} > ... fails when trying to parse it. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:36 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:36 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-644) Failing to create new REST endpoints In-Reply-To: <5731097.1711.1308825655356.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <370435254.536.1349276436194.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-644?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-644: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Failing to create new REST endpoints > ------------------------------------ > > Key: BIOCAT-644 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-644 > Project: BioCatalogue > Issue Type: Bug > Components: REST Services Support > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Minor > Fix For: 1.1.1 > > > To duplicate the issue: > # Log in > # Register a new REST service or go to an existing one > # Click on the "REST Endpoints" tab > # Click on "Add New Endpoints" > # Put in a valid new REST endpoint in the text box (e.g. "http://example.org/test/{id}") and submit > You will get the following error message in the web interface: > {code} > The following endpoints could not be added: > ... > {code} > Looking at the logs and db, it looks like a {{RestResource}} is being created (but an incorrect one) but a corresponding {{RestMethod}} is not being created. > Also, possibly not relevant, I keep seeing this in the logs multiple times: > {code} > ERROROAuth::Signature::UnknownSignatureMethod > {code} > *This needs some thorough investigation!* -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:40 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:40 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-651) Reorder service providers index by number of services In-Reply-To: <9184075.2280.1309277515392.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <407448856.538.1349276440657.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-651?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-651: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Reorder service providers index by number of services > ----------------------------------------------------- > > Key: BIOCAT-651 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-651 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.1 > > > Currently, service providers are sorted by latest, but this shows lots of new ones that have the default names based on the hostname, which doesn't look very good at all. > Change the default search order to order by number of services by a provider. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:49 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:49 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-664) New admin feature: activate users In-Reply-To: <12844958.2604.1309775395406.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2025510560.542.1349276449901.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-664?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-664: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > New admin feature: activate users > --------------------------------- > > Key: BIOCAT-664 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-664 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard > Reporter: Jiten Bhagat > Assignee: Robert Haines > Fix For: 1.1.1 > > > Need an admin feature to allow unactivated users to be activated. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:58 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-681) Implement the ability to directly set the display name of a service In-Reply-To: <19283279.132.1311777824765.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <589398535.546.1349276458791.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-681?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-681: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Implement the ability to directly set the display name of a service > ------------------------------------------------------------------- > > Key: BIOCAT-681 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-681 > Project: BioCatalogue > Issue Type: New Feature > Components: Web Interface > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > Right now, to set the display name of a service you need to add an alternative name and then "promote" it to be the display name. > Have a button to easily set the display name for a service in the UI. > Can use the code for the service provider profile page as a starting point / basis. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:56:32 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:56:32 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-709) JSON service summary is broken Message-ID: <1062644913.483.1349276192420.JavaMail.jira@proteus> JSON service summary is broken ------------------------------ Key: BIOCAT-709 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-709 Project: BioCatalogue Issue Type: Bug Components: REST API Affects Versions: 1.1.0 Reporter: Robert Haines Assignee: Robert Haines Priority: Critical Getting data from, e.g., http://www.biocatalogue.org/services/4/summary.json causes a complete breakage. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:58:32 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:58:32 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-691) Update ALL remaining parts of the codebase that has been affected by the polymorphic annotation value changes In-Reply-To: <32054700.15.1315308137266.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <48471094.484.1349276312443.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-691?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-691: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Update ALL remaining parts of the codebase that has been affected by the polymorphic annotation value changes > ------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-691 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-691 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:58:42 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:58:42 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-189) Improve search results ordering Message-ID: <1685808458.488.1349276322344.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-189?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-189: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Improve search results ordering > ------------------------------- > > Key: BIOCAT-189 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-189 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > Right now the ordering of search results isn't great. > Maybe use boosting to ensure that services that contain the word(s) in their names get higher up. > Also MUST look to using the scores directly from SOLR when doing the reordering of results. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:58:52 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:58:52 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-223) Update auto_tagger script to do tags to categories Message-ID: <1154212744.492.1349276332458.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-223?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-223: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Update auto_tagger script to do tags to categories > -------------------------------------------------- > > Key: BIOCAT-223 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-223 > Project: BioCatalogue > Issue Type: Improvement > Components: Misc Codebase > Reporter: Katy Wolstencroft > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > For categories with unambiguous labels, we can find tags with those labels and add categories automatically. > (As suggested by Katy) -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:01 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-249) error_to_home and other such should return appropriate HTTP codes Message-ID: <205556911.496.1349276341188.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-249?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-249: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > error_to_home and other such should return appropriate HTTP codes > ----------------------------------------------------------------- > > Key: BIOCAT-249 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-249 > Project: BioCatalogue > Issue Type: Improvement > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > Methods like error_to_home etc should return appropriate HTTP status codes. Right now there's just a redirect, and no way of telling that a genuine error has occurred. > Need to rethink this whole thing. Maybe beef up the 404 etc error pages and have those served up. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:00 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-591) Investigate running multiple delayed_job workers on the live EBI setup In-Reply-To: <14672693.779.1305818395351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <603489917.521.1349276400398.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-591?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-591: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Investigate running multiple delayed_job workers on the live EBI setup > ---------------------------------------------------------------------- > > Key: BIOCAT-591 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-591 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > Having only one delayed_job worker running means that if it get's clogged up or freezes then all jobs stop getting processed. > Look into having multiple (at least 2 delayed_job workers) running. Possibly one per node. > This needs to be done in a careful manner so as not to break the current set up. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:03 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:03 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-260) Tooltip hover issues Message-ID: <1797822563.497.1349276343474.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-260?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-260: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Tooltip hover issues > -------------------- > > Key: BIOCAT-260 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-260 > Project: BioCatalogue > Issue Type: Bug > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.1.1 > > > As reported by Sergey: > "I've just noticed that the tooltips over 'Latest Services Feed' and > the 'Follow me on Twitter' icons in the action bar appear under these > icons themselves (this doesn't normally happen with other tooltips - at > least not that I've seen)." > Occurs in FF and IE apparently. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:12 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:12 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-296) Add Favourites to the API Message-ID: <25412806.501.1349276352742.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-296?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-296: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Add Favourites to the API > ------------------------- > > Key: BIOCAT-296 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-296 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > Original Estimate: 2 days > Time Spent: 1 hour > Remaining Estimate: 1 day, 7 hours > > Need the ability to get a particular user's favourites -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:24 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:24 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-447) Test SSL on the BioCatalogue main site In-Reply-To: <337413.7600.1280153355313.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1090061109.506.1349276364883.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-447?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-447: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Test SSL on the BioCatalogue main site > -------------------------------------- > > Key: BIOCAT-447 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-447 > Project: BioCatalogue > Issue Type: Sub-task > Components: Misc Codebase > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.1.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:38 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:38 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-650) Docs don't indicate what test scripts should return In-Reply-To: <25235642.2127.1309249675351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1368747050.537.1349276438367.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-650?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-650: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Docs don't indicate what test scripts should return > --------------------------------------------------- > > Key: BIOCAT-650 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-650 > Project: BioCatalogue > Issue Type: Bug > Components: Documentation, Service Monitoring > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.1.1 > > > The script at http://www.biocatalogue.org/service_tests/4872 is failing possibly due to the return values (it returns back the content from the HTTP request). > My understanding is that scripts need to return an integer code where 0 means everything went okay and anything apart from that indicates an error code. > However *it's not clear anywhere* in the [documentation|http://www.biocatalogue.org/wiki/doku.php?id=development:testscripts_in_biocatalogue], nor the web interface, what script writers should return in their scripts to fit in with the monitoring framework! > We need to check the code for the test harness to see what exactly it requires as return values and then update the documentation and make it much clearer in the UI how people can go about submitting scripts, giving them adequate guidance in the process. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:58:47 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:58:47 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-219) Search indexing for annotations Message-ID: <743058162.490.1349276327393.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-219?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-219: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Search indexing for annotations > ------------------------------- > > Key: BIOCAT-219 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-219 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > 2 things here: > 1. Make sure that when you do the categories work, that the ID (which is what is stored as the value) is not what gets indexed, rather, the actual category label itself! > 2. Maybe certain types of annotations, like name aliases, should have a boost, when indexed. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:58 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-578) Add Services Responsible For to the API In-Reply-To: <14336558.12.1298290504895.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1692192319.520.1349276398114.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-578?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-578: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Add Services Responsible For to the API > --------------------------------------- > > Key: BIOCAT-578 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-578 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > Time Spent: 1 hour > Remaining Estimate: 0 minutes > > Need the ability to get the list of services a user is *responsible* for -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:01:00 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:01:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-684) /lookup call is not working when Accept header is set to application/xml In-Reply-To: <6211393.15.1313503781808.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <925274823.547.1349276460828.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-684?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-684: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > /lookup call is not working when Accept header is set to application/xml > ------------------------------------------------------------------------ > > Key: BIOCAT-684 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-684 > Project: BioCatalogue > Issue Type: Bug > Components: REST API > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.1 > > > The following lookup call: > http://sandbox.biocatalogue.org/lookup?wsdl_location=http://ws.adaptivedisclosure.org/axis/services/SearcherWS?wsdl > ... works OK in the browser. BUT when calling it via the command line (etc) using an Accept header of "application/xml" it fails with an HTTP 400. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:02 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-601) Annotation attributes need to store descriptions, labels, etc about themselves In-Reply-To: <23929179.1016.1307616355378.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <586436368.522.1349276402965.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-601?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-601: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Annotation attributes need to store descriptions, labels, etc about themselves > ------------------------------------------------------------------------------ > > Key: BIOCAT-601 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-601 > Project: BioCatalogue > Issue Type: Improvement > Components: Annotations (in App), Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:58:56 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:58:56 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-231) Enable tag filter not persisting Message-ID: <1179493056.494.1349276336723.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-231?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-231: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Enable tag filter not persisting > -------------------------------- > > Key: BIOCAT-231 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-231 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > the 'enable tag filter' doesn't stay. i have to keep on clicking on it anytime i want to browse for new services...very frustrating. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:58:50 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:58:50 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-709) JSON service summary is broken In-Reply-To: <1062644913.483.1349276192420.JavaMail.jira@proteus> Message-ID: <674436656.491.1349276330178.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-709?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel\#worklog-{worklog.getId()} ] Robert Haines logged work on BIOCAT-709: ---------------------------------------- Author: Robert Haines Created on: 2012-10-03 15:58 Start Date: 2012-10-03 15:58 Worklog Time Spent: 2 hours Work Description: Slightly delayed trying to navigate round JSON code Issue Time Tracking ------------------- Remaining Estimate: 0 minutes (was: 2 hours) Time Spent: 2 hours Worklog Id: (was: 10614) > JSON service summary is broken > ------------------------------ > > Key: BIOCAT-709 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-709 > Project: BioCatalogue > Issue Type: Bug > Components: REST API > Affects Versions: 1.1.0 > Reporter: Robert Haines > Assignee: Robert Haines > Priority: Critical > Original Estimate: 2 hours > Time Spent: 2 hours > Remaining Estimate: 0 minutes > > Getting data from, e.g., http://www.biocatalogue.org/services/4/summary.json causes a complete breakage. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:10 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:10 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-289) Filters disappear when I switch between different views Message-ID: <1011898201.500.1349276350586.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-289?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-289: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Filters disappear when I switch between different views > ------------------------------------------------------- > > Key: BIOCAT-289 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-289 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > When I filter services (e.g by provider, location etc.) and switch to simple view for example, it clears off all the selected filters. > Need to remember the filters selected when switching views. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:42 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:42 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-656) Change styling of all dropdown menus / buttons on the various show pages so that they are more prominent as actions In-Reply-To: <69462.2296.1309338715350.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <951419767.539.1349276442662.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-656?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-656: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Change styling of all dropdown menus / buttons on the various show pages so that they are more prominent as actions > ------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-656 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-656 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > Currently, the action buttons on pages like the services profile page are just not prominent enough. > Make this very obvious by turning it into a toolbar like thing. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:08 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:08 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-611) Create a staging server VM image that matches the EBI's set up In-Reply-To: <26593137.1328.1307699817683.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <431157894.524.1349276408653.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-611?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-611: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Create a staging server VM image that matches the EBI's set up > -------------------------------------------------------------- > > Key: BIOCAT-611 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-611 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > Time Spent: 2 weeks > Remaining Estimate: 0 minutes > > We need a VM image that closely matches the set up at the EBI, so we can use that as a staging environment before test and live deployments. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:17 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-620) Filtering options should only return those filter options that are available within the context In-Reply-To: <12682775.1380.1307975575355.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1986569132.528.1349276417632.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-620: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Filtering options should only return those filter options that are available within the context > ----------------------------------------------------------------------------------------------- > > Key: BIOCAT-620 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620 > Project: BioCatalogue > Issue Type: Bug > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.1 > > Time Spent: 4 hours > Remaining Estimate: 0 minutes > > Currently, whenever a set of filter options are returned, it will show ALL possible filter options on that resource rather than the just one's available within the current context. > For example, if you do: > http://sandbox.biocatalogue.org/soap_operations.xml?q=blast > ... and follow: > http://sandbox.biocatalogue.org/soap_operations/filters?q=blast > ... it **should** give you only the filter options that are available from there, not ALL filters on SOAP Operations. > This needs to be fixed both for the web interface AND API. > *NOTE*: the counts need to be fixed too. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:36 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:36 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-500) Document how to use and update the VM In-Reply-To: <16227861.9965.1286463195301.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1839510178.511.1349276376526.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-500?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-500: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Document how to use and update the VM > ------------------------------------- > > Key: BIOCAT-500 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-500 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > Original Estimate: 3 hours > Remaining Estimate: 3 hours > > Document how to set up, use and update the BioCatalogue VM. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:45 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:45 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-661) New admin feature: merge user accounts In-Reply-To: <13421585.2502.1309508095487.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <719581977.540.1349276445139.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-661?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-661: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > New admin feature: merge user accounts > -------------------------------------- > > Key: BIOCAT-661 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-661 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard > Reporter: Jiten Bhagat > Assignee: Robert Haines > Priority: Critical > Fix For: 1.1.1 > > > We need an admins only tool to merge user accounts in a sane, consistent and safe way. > An important case has come up from Marco. He has 2 user accounts: > - http://www.biocatalogue.org/users/48 > - http://www.biocatalogue.org/users/637 > He would like 637 to be merged *fully* into 48, i.e. all annotations, all credentials, and so on. > Build an admin tool in the Curation Dashboard too allow anyone logged in as an admin to do this. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:47 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:47 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-662) Allow those responsible for a service to edit it's WSDL location In-Reply-To: <22914152.2503.1309509295351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1462229621.541.1349276447637.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-662?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-662: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Allow those responsible for a service to edit it's WSDL location > ---------------------------------------------------------------- > > Key: BIOCAT-662 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-662 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API, Service Container, Web Interface > Reporter: Jiten Bhagat > Assignee: Robert Haines > Priority: Blocker > Fix For: 1.1.1 > > > Both Jose (from the INB services) and Marco have asked for the ability to edit the WSDL location for a service. > Implement a feature to allow this in the web interface AND API. > Make sure to store an activity log when this happens, with the old and new WSDL location values registered. > Can just reuse the {{wsdl_files}} table to store this change. > Also need to trigger a service update. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:44 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-536) Update the annotation field mappings both in the API docs and wiki In-Reply-To: <7210831.567.1289922389159.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <819366718.514.1349276384632.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-536: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Update the annotation field mappings both in the API docs and wiki > ------------------------------------------------------------------ > > Key: BIOCAT-536 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.1 > > > Update the annotation field mappings both in the [API docs|http://www.biocatalogue.org/wiki/doku.php?id=public:api#annotation_fields_breakdown] and the [Annotations wiki page|http://www.biocatalogue.org/wiki/doku.php?id=development:annotation] -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:05 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:05 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-607) Refactor out annotation values as first class polymorphic objects In-Reply-To: <22920035.1301.1307630815347.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <73608965.523.1349276405693.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-607?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-607: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Refactor out annotation values as first class polymorphic objects > ----------------------------------------------------------------- > > Key: BIOCAT-607 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-607 > Project: BioCatalogue > Issue Type: Improvement > Components: Annotations (in App), Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.1 > > Time Spent: 2 days, 4 hours > Remaining Estimate: 0 minutes > > Currently, values in annotations are just a string. This needs to be stripped out into first class objects such as: > - Tag > - Code / Script (?) > - TextValue (should be made available in plugin) > etc. > This will help with performance as then you wouldn't need to do GROUP BY queries on strings in the db, and in general it would be nicer model to worth with. > BUT NOTE: this would require some comprehensive and meticulous fine-combing of the whole system to ensure nothing breaks as a result. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:39 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:39 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-509) Document the user roles and privileges used in the system In-Reply-To: <16709321.10450.1288606635350.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1070847305.512.1349276379375.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-509?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-509: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Document the user roles and privileges used in the system > --------------------------------------------------------- > > Key: BIOCAT-509 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-509 > Project: BioCatalogue > Issue Type: Task > Components: Documentation > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.1.1 > > > George Atala asked... > {quote} > Hello, > We started experimenting with BioCatalogue, and were able to install an instance fairly easily -- thanks for the excellent documentation. > I was wondering how users can be assigned admin roles. Are there other roles one should be using for basic operation? > Many thanks, > George > {quote} > Jits responded with... > {quote} > At the moment it's a fairly lightweight roles system - admins (value: 1) and curators (value: 2) are the only real roles used. If role_id is not specified then these are just "normal" users. > Curators and admins basically have full permissions to do things in the catalogue - delete services, annotations and so on. Admins have slightly more priviledges. > Currently, to set the roles you would have to manually update the entry in the database (or via the Rails console). We hope to have much nicer roles management in the future. > {quote} > We need to document the exact roles and privileges used in the system. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 14:59:06 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 15:59:06 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-267) In Annotations plugin - check the setting of "source" when creating annotations Message-ID: <363219255.498.1349276346090.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-267?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-267: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > In Annotations plugin - check the setting of "source" when creating annotations > ------------------------------------------------------------------------------- > > Key: BIOCAT-267 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-267 > Project: BioCatalogue > Issue Type: Task > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.1 > > > Currently the create method will set the source to the current_user if no source data is provided in the params hash. Should we allow setting an arbitrary source via params? How about having a configuration setting "restricted_source_types" that prevents creation of annotation (via params) that have those source types. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:29 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:29 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-634) Figure out how to properly record monitoring information for REST endpoints tested using example_endpoint annotations In-Reply-To: <9393676.1563.1308306595396.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1832886370.533.1349276429653.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-634?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-634: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Figure out how to properly record monitoring information for REST endpoints tested using example_endpoint annotations > --------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-634 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-634 > Project: BioCatalogue > Issue Type: Task > Components: REST Services Support, Service Monitoring > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > Fix For: 1.1.1 > > > The monitoring framework uses example_endpoint annotations to monitor the availability of REST services. Some of these annotations contain: > * multiple valid URIs separated by some delimiter; > * one or more valid URIs embedded within some other descriptive text; > * no valid URIs; > * a combination of the above cases. > A patch was added in rev. 2420 so that a UrlMonitor is either not created or is deleted if no valid URI can be found within the annotation. > Also, there is also no obvious way of recording which endpoint has been pinged for the case of example_endpoint annotations with multiple valid URIs; this patch pings the first valid endpoint from the annotation and embeds this information within the message attribute of a TestResult object. A "proper" way of storing this information is needed as the message attribute of TestResult is reserved for HTTP header info. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:54 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:54 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-678) Create update script on staging VM image In-Reply-To: <18461761.4.1311758924787.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1484727422.544.1349276454242.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-678?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-678: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Create update script on staging VM image > ---------------------------------------- > > Key: BIOCAT-678 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-678 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.1 > > > Need an update script, like the one on the sandbox server, that performs the basic update steps (including starting/stopping Solr). -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:13 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:13 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-617) Investigate the breakage related to the service monitoring framework In-Reply-To: <19384335.1347.1307706955354.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1228222538.526.1349276413269.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-617?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-617: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Investigate the breakage related to the service monitoring framework > -------------------------------------------------------------------- > > Key: BIOCAT-617 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-617 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > Fix For: 1.1.1 > > Time Spent: 3 hours > Remaining Estimate: 0 minutes > > Test scripts are not being executed -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:56 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:56 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-679) Test SSL on the BioCatalogue sandbox In-Reply-To: <7008757.20.1311763964719.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <884030859.545.1349276456457.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-679?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-679: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Test SSL on the BioCatalogue sandbox > ------------------------------------ > > Key: BIOCAT-679 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-679 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > Fix For: 1.1.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:20 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:20 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-621) Incorrect number of results being returned from filtering In-Reply-To: <12562916.1399.1308049975350.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <673361499.529.1349276420348.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-621?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-621: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Incorrect number of results being returned from filtering > --------------------------------------------------------- > > Key: BIOCAT-621 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-621 > Project: BioCatalogue > Issue Type: Bug > Components: Search / Filtering / Browsing > Reporter: Alan Williams > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.1 > > > if you look at: > http://sandbox.biocatalogue.org/soap_operations/filters.xml?q=fasta > ... and take the filter: > {code} > > {code} > ... i.e. the filtered index: > http://sandbox.biocatalogue.org/soap_operations.xml?q=fasta&tag_ops=%5Bblast%5D > ... it returns 4 items instead of the reported 3. > Investigate. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:51 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:51 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-674) Possibly open up the Annotations bulk_create endpoint for all users In-Reply-To: <26739837.3024.1310477575433.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <842036059.543.1349276451922.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-674?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-674: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Possibly open up the Annotations bulk_create endpoint for all users > ------------------------------------------------------------------- > > Key: BIOCAT-674 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-674 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.1 > > > Currently, the bulk annotations endpoint (/annotations/bulk_create) is protected and only usable by admins and curators. We need to consider opening this up all users as it is needed by Manolis (Sean's provenance student), and may be needed by others. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:00:10 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:00:10 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-616) Need to deal with the deprecation/retiring of the Creative Commons Public Domain License In-Reply-To: <18000113.1340.1307703235352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1594040633.525.1349276410892.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-616?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-616: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Need to deal with the deprecation/retiring of the Creative Commons Public Domain License > ---------------------------------------------------------------------------------------- > > Key: BIOCAT-616 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-616 > Project: BioCatalogue > Issue Type: Task > Components: Data > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.1 > > > According to the [Terms of Use|http://www.biocatalogue.org/termsofuse], the content of the BioCatalogue is licensed under the [Creative Commons Public Domain License|http://creativecommons.org/licenses/publicdomain/]. However, this has been [_retired_ late in 2010|http://creativecommons.org/retiredlicenses]. > Need to look into alternative licensing of content and prepare a transition process, which includes notifying everyone. > Possible alternative licenses (that are compatible): > * [CC0 1.0 Universal (Public Domain License)|http://creativecommons.org/publicdomain/zero/1.0/] -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 3 15:01:03 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 3 Oct 2012 16:01:03 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-685) Search for existing services based on old WSDL URLs In-Reply-To: <14338417.148.1314200201760.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <537877423.548.1349276463577.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-685?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-685: --------------------------------- Fix Version/s: 1.1.1 (was: 1.1.0) > Search for existing services based on old WSDL URLs > ---------------------------------------------------- > > Key: BIOCAT-685 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-685 > Project: BioCatalogue > Issue Type: Sub-task > Components: Search / Filtering / Browsing > Affects Versions: 1.0.1 > Reporter: Robert Haines > Assignee: Robert Haines > Fix For: 1.1.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Wed Oct 3 15:16:05 2012 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Oct 2012 15:16:05 +0000 (UTC) Subject: [BioCatalogue-developers] [2547] trunk/version_info.yml: Bump version number to 1.1.1 Message-ID: <20121003151605.DB3A62E060@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Oct 4 11:23:33 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 4 Oct 2012 12:23:33 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-710) Service 3322 errors on examples page/tab Message-ID: <1042012323.549.1349349813854.JavaMail.jira@proteus> Service 3322 errors on examples page/tab ---------------------------------------- Key: BIOCAT-710 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-710 Project: BioCatalogue Issue Type: Bug Components: Data, Misc Codebase Reporter: Robert Haines Assignee: Robert Haines I *looks* like there is a data inconsistency in the database. Maybe there is a RestMethod with a null parameter? I could just test for nil in the relevant places, but there are plenty of other services without this problem so I suspect bad data. I need to check the actual DB so I will ask for the latest dump to confirm this. Error transcript follows: {code} A NoMethodError occurred in services#examples: undefined method `annotations_with_attribute' for nil:NilClass [RAILS_ROOT]/app/models/service.rb:437:in `data_example_annotations' ------------------------------- Request: ------------------------------- * URL : http://www.biocatalogue.org/services/3322/examples?authenticity_token=Izs4mo8NXDDlzPTbMK%2FIKUtB6R43GJKlsaC55TPOK4M%3D * Method : GET * IP address: 94.192.243.24 * Parameters: {"action"=>"examples", "protocol"=>"http", "authenticity_token"=>"Izs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M=", "id"=>"3322", "controller"=>"services"} * Rails root: /net/isilonP/public/rw/es/projects/biocatalogue/live/trunk_2545 ------------------------------- Session: ------------------------------- * session id: nil * data: nil ------------------------------- Environment: ------------------------------- * DOCUMENT_ROOT : /nfs/public/rw/es/projects/biocatalogue/live/current/public * HTTP_ACCEPT : text/javascript, text/html, application/xml, text/xml, */* * HTTP_ACCEPT_CHARSET : ISO-8859-1,utf-8;q=0.7,*;q=0.3 * HTTP_ACCEPT_ENCODING : gzip,deflate,sdch * HTTP_ACCEPT_LANGUAGE : en-GB,en-US;q=0.8,en;q=0.6 * HTTP_CONNECTION : keep-alive * HTTP_COOKIE : service-tabs_tabber=2; stats-tabs_tabber=0; _session_id=98f68899cde3694341b7ecca70508874; __utma=15951013.1947546072.1321612577.1349281130.1349343123.104; __utmb=15951013.28.10.1349343123; __utmc=15951013; __utmz=15951013.1337894854.65.3.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=http://www.biocatalogue.org/; __atuvc=38%7C36%2C2%7C37%2C0%7C38%2C0%7C39%2C31%7C40 * HTTP_HOST : www.biocatalogue.org * HTTP_REFERER : http://www.biocatalogue.org/services/3322 * HTTP_USER_AGENT : Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.79 Safari/537.4 * HTTP_X_CLUSTER_CLIENT_IP : 94.192.243.24 * HTTP_X_PROTOTYPE_VERSION : 1.6.0.3 * HTTP_X_REQUESTED_WITH : XMLHttpRequest * PATH_INFO : /services/3322/examples * QUERY_STRING : authenticity_token=Izs4mo8NXDDlzPTbMK%2FIKUtB6R43GJKlsaC55TPOK4M%3D * REMOTE_ADDR : 94.192.243.24 * REMOTE_PORT : 36442 * REQUEST_METHOD : GET * REQUEST_URI : /services/3322/examples?authenticity_token=Izs4mo8NXDDlzPTbMK%2FIKUtB6R43GJKlsaC55TPOK4M%3D * SCRIPT_NAME : * SERVER_ADDR : 10.3.0.47 * 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) * ZEUS_LOAD_BALANCER_ADDR : 193.62.197.26 * _ : _ * action_controller.request.query_parameters : authenticity_tokenIzs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M= * 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 : __utma15951013.1947546072.1321612577.1349281130.1349343123.104__utmb15951013.28.10.1349343123service-tabs_tabber2_session_id98f68899cde3694341b7ecca70508874__utmc15951013stats-tabs_tabber0__utmz15951013.1337894854.65.3.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=http://www.biocatalogue.org/__atuvc38|36,2|37,0|38,0|39,31|40 * rack.request.cookie_string : service-tabs_tabber=2; stats-tabs_tabber=0; _session_id=98f68899cde3694341b7ecca70508874; __utma=15951013.1947546072.1321612577.1349281130.1349343123.104; __utmb=15951013.28.10.1349343123; __utmc=15951013; __utmz=15951013.1337894854.65.3.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=http://www.biocatalogue.org/; __atuvc=38%7C36%2C2%7C37%2C0%7C38%2C0%7C39%2C31%7C40 * rack.request.query_hash : authenticity_tokenIzs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M= * rack.request.query_string : authenticity_token=Izs4mo8NXDDlzPTbMK%2FIKUtB6R43GJKlsaC55TPOK4M%3D * rack.routing_args : protocolhttpactionexamplesid3322controllerservices * rack.run_once : false * rack.session : previous_url/services/3322user_id829use_tab_cookiefalse_csrf_tokenIzs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M=flash * rack.session.options : key_session_idpath/expire_afterdomainhttponlytrueid98f68899cde3694341b7ecca70508874cookie_onlytruesecurefalse * rack.session.record : # * rack.url_scheme : http * rack.version : 10 * Process: 31486 * Server : ves-hx-2f * request.format: text/javascript ------------------------------- Backtrace: ------------------------------- [RAILS_ROOT]/app/models/service.rb:437:in `data_example_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]/app/models/service.rb:433:in `data_example_annotations' [RAILS_ROOT]/app/models/service.rb:426:in `each' [RAILS_ROOT]/app/models/service.rb:426:in `data_example_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]/app/models/service.rb:413:in `data_example_annotations' [RAILS_ROOT]/app/controllers/services_controller.rb:321:in `examples' [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' /nfs/public/rw/webadmin/ruby/ruby-enterprise-1.8.7-2010.02/lib/ruby/1.8/benchmark.rb:308: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' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:92:in `process_request' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_request_handler.rb:207:in `main_loop' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:441:in `start_request_handler' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:381:in `handle_spawn_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/utils.rb:252:in `safe_fork' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:377:in `handle_spawn_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:163:in `start' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:222:in `start' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:253:in `spawn_rails_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:247:in `spawn_rails_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:246:in `spawn_rails_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:145:in `spawn_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:278:in `handle_spawn_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/bin/passenger-spawn-server:61 {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 4 11:23:36 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 4 Oct 2012 12:23:36 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-710) Service 3322 errors on examples page/tab In-Reply-To: <1042012323.549.1349349813854.JavaMail.jira@proteus> Message-ID: <1416199619.550.1349349816354.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-710?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel\#worklog-{worklog.getId()} ] Robert Haines logged work on BIOCAT-710: ---------------------------------------- Author: Robert Haines Created on: 2012-10-04 12:23 Start Date: 2012-10-04 12:23 Worklog Time Spent: 1 day Issue Time Tracking ------------------- Remaining Estimate: 1 day (was: 2 days) Time Spent: 1 day Worklog Id: (was: 10615) > Service 3322 errors on examples page/tab > ---------------------------------------- > > Key: BIOCAT-710 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-710 > Project: BioCatalogue > Issue Type: Bug > Components: Data, Misc Codebase > Reporter: Robert Haines > Assignee: Robert Haines > Original Estimate: 2 days > Time Spent: 1 day > Remaining Estimate: 1 day > > I *looks* like there is a data inconsistency in the database. Maybe there is a RestMethod with a null parameter? > I could just test for nil in the relevant places, but there are plenty of other services without this problem so I suspect bad data. I need to check the actual DB so I will ask for the latest dump to confirm this. > Error transcript follows: > {code} > A NoMethodError occurred in services#examples: > undefined method `annotations_with_attribute' for nil:NilClass > [RAILS_ROOT]/app/models/service.rb:437:in `data_example_annotations' > ------------------------------- > Request: > ------------------------------- > * URL : http://www.biocatalogue.org/services/3322/examples?authenticity_token=Izs4mo8NXDDlzPTbMK%2FIKUtB6R43GJKlsaC55TPOK4M%3D > * Method : GET > * IP address: 94.192.243.24 > * Parameters: {"action"=>"examples", "protocol"=>"http", "authenticity_token"=>"Izs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M=", "id"=>"3322", "controller"=>"services"} > * Rails root: /net/isilonP/public/rw/es/projects/biocatalogue/live/trunk_2545 > ------------------------------- > Session: > ------------------------------- > * session id: nil > * data: nil > ------------------------------- > Environment: > ------------------------------- > * DOCUMENT_ROOT : /nfs/public/rw/es/projects/biocatalogue/live/current/public > * HTTP_ACCEPT : text/javascript, text/html, application/xml, text/xml, */* > * HTTP_ACCEPT_CHARSET : ISO-8859-1,utf-8;q=0.7,*;q=0.3 > * HTTP_ACCEPT_ENCODING : gzip,deflate,sdch > * HTTP_ACCEPT_LANGUAGE : en-GB,en-US;q=0.8,en;q=0.6 > * HTTP_CONNECTION : keep-alive > * HTTP_COOKIE : service-tabs_tabber=2; stats-tabs_tabber=0; _session_id=98f68899cde3694341b7ecca70508874; __utma=15951013.1947546072.1321612577.1349281130.1349343123.104; __utmb=15951013.28.10.1349343123; __utmc=15951013; __utmz=15951013.1337894854.65.3.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=http://www.biocatalogue.org/; __atuvc=38%7C36%2C2%7C37%2C0%7C38%2C0%7C39%2C31%7C40 > * HTTP_HOST : www.biocatalogue.org > * HTTP_REFERER : http://www.biocatalogue.org/services/3322 > * HTTP_USER_AGENT : Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.79 Safari/537.4 > * HTTP_X_CLUSTER_CLIENT_IP : 94.192.243.24 > * HTTP_X_PROTOTYPE_VERSION : 1.6.0.3 > * HTTP_X_REQUESTED_WITH : XMLHttpRequest > * PATH_INFO : /services/3322/examples > * QUERY_STRING : authenticity_token=Izs4mo8NXDDlzPTbMK%2FIKUtB6R43GJKlsaC55TPOK4M%3D > * REMOTE_ADDR : 94.192.243.24 > * REMOTE_PORT : 36442 > * REQUEST_METHOD : GET > * REQUEST_URI : /services/3322/examples?authenticity_token=Izs4mo8NXDDlzPTbMK%2FIKUtB6R43GJKlsaC55TPOK4M%3D > * SCRIPT_NAME : > * SERVER_ADDR : 10.3.0.47 > * 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) > * ZEUS_LOAD_BALANCER_ADDR : 193.62.197.26 > * _ : _ > * action_controller.request.query_parameters : authenticity_tokenIzs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M= > * 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 : __utma15951013.1947546072.1321612577.1349281130.1349343123.104__utmb15951013.28.10.1349343123service-tabs_tabber2_session_id98f68899cde3694341b7ecca70508874__utmc15951013stats-tabs_tabber0__utmz15951013.1337894854.65.3.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=http://www.biocatalogue.org/__atuvc38|36,2|37,0|38,0|39,31|40 > * rack.request.cookie_string : service-tabs_tabber=2; stats-tabs_tabber=0; _session_id=98f68899cde3694341b7ecca70508874; __utma=15951013.1947546072.1321612577.1349281130.1349343123.104; __utmb=15951013.28.10.1349343123; __utmc=15951013; __utmz=15951013.1337894854.65.3.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=http://www.biocatalogue.org/; __atuvc=38%7C36%2C2%7C37%2C0%7C38%2C0%7C39%2C31%7C40 > * rack.request.query_hash : authenticity_tokenIzs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M= > * rack.request.query_string : authenticity_token=Izs4mo8NXDDlzPTbMK%2FIKUtB6R43GJKlsaC55TPOK4M%3D > * rack.routing_args : protocolhttpactionexamplesid3322controllerservices > * rack.run_once : false > * rack.session : previous_url/services/3322user_id829use_tab_cookiefalse_csrf_tokenIzs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M=flash > * rack.session.options : key_session_idpath/expire_afterdomainhttponlytrueid98f68899cde3694341b7ecca70508874cookie_onlytruesecurefalse > * rack.session.record : # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 31486 > * Server : ves-hx-2f > > * request.format: text/javascript > ------------------------------- > Backtrace: > ------------------------------- > [RAILS_ROOT]/app/models/service.rb:437:in `data_example_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]/app/models/service.rb:433:in `data_example_annotations' > [RAILS_ROOT]/app/models/service.rb:426:in `each' > [RAILS_ROOT]/app/models/service.rb:426:in `data_example_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]/app/models/service.rb:413:in `data_example_annotations' > [RAILS_ROOT]/app/controllers/services_controller.rb:321:in `examples' > [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' > /nfs/public/rw/webadmin/ruby/ruby-enterprise-1.8.7-2010.02/lib/ruby/1.8/benchmark.rb:308: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' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:92:in `process_request' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_request_handler.rb:207:in `main_loop' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:441:in `start_request_handler' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:381:in `handle_spawn_application' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/utils.rb:252:in `safe_fork' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:377:in `handle_spawn_application' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:163:in `start' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:222:in `start' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:253:in `spawn_rails_application' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:247:in `spawn_rails_application' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:246:in `spawn_rails_application' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:145:in `spawn_application' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:278:in `handle_spawn_application' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/bin/passenger-spawn-server:61 > {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 4 11:25:32 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 4 Oct 2012 12:25:32 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-710) Service 3322 errors on examples page/tab In-Reply-To: <1042012323.549.1349349813854.JavaMail.jira@proteus> Message-ID: <2129409938.551.1349349932429.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-710?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-710: --------------------------------- Priority: Minor (was: Major) > Service 3322 errors on examples page/tab > ---------------------------------------- > > Key: BIOCAT-710 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-710 > Project: BioCatalogue > Issue Type: Bug > Components: Data, Misc Codebase > Reporter: Robert Haines > Assignee: Robert Haines > Priority: Minor > Original Estimate: 2 days > Time Spent: 1 day > Remaining Estimate: 1 day > > I *looks* like there is a data inconsistency in the database. Maybe there is a RestMethod with a null parameter? > I could just test for nil in the relevant places, but there are plenty of other services without this problem so I suspect bad data. I need to check the actual DB so I will ask for the latest dump to confirm this. > Error transcript follows: > {code} > A NoMethodError occurred in services#examples: > undefined method `annotations_with_attribute' for nil:NilClass > [RAILS_ROOT]/app/models/service.rb:437:in `data_example_annotations' > ------------------------------- > Request: > ------------------------------- > * URL : http://www.biocatalogue.org/services/3322/examples?authenticity_token=Izs4mo8NXDDlzPTbMK%2FIKUtB6R43GJKlsaC55TPOK4M%3D > * Method : GET > * IP address: 94.192.243.24 > * Parameters: {"action"=>"examples", "protocol"=>"http", "authenticity_token"=>"Izs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M=", "id"=>"3322", "controller"=>"services"} > * Rails root: /net/isilonP/public/rw/es/projects/biocatalogue/live/trunk_2545 > ------------------------------- > Session: > ------------------------------- > * session id: nil > * data: nil > ------------------------------- > Environment: > ------------------------------- > * DOCUMENT_ROOT : /nfs/public/rw/es/projects/biocatalogue/live/current/public > * HTTP_ACCEPT : text/javascript, text/html, application/xml, text/xml, */* > * HTTP_ACCEPT_CHARSET : ISO-8859-1,utf-8;q=0.7,*;q=0.3 > * HTTP_ACCEPT_ENCODING : gzip,deflate,sdch > * HTTP_ACCEPT_LANGUAGE : en-GB,en-US;q=0.8,en;q=0.6 > * HTTP_CONNECTION : keep-alive > * HTTP_COOKIE : service-tabs_tabber=2; stats-tabs_tabber=0; _session_id=98f68899cde3694341b7ecca70508874; __utma=15951013.1947546072.1321612577.1349281130.1349343123.104; __utmb=15951013.28.10.1349343123; __utmc=15951013; __utmz=15951013.1337894854.65.3.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=http://www.biocatalogue.org/; __atuvc=38%7C36%2C2%7C37%2C0%7C38%2C0%7C39%2C31%7C40 > * HTTP_HOST : www.biocatalogue.org > * HTTP_REFERER : http://www.biocatalogue.org/services/3322 > * HTTP_USER_AGENT : Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.79 Safari/537.4 > * HTTP_X_CLUSTER_CLIENT_IP : 94.192.243.24 > * HTTP_X_PROTOTYPE_VERSION : 1.6.0.3 > * HTTP_X_REQUESTED_WITH : XMLHttpRequest > * PATH_INFO : /services/3322/examples > * QUERY_STRING : authenticity_token=Izs4mo8NXDDlzPTbMK%2FIKUtB6R43GJKlsaC55TPOK4M%3D > * REMOTE_ADDR : 94.192.243.24 > * REMOTE_PORT : 36442 > * REQUEST_METHOD : GET > * REQUEST_URI : /services/3322/examples?authenticity_token=Izs4mo8NXDDlzPTbMK%2FIKUtB6R43GJKlsaC55TPOK4M%3D > * SCRIPT_NAME : > * SERVER_ADDR : 10.3.0.47 > * 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) > * ZEUS_LOAD_BALANCER_ADDR : 193.62.197.26 > * _ : _ > * action_controller.request.query_parameters : authenticity_tokenIzs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M= > * 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 : __utma15951013.1947546072.1321612577.1349281130.1349343123.104__utmb15951013.28.10.1349343123service-tabs_tabber2_session_id98f68899cde3694341b7ecca70508874__utmc15951013stats-tabs_tabber0__utmz15951013.1337894854.65.3.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=http://www.biocatalogue.org/__atuvc38|36,2|37,0|38,0|39,31|40 > * rack.request.cookie_string : service-tabs_tabber=2; stats-tabs_tabber=0; _session_id=98f68899cde3694341b7ecca70508874; __utma=15951013.1947546072.1321612577.1349281130.1349343123.104; __utmb=15951013.28.10.1349343123; __utmc=15951013; __utmz=15951013.1337894854.65.3.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=http://www.biocatalogue.org/; __atuvc=38%7C36%2C2%7C37%2C0%7C38%2C0%7C39%2C31%7C40 > * rack.request.query_hash : authenticity_tokenIzs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M= > * rack.request.query_string : authenticity_token=Izs4mo8NXDDlzPTbMK%2FIKUtB6R43GJKlsaC55TPOK4M%3D > * rack.routing_args : protocolhttpactionexamplesid3322controllerservices > * rack.run_once : false > * rack.session : previous_url/services/3322user_id829use_tab_cookiefalse_csrf_tokenIzs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M=flash > * rack.session.options : key_session_idpath/expire_afterdomainhttponlytrueid98f68899cde3694341b7ecca70508874cookie_onlytruesecurefalse > * rack.session.record : # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 31486 > * Server : ves-hx-2f > > * request.format: text/javascript > ------------------------------- > Backtrace: > ------------------------------- > [RAILS_ROOT]/app/models/service.rb:437:in `data_example_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]/app/models/service.rb:433:in `data_example_annotations' > [RAILS_ROOT]/app/models/service.rb:426:in `each' > [RAILS_ROOT]/app/models/service.rb:426:in `data_example_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]/app/models/service.rb:413:in `data_example_annotations' > [RAILS_ROOT]/app/controllers/services_controller.rb:321:in `examples' > [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' > /nfs/public/rw/webadmin/ruby/ruby-enterprise-1.8.7-2010.02/lib/ruby/1.8/benchmark.rb:308: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' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:92:in `process_request' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_request_handler.rb:207:in `main_loop' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:441:in `start_request_handler' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:381:in `handle_spawn_application' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/utils.rb:252:in `safe_fork' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:377:in `handle_spawn_application' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:163:in `start' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:222:in `start' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:253:in `spawn_rails_application' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:247:in `spawn_rails_application' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:246:in `spawn_rails_application' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:145:in `spawn_application' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:278:in `handle_spawn_application' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' > /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/bin/passenger-spawn-server:61 > {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 4 11:30:32 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 4 Oct 2012 12:30:32 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-711) Search by data appears to be broken Message-ID: <1819803778.552.1349350232407.JavaMail.jira@proteus> Search by data appears to be broken ----------------------------------- Key: BIOCAT-711 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-711 Project: BioCatalogue Issue Type: Bug Components: Search / Filtering / Browsing Affects Versions: 1.1.0 Reporter: Robert Haines Assignee: Robert Haines Fix For: 1.1.1 This could have happened in the 1.1.0 update. Error transcript follows: {code} A ActiveRecord::StatementInvalid occurred in search#by_data: Mysql::Error: Unknown column 'annotations.value' in 'where clause': SELECT `annotation_properties`.* FROM `annotation_properties` INNER JOIN `annotations` ON `annotations`.id = `annotation_properties`.annotation_id WHERE (annotations.annotatable_type = 'SoapInput' AND annotation_properties.property_type= 'DataSearchRegex' AND annotation_properties.value='1' AND CHAR_LENGTH(annotations.value)>=0) [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract_adapter.rb:212:in `log' ------------------------------- Request: ------------------------------- * URL : http://www.biocatalogue.org/search/by_data * Method : POST * IP address: 94.192.243.24 * Parameters: {"commit"=>"", "action"=>"by_data", "protocol"=>"http", "authenticity_token"=>"Izs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M=", "search_by_data"=>{"data"=>"", "search_type"=>"input", "limit"=>"20"}, "controller"=>"search"} * Rails root: /net/isilonP/public/rw/es/projects/biocatalogue/live/trunk_2545 ------------------------------- Session: ------------------------------- * session id: nil * data: nil ------------------------------- Environment: ------------------------------- * CONTENT_LENGTH : 214 * CONTENT_TYPE : application/x-www-form-urlencoded * DOCUMENT_ROOT : /nfs/public/rw/es/projects/biocatalogue/live/current/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=0.3 * HTTP_ACCEPT_ENCODING : gzip,deflate,sdch * HTTP_ACCEPT_LANGUAGE : en-GB,en-US;q=0.8,en;q=0.6 * HTTP_CACHE_CONTROL : max-age=0 * HTTP_CONNECTION : keep-alive * HTTP_COOKIE : stats-tabs_tabber=0; _session_id=98f68899cde3694341b7ecca70508874; __utma=15951013.1947546072.1321612577.1349281130.1349343123.104; __utmb=15951013.31.10.1349343123; __utmc=15951013; __utmz=15951013.1337894854.65.3.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=http://www.biocatalogue.org/; __atuvc=38%7C36%2C2%7C37%2C0%7C38%2C0%7C39%2C34%7C40 * HTTP_HOST : www.biocatalogue.org * HTTP_ORIGIN : http://www.biocatalogue.org * HTTP_REFERER : http://www.biocatalogue.org/search/by_data * HTTP_USER_AGENT : Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.79 Safari/537.4 * HTTP_X_CLUSTER_CLIENT_IP : 94.192.243.24 * PATH_INFO : /search/by_data * QUERY_STRING : * REMOTE_ADDR : 94.192.243.24 * REMOTE_PORT : 51861 * REQUEST_METHOD : POST * REQUEST_URI : /search/by_data * SCRIPT_NAME : * SERVER_ADDR : 10.3.0.47 * 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) * ZEUS_LOAD_BALANCER_ADDR : 193.62.197.26 * _ : _ * action_controller.request.query_parameters : * action_controller.request.request_parameters: commitauthenticity_tokenIzs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M=search_by_datadatasearch_typeinputlimit20 * action_controller.rescue.request : # * action_controller.rescue.response : # * rack.errors : # * rack.input : # * rack.multiprocess : true * rack.multithread : false * rack.request : # * rack.request.cookie_hash : __utma15951013.1947546072.1321612577.1349281130.1349343123.104__utmb15951013.31.10.1349343123_session_id98f68899cde3694341b7ecca70508874__utmc15951013stats-tabs_tabber0__utmz15951013.1337894854.65.3.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=http://www.biocatalogue.org/__atuvc38|36,2|37,0|38,0|39,34|40 * rack.request.cookie_string : stats-tabs_tabber=0; _session_id=98f68899cde3694341b7ecca70508874; __utma=15951013.1947546072.1321612577.1349281130.1349343123.104; __utmb=15951013.31.10.1349343123; __utmc=15951013; __utmz=15951013.1337894854.65.3.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=http://www.biocatalogue.org/; __atuvc=38%7C36%2C2%7C37%2C0%7C38%2C0%7C39%2C34%7C40 * rack.request.form_hash : commitauthenticity_tokenIzs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M=search_by_datadatasearch_typeinputlimit20 * rack.request.form_input : # * rack.request.form_vars : authenticity_token=Izs4mo8NXDDlzPTbMK%2FIKUtB6R43GJKlsaC55TPOK4M%3D&search_by_data%5Bdata%5D=%3Cdata%3E%3Ctest%3E%3C%2Ftest%3E%3C%2Fdata%3E&search_by_data%5Blimit%5D=20&search_by_data%5Bsearch_type%5D=input&commit= * rack.request.query_hash : * rack.request.query_string : * rack.routing_args : protocolhttpactionby_datacontrollersearch * rack.run_once : false * rack.session : previous_url/search/by_datauser_id829use_tab_cookiefalse_csrf_tokenIzs4mo8NXDDlzPTbMK/IKUtB6R43GJKlsaC55TPOK4M=flash * rack.session.options : key_session_idpath/expire_afterdomainhttponlytrueid98f68899cde3694341b7ecca70508874cookie_onlytruesecurefalse * rack.session.record : # * rack.url_scheme : http * rack.version : 10 * Process: 31551 * Server : ves-hx-2f * 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/mysql_adapter.rb:595:in `select' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/database_statements.rb:7:in `select_all_without_query_cache' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:60:in `select_all' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:81:in `cache_sql' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:60:in `select_all' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:661:in `find_by_sql' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:1553:in `find_every' [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/base.rb:615:in `find' [RAILS_ROOT]/lib/bio_catalogue/search_by_data.rb:177:in `get_database_positive_properties_input' [RAILS_ROOT]/lib/bio_catalogue/search_by_data.rb:195:in `get_matching_input_ports_for_data' [RAILS_ROOT]/app/controllers/search_controller.rb:112:in `by_data' [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' /nfs/public/rw/webadmin/ruby/ruby-enterprise-1.8.7-2010.02/lib/ruby/1.8/benchmark.rb:308: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' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:92:in `process_request' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_request_handler.rb:207:in `main_loop' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:441:in `start_request_handler' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:381:in `handle_spawn_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/utils.rb:252:in `safe_fork' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:377:in `handle_spawn_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:163:in `start' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:222:in `start' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:253:in `spawn_rails_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:247:in `spawn_rails_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:246:in `spawn_rails_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:145:in `spawn_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:278:in `handle_spawn_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/bin/passenger-spawn-server:61 {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 4 12:46:32 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 4 Oct 2012 13:46:32 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-712) Multiple search scopes cause error Message-ID: <2123904742.553.1349354792411.JavaMail.jira@proteus> Multiple search scopes cause error ---------------------------------- Key: BIOCAT-712 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-712 Project: BioCatalogue Issue Type: Bug Components: Search / Filtering / Browsing Affects Versions: 1.1.0 Reporter: Robert Haines Assignee: Robert Haines Fix For: 1.1.1 Not sure if multiple search scopes make any sense but we do seem to be seeing these happen so we should at least handle them. If there are multiple scopes then we see them as an array so we should do something sensible with it. Error transcript below: {code} A NoMethodError occurred in search#show: undefined method `titleize' for ["services", "soap_operations"]:Array [RAILS_ROOT]/lib/bio_catalogue/search.rb:36:in `scope_to_visible_search_type' ------------------------------- Request: ------------------------------- * URL : http://www.biocatalogue.org/search?page=2&q=blast+sequence&scope=services,soap_operations * Method : GET * IP address: 150.128.131.7 * Parameters: {"scope"=>"services,soap_operations", "action"=>"show", "protocol"=>"http", "page"=>"2", "q"=>"blast sequence", "controller"=>"search"} * Rails root: /net/isilonP/public/rw/es/projects/biocatalogue/live/trunk_2545 ------------------------------- Session: ------------------------------- * session id: nil * data: nil ------------------------------- Environment: ------------------------------- * DOCUMENT_ROOT : /nfs/public/rw/es/projects/biocatalogue/live/current/public * HTTP_ACCEPT : text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 * HTTP_ACCEPT_ENCODING : gzip, deflate * HTTP_ACCEPT_LANGUAGE : es-es,es;q=0.8,en-us;q=0.5,en;q=0.3 * HTTP_CONNECTION : keep-alive * HTTP_COOKIE : __utma=15951013.314098215.1340263485.1347521581.1347865181.58; __utmz=15951013.1340263485.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none); __atuvc=0%7C34%2C3%7C35%2C0%7C36%2C33%7C37%2C3%7C38; _session_id=6ca7f45ff43738605290beb0d28b7d67; __utmb=15951013.3.10.1347865181; __utmc=15951013 * HTTP_HOST : www.biocatalogue.org * HTTP_USER_AGENT : Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 Firefox/15.0.1 * HTTP_X_CLUSTER_CLIENT_IP : 150.128.131.7 * PATH_INFO : /search * QUERY_STRING : page=2&q=blast+sequence&scope=services,soap_operations * REMOTE_ADDR : 150.128.131.7 * REMOTE_PORT : 38502 * REQUEST_METHOD : GET * REQUEST_URI : /search?page=2&q=blast+sequence&scope=services,soap_operations * SCRIPT_NAME : * SERVER_ADDR : 10.3.0.46 * 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) * ZEUS_LOAD_BALANCER_ADDR : 193.62.197.26 * _ : _ * action_controller.request.query_parameters : scopeservices,soap_operationsqblast sequencepage2 * 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 : __utma15951013.314098215.1340263485.1347521581.1347865181.58__utmb15951013.3.10.1347865181_session_id6ca7f45ff43738605290beb0d28b7d67__utmc15951013__utmz15951013.1340263485.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none)__atuvc0|34,3|35,0|36,33|37,3|38 * rack.request.cookie_string : __utma=15951013.314098215.1340263485.1347521581.1347865181.58; __utmz=15951013.1340263485.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none); __atuvc=0%7C34%2C3%7C35%2C0%7C36%2C33%7C37%2C3%7C38; _session_id=6ca7f45ff43738605290beb0d28b7d67; __utmb=15951013.3.10.1347865181; __utmc=15951013 * rack.request.query_hash : scopeservices,soap_operationsqblast sequencepage2 * rack.request.query_string : page=2&q=blast+sequence&scope=services,soap_operations * rack.routing_args : protocolhttpactionshowcontrollersearch * rack.run_once : false * rack.session : search_show_listing_typesimplelast_searchhttp://www.biocatalogue.org/search?q=genes&commit=previous_url/search?page=2&q=blast+sequence&scope=services,soap_operationsuse_tab_cookietrue_csrf_tokenWEcM8SCvToJ2sGxjGX+LbN4Z+v9wfg3edPFN/crNa1s=flash * rack.session.options : key_session_idpath/expire_afterdomainhttponlytrueid6ca7f45ff43738605290beb0d28b7d67cookie_onlytruesecurefalse * rack.session.record : # * rack.url_scheme : http * rack.version : 10 * Process: 7275 * Server : ves-hx-2e * request.format: text/html ------------------------------- Backtrace: ------------------------------- [RAILS_ROOT]/lib/bio_catalogue/search.rb:36:in `scope_to_visible_search_type' [RAILS_ROOT]/app/controllers/search_controller.rb:185:in `validate_and_setup_search' [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/actionpack/lib/action_controller/filters.rb:225:in `call' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:629:in `run_before_filters' [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:615: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' /nfs/public/rw/webadmin/ruby/ruby-enterprise-1.8.7-2010.02/lib/ruby/1.8/benchmark.rb:308: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' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/rack/request_handler.rb:92:in `process_request' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_request_handler.rb:207:in `main_loop' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:441:in `start_request_handler' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:381:in `handle_spawn_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/utils.rb:252:in `safe_fork' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:377:in `handle_spawn_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:163:in `start' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/railz/application_spawner.rb:222:in `start' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:253:in `spawn_rails_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:247:in `spawn_rails_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:246:in `spawn_rails_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:145:in `spawn_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/spawn_manager.rb:278:in `handle_spawn_application' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `__send__' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:352:in `main_loop' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/lib/phusion_passenger/abstract_server.rb:196:in `start_synchronously' /nfs/public/rw/webadmin/ruby/build/passenger-2.2.15/bin/passenger-spawn-server:61 {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 4 15:13:32 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 4 Oct 2012 16:13:32 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-713) Invalid search scope causes error Message-ID: <919836707.559.1349363612440.JavaMail.jira@proteus> Invalid search scope causes error --------------------------------- Key: BIOCAT-713 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-713 Project: BioCatalogue Issue Type: Bug Components: Search / Filtering / Browsing Affects Versions: 1.1.0 Reporter: Robert Haines Assignee: Robert Haines Fix For: 1.1.1 If an invalid search scope is specified an error is raised. It would probably be better if a warning was posted instead and the invalid scope ignored. Example invalid request: {http://www.biocatalogue.org/search?q=blast&scope=wrong} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 4 15:13:35 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 4 Oct 2012 16:13:35 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-713) Invalid search scope causes error In-Reply-To: <919836707.559.1349363612440.JavaMail.jira@proteus> Message-ID: <46568018.560.1349363615309.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-713?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-713: --------------------------------- Description: If an invalid search scope is specified an error is raised. It would probably be better if a warning was posted instead and the invalid scope ignored. Example invalid request: {{http://www.biocatalogue.org/search?q=blast&scope=wrong}} was: If an invalid search scope is specified an error is raised. It would probably be better if a warning was posted instead and the invalid scope ignored. Example invalid request: {http://www.biocatalogue.org/search?q=blast&scope=wrong} > Invalid search scope causes error > --------------------------------- > > Key: BIOCAT-713 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-713 > Project: BioCatalogue > Issue Type: Bug > Components: Search / Filtering / Browsing > Affects Versions: 1.1.0 > Reporter: Robert Haines > Assignee: Robert Haines > Fix For: 1.1.1 > > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > If an invalid search scope is specified an error is raised. It would probably be better if a warning was posted instead and the invalid scope ignored. > Example invalid request: {{http://www.biocatalogue.org/search?q=blast&scope=wrong}} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 4 15:34:32 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 4 Oct 2012 16:34:32 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-713) Invalid search scope causes error In-Reply-To: <919836707.559.1349363612440.JavaMail.jira@proteus> Message-ID: <1896947381.562.1349364872421.JavaMail.jira@proteus> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-713?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=18382#comment-18382 ] Robert Haines commented on BIOCAT-713: -------------------------------------- Set search scope to all on error instead? > Invalid search scope causes error > --------------------------------- > > Key: BIOCAT-713 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-713 > Project: BioCatalogue > Issue Type: Bug > Components: Search / Filtering / Browsing > Affects Versions: 1.1.0 > Reporter: Robert Haines > Assignee: Robert Haines > Fix For: 1.1.1 > > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > If an invalid search scope is specified an error is raised. It would probably be better if a warning was posted instead and the invalid scope ignored. > Example invalid request: {{http://www.biocatalogue.org/search?q=blast&scope=wrong}} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Wed Oct 24 13:02:01 2012 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 24 Oct 2012 13:02:01 +0000 (UTC) Subject: [BioCatalogue-developers] [2548] trunk/app/models/service.rb: [BIOCAT-709] JSON service summary is broken Message-ID: <20121024130202.17D2F2E061@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Oct 25 08:37:32 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 25 Oct 2012 09:37:32 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-714) Mis-aligned footer links Message-ID: <810549859.901.1351154252423.JavaMail.jira@proteus> Mis-aligned footer links ------------------------ Key: BIOCAT-714 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-714 Project: BioCatalogue Issue Type: Bug Components: Web Interface Affects Versions: 1.1.0 Reporter: Robert Haines Assignee: Robert Haines Priority: Trivial Fix For: 1.1.1 The "Terms of use" link is not vertically aligned with any of the other footer links. Finn has isolated the issue (the links with a separator are vertically aligned but the first one isn't) but we are waiting for a suitable time to make this trivial fix. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira