From issues at mygrid.org.uk Mon Feb 6 11:02:24 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Mon, 6 Feb 2012 16:02:24 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-698) WSDL loader should declare itself in the user agent HTTP header In-Reply-To: <29056142.37.1323109055942.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22950818.1456.1328544144042.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-698?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17881#comment-17881 ] Robert Haines commented on BIOCAT-698: -------------------------------------- This looks like it can be fixed in the WSDLUtils.php file. Awaiting confirmation via testing against a locked-down server! > WSDL loader should declare itself in the user agent HTTP header > --------------------------------------------------------------- > > Key: BIOCAT-698 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-698 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Affects Versions: 1.0.1 > Reporter: Robert Haines > Assignee: Robert Haines > Priority: Critical > Fix For: Future > > > Email from Marco: > > Our developer Reinout van Schouwen found a bottleneck in submitting one > > of our services. As I understood it, the security system on our server > > requires that the agent that does a request makes itself known; this > > happens for instance when the wsdl is read. > > > > Reinout writes: > > > > The BioCatalogue WSDL preview function triggers a rule in the Apache > > mod-security module: > > > > "/etc/apache2/conf.d/modsecurity/base_rules/modsecurity_crs_21_protocol_anomalies.conf"] [line"65"] [id"960009"] [rev"2.1.2"] [msg"Request Missing a User Agent Header"] [severity"NOTICE"] [tag"PROTOCOL_VIOLATION/MISSING_HEADER_UA"] [tag"WASCTC/WASC-21"] [tag"OWASP_TOP_10/A7"] [tag"PCI/6.5.10"] [hostname"ws.biosemantics.org"] [uri"/ConceptRecognizerService"] [unique_id"TtiaXJFY0ugAAH6W8psAAAAE"] > > > > Therefore the web server response is 403 Forbidden and I cannot add my > > service without disabling mod-security first. The reason for this rule > > to be triggered is because BioCatalogue doesn't send a User Agent > > header, as can be confirmed from this Apache log entry: > > > > 193.62.196.8 - - [02/Dec/2011:10:29:00+0100]"GET /ConceptRecognizerService?wsdl HTTP/1.0" 403 519"-" "-" > > > > Please fix the BioCatalogue WSDL loader so that it includes a User Agent > > in its HTTP requests. Thanks! -- 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 Mon Feb 6 11:31:26 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Mon, 6 Feb 2012 16:31:26 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-702) Requesting activity.atom for a service that does not exist causes error Message-ID: <945187.1471.1328545886566.JavaMail.jira@rosalind.cs.man.ac.uk> Requesting activity.atom for a service that does not exist causes error ----------------------------------------------------------------------- Key: BIOCAT-702 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-702 Project: BioCatalogue Issue Type: Bug Components: Web Interface Affects Versions: 1.1.0 Reporter: Robert Haines Assignee: Robert Haines Fix For: 1.1.0 Example: http://test.biocatalogue.org/services/2710/activity.atom causes an error, but: http://test.biocatalogue.org/services/2710/activity produces a 404. The former should produce a 404 too - not crash! Other examples: http://test.biocatalogue.org/services/11/activity.atom http://test.biocatalogue.org/services/134/activity.atom http://test.biocatalogue.org/services/6/activity.atom http://test.biocatalogue.org/services/2065/activity.atom Full error: {code} A ActionView::TemplateError occurred in services#activity: service_url failed to generate from {:action=>"show", :controller=>"services", :format=>:atom, :protocol=>"http", :id=>nil}, expected: {:action=>"show", :controller=>"services", :protocol=>"http"}, diff: {:format=>:atom, :id=>nil} On line #8 of app/views/services/activity.atom.builder 5: # See license.txt for details 6: 7: 8: atom_feed :url => service_url(@service, :format => :atom), 9: :root_url => service_url(@service), 10: :schema_date => "2009" do |feed| 11: (eval):16:in `service_url' app/views/services/activity.atom.builder:8:in `_run_builder_app47views47services47activity46atom46builder' app/controllers/application_controller.rb:355:in `error' app/controllers/application_controller.rb:339:in `error' app/controllers/application_controller.rb:368:in `error_to_back_or_home' app/controllers/services_controller.rb:430:in `find_service' /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' ------------------------------- Request: ------------------------------- * URL : http://test.biocatalogue.org/services/2704/activity.atom * Method : GET * IP address: 66.249.72.168 * Parameters: {"format"=>"atom", "action"=>"activity", "protocol"=>"http", "id"=>"2704", "controller"=>"services"} * Rails root: /net/isilonP/public/rw/es/projects/biocatalogue/test/trunk_2533 ------------------------------- Session: ------------------------------- * session id: nil * data: nil ------------------------------- Environment: ------------------------------- * DOCUMENT_ROOT : /nfs/public/rw/es/projects/biocatalogue/test/current/public * HTTP_ACCEPT : */* * HTTP_ACCEPT_ENCODING : gzip,deflate * HTTP_CONNECTION : Keep-alive * HTTP_FROM : googlebot(at)googlebot.com * HTTP_HOST : test.biocatalogue.org * HTTP_USER_AGENT : Mozilla/5.0 (compatible; Googlebot/2.1; +http://www.google.com/bot.html) * HTTP_X_CLUSTER_CLIENT_IP : 66.249.72.168 * PATH_INFO : /services/2704/activity.atom * QUERY_STRING : * REMOTE_ADDR : 66.249.72.168 * REMOTE_PORT : 41936 * REQUEST_METHOD : GET * REQUEST_URI : /services/2704/activity.atom * SCRIPT_NAME : * SERVER_ADDR : 10.3.0.45 * SERVER_ADMIN : root at localhost * SERVER_NAME : test.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: * action_controller.rescue.request : # * action_controller.rescue.response : # * rack.errors : # * rack.input : # * rack.multiprocess : true * rack.multithread : false * rack.request : # * rack.request.query_hash : * rack.request.query_string : * rack.routing_args : formatatomprotocolhttpactionactivityid2704controllerservices * rack.run_once : false * rack.session : use_tab_cookiefalseflasherrorService with ID 2704 not found. * rack.session.options : key_session_idpath/expire_afterdomainhttponlytrueid5da8d5b405e72afc5cba58a6ed7a30b8cookie_onlytruesecurefalse * rack.session.record : # * rack.url_scheme : http * rack.version : 10 * Process: 16179 * Server : ves-hx-2d * request.format: application/atom+xml ------------------------------- Backtrace: ------------------------------- On line #8 of app/views/services/activity.atom.builder 5: # See license.txt for details 6: 7: 8: atom_feed :url => service_url(@service, :format => :atom), 9: :root_url => service_url(@service), 10: :schema_date => "2009" do |feed| 11: (eval):16:in `service_url' app/views/services/activity.atom.builder:8:in `_run_builder_app47views47services47activity46atom46builder' app/controllers/application_controller.rb:355:in `error' app/controllers/application_controller.rb:339:in `error' app/controllers/application_controller.rb:368:in `error_to_back_or_home' app/controllers/services_controller.rb:430:in `find_service' /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' {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 Tue Feb 7 11:42:22 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Tue, 7 Feb 2012 16:42:22 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-702) Requesting activity.atom for a service that does not exist causes error In-Reply-To: <945187.1471.1328545886566.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <33499975.2123.1328632942198.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-702?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines resolved BIOCAT-702. ---------------------------------- Resolution: Fixed Not sure why but the error handling code for atom feeds wasn't actually rendering anything so the error wasn't really caught. This now renders :nothing and returns a 404. > Requesting activity.atom for a service that does not exist causes error > ----------------------------------------------------------------------- > > Key: BIOCAT-702 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-702 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.1.0 > Reporter: Robert Haines > Assignee: Robert Haines > Fix For: 1.1.0 > > > Example: > http://test.biocatalogue.org/services/2710/activity.atom > causes an error, but: > http://test.biocatalogue.org/services/2710/activity > produces a 404. The former should produce a 404 too - not crash! > Other examples: > http://test.biocatalogue.org/services/11/activity.atom > http://test.biocatalogue.org/services/134/activity.atom > http://test.biocatalogue.org/services/6/activity.atom > http://test.biocatalogue.org/services/2065/activity.atom > Full error: > {code} > A ActionView::TemplateError occurred in services#activity: > service_url failed to generate from {:action=>"show", :controller=>"services", :format=>:atom, :protocol=>"http", :id=>nil}, expected: {:action=>"show", :controller=>"services", :protocol=>"http"}, diff: {:format=>:atom, :id=>nil} > On line #8 of app/views/services/activity.atom.builder > 5: # See license.txt for details > 6: > 7: > 8: atom_feed :url => service_url(@service, :format => :atom), > 9: :root_url => service_url(@service), > 10: :schema_date => "2009" do |feed| > 11: > (eval):16:in `service_url' > app/views/services/activity.atom.builder:8:in `_run_builder_app47views47services47activity46atom46builder' > app/controllers/application_controller.rb:355:in `error' > app/controllers/application_controller.rb:339:in `error' > app/controllers/application_controller.rb:368:in `error_to_back_or_home' > app/controllers/services_controller.rb:430:in `find_service' > /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' > ------------------------------- > Request: > ------------------------------- > * URL : http://test.biocatalogue.org/services/2704/activity.atom > * Method : GET > * IP address: 66.249.72.168 > * Parameters: {"format"=>"atom", "action"=>"activity", "protocol"=>"http", "id"=>"2704", "controller"=>"services"} > * Rails root: /net/isilonP/public/rw/es/projects/biocatalogue/test/trunk_2533 > ------------------------------- > Session: > ------------------------------- > * session id: nil > * data: nil > ------------------------------- > Environment: > ------------------------------- > * DOCUMENT_ROOT : /nfs/public/rw/es/projects/biocatalogue/test/current/public > * HTTP_ACCEPT : */* > * HTTP_ACCEPT_ENCODING : gzip,deflate > * HTTP_CONNECTION : Keep-alive > * HTTP_FROM : googlebot(at)googlebot.com > * HTTP_HOST : test.biocatalogue.org > * HTTP_USER_AGENT : Mozilla/5.0 (compatible; Googlebot/2.1; +http://www.google.com/bot.html) > * HTTP_X_CLUSTER_CLIENT_IP : 66.249.72.168 > * PATH_INFO : /services/2704/activity.atom > * QUERY_STRING : > * REMOTE_ADDR : 66.249.72.168 > * REMOTE_PORT : 41936 > * REQUEST_METHOD : GET > * REQUEST_URI : /services/2704/activity.atom > * SCRIPT_NAME : > * SERVER_ADDR : 10.3.0.45 > * SERVER_ADMIN : root at localhost > * SERVER_NAME : test.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: > * action_controller.rescue.request : # > * action_controller.rescue.response : # > * rack.errors : # > * rack.input : # > * rack.multiprocess : true > * rack.multithread : false > * rack.request : # > * rack.request.query_hash : > * rack.request.query_string : > * rack.routing_args : formatatomprotocolhttpactionactivityid2704controllerservices > * rack.run_once : false > * rack.session : use_tab_cookiefalseflasherrorService with ID 2704 not found. > * rack.session.options : key_session_idpath/expire_afterdomainhttponlytrueid5da8d5b405e72afc5cba58a6ed7a30b8cookie_onlytruesecurefalse > * rack.session.record : # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 16179 > * Server : ves-hx-2d > > * request.format: application/atom+xml > ------------------------------- > Backtrace: > ------------------------------- > On line #8 of app/views/services/activity.atom.builder > > 5: # See license.txt for details > 6: > 7: > 8: atom_feed :url => service_url(@service, :format => :atom), > 9: :root_url => service_url(@service), > 10: :schema_date => "2009" do |feed| > 11: > > (eval):16:in `service_url' > app/views/services/activity.atom.builder:8:in `_run_builder_app47views47services47activity46atom46builder' > app/controllers/application_controller.rb:355:in `error' > app/controllers/application_controller.rb:339:in `error' > app/controllers/application_controller.rb:368:in `error_to_back_or_home' > app/controllers/services_controller.rb:430:in `find_service' > /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' > {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue Feb 7 11:58:30 2012 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 7 Feb 2012 11:58:30 -0500 (EST) Subject: [BioCatalogue-developers] [2538] trunk/app/controllers/application_controller.rb: [BIOCAT-702] Req. Message-ID: <20120207165830.B86551678364@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Feb 7 12:00:13 2012 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 7 Feb 2012 12:00:13 -0500 (EST) Subject: [BioCatalogue-developers] [2539] trunk/.gitignore: Add . gitignore file to ensure config files are not committed accidentally. Message-ID: <20120207170013.C4BD01678364@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Feb 7 12:01:58 2012 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 7 Feb 2012 12:01:58 -0500 (EST) Subject: [BioCatalogue-developers] [2540] trunk/.rvmrc: Update . rvmrc to be less picky about which version of ree is used. Message-ID: <20120207170158.95E8C1678364@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Feb 8 11:37:22 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 8 Feb 2012 16:37:22 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-654) Make Carole a Curator on the live site In-Reply-To: <7163612.2293.1309338355454.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7121521.2236.1328719042264.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-654?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines reassigned BIOCAT-654: ------------------------------------ Assignee: Robert Haines (was: Jiten Bhagat) > Make Carole a Curator on the live site > -------------------------------------- > > Key: BIOCAT-654 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-654 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Robert Haines > Priority: Critical > Fix For: 1.1.0 > > > With the new ability to make users curators through the web interface, make Carole a curator too. > Need to first check with Carole that this is okay as lots of emails would get sent. -- 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 Feb 8 11:37:24 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 8 Feb 2012 16:37:24 +0000 (GMT) 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: <3798954.2237.1328719044707.JavaMail.jira@rosalind.cs.man.ac.uk> [ 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: 1.1.0 (was: 1.0.1) > 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: 1.1.0 > > > 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 Feb 8 11:37:27 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 8 Feb 2012 16:37:27 +0000 (GMT) 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: <17307893.2238.1328719047421.JavaMail.jira@rosalind.cs.man.ac.uk> [ 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: 1.1.0 (was: 1.0.1) > 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: 1.1.0 > > > 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 Feb 8 11:37:29 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 8 Feb 2012 16:37:29 +0000 (GMT) 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: <4174670.2239.1328719049708.JavaMail.jira@rosalind.cs.man.ac.uk> [ 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: 1.1.0 (was: 1.0.1) > 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: 1.1.0 > > > 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 Feb 8 11:37:31 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 8 Feb 2012 16:37:31 +0000 (GMT) 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: <20617622.2240.1328719051905.JavaMail.jira@rosalind.cs.man.ac.uk> [ 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: 1.1.0 (was: 1.0.1) > 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: 1.1.0 > > 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 Feb 8 11:37:34 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 8 Feb 2012 16:37:34 +0000 (GMT) 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: <5924168.2241.1328719054261.JavaMail.jira@rosalind.cs.man.ac.uk> [ 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: 1.1.0 (was: 1.0.1) > 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: 1.1.0 > > -- 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 Feb 8 11:37:36 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Wed, 8 Feb 2012 16:37:36 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-654) Make Carole a Curator on the live site In-Reply-To: <7163612.2293.1309338355454.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6682784.2242.1328719056451.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-654?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-654: --------------------------------- Fix Version/s: 1.1.0 (was: 1.0.1) > Make Carole a Curator on the live site > -------------------------------------- > > Key: BIOCAT-654 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-654 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Robert Haines > Priority: Critical > Fix For: 1.1.0 > > > With the new ability to make users curators through the web interface, make Carole a curator too. > Need to first check with Carole that this is okay as lots of emails would get sent. -- 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 Feb 9 06:27:29 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 9 Feb 2012 11:27:29 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-703) Update copyright in page footers to always show the current year Message-ID: <20458604.2269.1328786849352.JavaMail.jira@rosalind.cs.man.ac.uk> Update copyright in page footers to always show the current year ---------------------------------------------------------------- Key: BIOCAT-703 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-703 Project: BioCatalogue Issue Type: Task Components: Web Interface Affects Versions: 1.1.0 Reporter: Robert Haines Assignee: Robert Haines Priority: Trivial Fix For: 1.1.0 Time.now.year should do 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 Thu Feb 9 06:27:31 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 9 Feb 2012 11:27:31 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-703) Update copyright in page footers to always show the current year In-Reply-To: <20458604.2269.1328786849352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19562922.2270.1328786851398.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-703?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-703: --------------------------------- Description: {{Time.now.year}} should do it. (was: Time.now.year should do it.) > Update copyright in page footers to always show the current year > ---------------------------------------------------------------- > > Key: BIOCAT-703 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-703 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Affects Versions: 1.1.0 > Reporter: Robert Haines > Assignee: Robert Haines > Priority: Trivial > Fix For: 1.1.0 > > > {{Time.now.year}} should do it. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Feb 9 09:03:14 2012 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 9 Feb 2012 09:03:14 -0500 (EST) Subject: [BioCatalogue-developers] [2541] trunk/app/views/layouts/_footer.html.erb: [BIOCAT-703] Update copyright in page footers to always show the current year. Message-ID: <20120209140314.3E09F185837C@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Feb 9 09:17:22 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 9 Feb 2012 14:17:22 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-703) Update copyright in page footers to always show the current year In-Reply-To: <20458604.2269.1328786849352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32694730.2318.1328797042188.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-703?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines resolved BIOCAT-703. ---------------------------------- Resolution: Fixed Trivial fix with Time.now.year > Update copyright in page footers to always show the current year > ---------------------------------------------------------------- > > Key: BIOCAT-703 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-703 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Affects Versions: 1.1.0 > Reporter: Robert Haines > Assignee: Robert Haines > Priority: Trivial > Fix For: 1.1.0 > > > {{Time.now.year}} should do 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 Thu Feb 9 09:38:22 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 9 Feb 2012 14:38:22 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-106) Allow the submitter to select a display name for a service Message-ID: <23875929.2319.1328798302227.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-106?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines reassigned BIOCAT-106: ------------------------------------ Assignee: Robert Haines (was: Jiten Bhagat) > 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: 1.1.0 > > > "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 Thu Feb 9 12:17:22 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 9 Feb 2012 17:17:22 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Assigned: (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: <33115101.2320.1328807842242.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-490?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines reassigned BIOCAT-490: ------------------------------------ Assignee: Robert Haines (was: Jiten Bhagat) > 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: 1.1.0 > > > 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 Thu Feb 9 12:19:22 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Thu, 9 Feb 2012 17:19:22 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-664) New admin feature: activate users In-Reply-To: <12844958.2604.1309775395406.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13326228.2321.1328807962193.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-664?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines reassigned BIOCAT-664: ------------------------------------ Assignee: Robert Haines (was: Jiten Bhagat) > 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: 1.1.0 > > > 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 Fri Feb 10 05:36:22 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Fri, 10 Feb 2012 10:36:22 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (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: <16741580.2346.1328870182231.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-642?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17892#comment-17892 ] Robert Haines commented on BIOCAT-642: -------------------------------------- Error is: {code} Failed to access XML Schema component, invalid URL : ../common/ws_common_1_0b.xsd {code} So, it's having trouble parsing relative paths? > 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: 1.1.0 > > > 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 Fri Feb 10 05:36:24 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Fri, 10 Feb 2012 10:36:24 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-661) New admin feature: merge user accounts In-Reply-To: <13421585.2502.1309508095487.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27849184.2347.1328870184663.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-661?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines reassigned BIOCAT-661: ------------------------------------ Assignee: Robert Haines (was: Jiten Bhagat) > 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: 1.1.0 > > > 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 Fri Feb 10 05:40:22 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Fri, 10 Feb 2012 10:40:22 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-661) New admin feature: merge user accounts In-Reply-To: <13421585.2502.1309508095487.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30208304.2348.1328870422177.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-661?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17893#comment-17893 ] Robert Haines commented on BIOCAT-661: -------------------------------------- How do we ensure that the two accounts are owned by the same person? There might be a case for someone wanting to merge another person's account into their own if they are taking over ownership of a set of services from someone but we would need to be very careful that we didn't merge accounts without permission from *BOTH* sides. > 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: 1.1.0 > > > 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 Fri Feb 10 13:48:22 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Fri, 10 Feb 2012 18:48:22 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-704) URLs with , or : in the parameters not rendered correctly Message-ID: <7469241.2359.1328899702183.JavaMail.jira@rosalind.cs.man.ac.uk> URLs with , or : in the parameters not rendered correctly --------------------------------------------------------- Key: BIOCAT-704 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-704 Project: BioCatalogue Issue Type: Bug Components: Web Interface Affects Versions: 1.1.0 Reporter: Robert Haines Assignee: Robert Haines Fix For: 1.2.0 Examples: http://www.biocatalogue.org/rest_methods/195 http://www.biocatalogue.org/rest_methods/196 The URL rendering gets cut off at the first occurrence of a comma or a colon. -- 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 Mon Feb 13 07:05:22 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Mon, 13 Feb 2012 12:05:22 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-654) Make Carole a Curator on the live site In-Reply-To: <7163612.2293.1309338355454.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30000790.2360.1329134722304.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-654?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines resolved BIOCAT-654. ---------------------------------- Resolution: Implemented Carole was consulted and agreed to be a curator. If the amount of emails is too much, we can always turn it off again! > Make Carole a Curator on the live site > -------------------------------------- > > Key: BIOCAT-654 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-654 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Robert Haines > Priority: Critical > Fix For: 1.1.0 > > > With the new ability to make users curators through the web interface, make Carole a curator too. > Need to first check with Carole that this is okay as lots of emails would get sent. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri Feb 17 04:43:42 2012 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 17 Feb 2012 04:43:42 -0500 (EST) Subject: [BioCatalogue-developers] [2542] trunk/public/stylesheets/styles.css: Fixed wide page issue Message-ID: <20120217094342.65AE7185837E@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Feb 17 05:00:26 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Fri, 17 Feb 2012 10:00:26 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-705) Parametrized skinning for the catalogue Message-ID: <3103129.2411.1329472826235.JavaMail.jira@rosalind.cs.man.ac.uk> Parametrized skinning for the catalogue --------------------------------------- Key: BIOCAT-705 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-705 Project: BioCatalogue Issue Type: New Feature Components: Web Interface Affects Versions: 1.1.0 Reporter: Robert Haines Assignee: Finn Bacall Fix For: Future Make the look of the BioCatalogue customizable from a single point of configuration. * Colours * Logo * Text - make phrases such as "... BioCatalogue ..." parametrized. This is not intended to be a big change of style sheets or moving things about. See the SCAPE changes for 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 Fri Feb 17 13:20:22 2012 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Fri, 17 Feb 2012 18:20:22 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-698) WSDL loader should declare itself in the user agent HTTP header In-Reply-To: <29056142.37.1323109055942.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <498089.2421.1329502822216.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-698?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines resolved BIOCAT-698. ---------------------------------- Resolution: Fixed This fixed locally. Awaiting deployment to BioCat test site. Required config was present in the file, just not provided for a proxied connection. > WSDL loader should declare itself in the user agent HTTP header > --------------------------------------------------------------- > > Key: BIOCAT-698 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-698 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Affects Versions: 1.0.1 > Reporter: Robert Haines > Assignee: Robert Haines > Priority: Critical > Fix For: Future > > > Email from Marco: > > Our developer Reinout van Schouwen found a bottleneck in submitting one > > of our services. As I understood it, the security system on our server > > requires that the agent that does a request makes itself known; this > > happens for instance when the wsdl is read. > > > > Reinout writes: > > > > The BioCatalogue WSDL preview function triggers a rule in the Apache > > mod-security module: > > > > "/etc/apache2/conf.d/modsecurity/base_rules/modsecurity_crs_21_protocol_anomalies.conf"] [line"65"] [id"960009"] [rev"2.1.2"] [msg"Request Missing a User Agent Header"] [severity"NOTICE"] [tag"PROTOCOL_VIOLATION/MISSING_HEADER_UA"] [tag"WASCTC/WASC-21"] [tag"OWASP_TOP_10/A7"] [tag"PCI/6.5.10"] [hostname"ws.biosemantics.org"] [uri"/ConceptRecognizerService"] [unique_id"TtiaXJFY0ugAAH6W8psAAAAE"] > > > > Therefore the web server response is 403 Forbidden and I cannot add my > > service without disabling mod-security first. The reason for this rule > > to be triggered is because BioCatalogue doesn't send a User Agent > > header, as can be confirmed from this Apache log entry: > > > > 193.62.196.8 - - [02/Dec/2011:10:29:00+0100]"GET /ConceptRecognizerService?wsdl HTTP/1.0" 403 519"-" "-" > > > > Please fix the BioCatalogue WSDL loader so that it includes a User Agent > > in its HTTP requests. Thanks! -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira