From issues at mygrid.org.uk Mon Dec 5 13:17:35 2011 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Mon, 5 Dec 2011 18:17:35 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-698) WSDL loader should declare itself in the user agent HTTP header Message-ID: <29056142.37.1323109055942.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.1.0 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 Dec 5 13:29:36 2011 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Mon, 5 Dec 2011 18:29:36 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-699) Mark services as "Under Test" Message-ID: <19024566.38.1323109776204.JavaMail.jira@rosalind.cs.man.ac.uk> Mark services as "Under Test" ----------------------------- Key: BIOCAT-699 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-699 Project: BioCatalogue Issue Type: New Feature Components: Web Interface Affects Versions: 1.0.1 Reporter: Robert Haines Assignee: Robert Haines Priority: Minor Email from Marco: We would like to be able to indicate the development status of a service, or did we miss this feature? In our case the service is in testing phase. It it really helpful to start using BioCatalogue in this phase. It gives a convenient link to send to users who can then help testing and annotating. Maybe test.biocatalogue.org could be used for this? But then services would need to be migrated to the main site somehow... -- 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 Dec 7 11:16:54 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 7 Dec 2011 11:16:54 -0500 (EST) Subject: [BioCatalogue-developers] [2529] branches/scape: Adding controller and page for ' Executing Web services' page. Message-ID: <20111207161654.B643A1D782A1@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Dec 8 06:13:06 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 8 Dec 2011 06:13:06 -0500 (EST) Subject: [BioCatalogue-developers] [2530] branches/scape/app: Changed terms of use to refer to SCAPE Catalogue instead on BioCatalogue. Message-ID: <20111208111307.9D1811678362@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Dec 13 05:58:49 2011 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Tue, 13 Dec 2011 10:58:49 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-700) Splitting up params passed in the url is not robust to empty param lists Message-ID: <25573476.5.1323773929583.JavaMail.jira@rosalind.cs.man.ac.uk> Splitting up params passed in the url is not robust to empty param lists ------------------------------------------------------------------------ Key: BIOCAT-700 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-700 Project: BioCatalogue Issue Type: Bug Components: Web Interface Affects Versions: 1.0.0 Reporter: Robert Haines Assignee: Robert Haines Fix For: 1.1.0 A URL such as http://www.biocatalogue.org/services.xml?t= creates a 500 server error simply because parsing the options after the ? is not checking for empty. -- 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 Dec 13 05:58:53 2011 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Tue, 13 Dec 2011 10:58:53 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-700) Splitting up params passed in the url is not robust to empty param lists In-Reply-To: <25573476.5.1323773929583.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21099469.6.1323773933677.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-700?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-700 started by Robert Haines. > Splitting up params passed in the url is not robust to empty param lists > ------------------------------------------------------------------------ > > Key: BIOCAT-700 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-700 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Robert Haines > Assignee: Robert Haines > Fix For: 1.1.0 > > > A URL such as http://www.biocatalogue.org/services.xml?t= creates a 500 server error simply because parsing the options after the ? is not checking for empty. -- 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 Dec 13 08:34:49 2011 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Tue, 13 Dec 2011 13:34:49 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-700) Splitting up params passed in the url is not robust to empty param lists In-Reply-To: <25573476.5.1323773929583.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18136575.8.1323783289583.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-700?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines updated BIOCAT-700: --------------------------------- Description: A URL such as http://www.biocatalogue.org/services.xml?t= generates a 500 server error simply because parsing the options after the ? is not checking for empty. (was: A URL such as http://www.biocatalogue.org/services.xml?t= creates a 500 server error simply because parsing the options after the ? is not checking for empty.) > Splitting up params passed in the url is not robust to empty param lists > ------------------------------------------------------------------------ > > Key: BIOCAT-700 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-700 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Robert Haines > Assignee: Robert Haines > Fix For: 1.1.0 > > > A URL such as http://www.biocatalogue.org/services.xml?t= generates a 500 server error simply because parsing the options after the ? is not checking for empty. -- 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 Dec 13 08:40:49 2011 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Tue, 13 Dec 2011 13:40:49 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-701) Fix whitespace issues in the entire codebase Message-ID: <25133475.13.1323783649479.JavaMail.jira@rosalind.cs.man.ac.uk> Fix whitespace issues in the entire codebase -------------------------------------------- Key: BIOCAT-701 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-701 Project: BioCatalogue Issue Type: Task Affects Versions: 1.1.0 Reporter: Robert Haines Assignee: Robert Haines Every time a half-decent whitespace aware editor is used it changes so many lines that the important functional change is hidden. The entire code base needs to be processed in the same commit to solve this issue. -- 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 Dec 13 08:52:49 2011 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Tue, 13 Dec 2011 13:52:49 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-700) Splitting up params passed in the url is not robust to empty param lists In-Reply-To: <25573476.5.1323773929583.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16816270.14.1323784369360.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-700?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Robert Haines resolved BIOCAT-700. ---------------------------------- Resolution: Fixed This is fixed by ensuring that the split value list isn't empty before further munging. > Splitting up params passed in the url is not robust to empty param lists > ------------------------------------------------------------------------ > > Key: BIOCAT-700 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-700 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Robert Haines > Assignee: Robert Haines > Fix For: 1.1.0 > > > A URL such as http://www.biocatalogue.org/services.xml?t= generates a 500 server error simply because parsing the options after the ? is not checking for empty. -- 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 Dec 13 12:41:58 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Dec 2011 12:41:58 -0500 (EST) Subject: [BioCatalogue-developers] [2531] trunk/app/controllers/services_controller.rb: [BIOCAT-697] Error in services#show for non-existent service. Message-ID: <20111213174158.F24E01218277@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 13 12:42:04 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Dec 2011 12:42:04 -0500 (EST) Subject: [BioCatalogue-developers] [2532] trunk/app/controllers/services_controller.rb: [BIOCAT-696] View error in services#monitoring on updated test site. Message-ID: <20111213174204.1A8C61218277@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 13 12:42:09 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Dec 2011 12:42:09 -0500 (EST) Subject: [BioCatalogue-developers] [2533] trunk/lib/bio_catalogue/filtering.rb: [BIOCAT-700] Splitting up params passed in the url is not robust. Message-ID: <20111213174209.6A8EB121827A@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Dec 13 13:28:49 2011 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Tue, 13 Dec 2011 18:28:49 +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: <25545376.15.1323800929170.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=17688#comment-17688 ] Robert Haines commented on BIOCAT-698: -------------------------------------- The fix for this might need to go in one of two places: * The WSDL utils library code * WSDL utils PHP code > 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: 1.1.0 > > > 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 Tue Dec 13 14:36:49 2011 From: issues at mygrid.org.uk (Robert Haines (JIRA)) Date: Tue, 13 Dec 2011 19:36:49 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Updated: (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: <16565741.16.1323805009711.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 updated BIOCAT-698: --------------------------------- Fix Version/s: Future (was: 1.1.0) > 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 noreply at rubyforge.org Wed Dec 21 07:16:25 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Dec 2011 07:16:25 -0500 (EST) Subject: [BioCatalogue-developers] [2534] branches/scape/app/views/user_mailer/registration_notification.html. erb: Changed the signature in the email that gets sent to the users Message-ID: <20111221121627.E89AE185836C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 21 08:50:33 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Dec 2011 08:50:33 -0500 (EST) Subject: [BioCatalogue-developers] [2535] branches/scape/app: Changed subject [BioCatalogue] to [ SCAPE Service Catalogue] for all emails being sent Message-ID: <20111221135034.376E8177994F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 21 09:38:30 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Dec 2011 09:38:30 -0500 (EST) Subject: [BioCatalogue-developers] [2536] branches/scape/app/views/tags/index.html.erb: changed the title in the tags not to contain biocatalogue workd Message-ID: <20111221143830.E72041858378@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 21 10:17:28 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Dec 2011 10:17:28 -0500 (EST) Subject: [BioCatalogue-developers] [2537] branches/scape/app/views/services/_index_tag_cloud.html.erb: Changed BioCatalogue wording in /services (file app/views/services/ _index_tag_cloud.html.erb) not to contain the word 'biocatalogue Message-ID: <20111221151728.9E27E185837A@rubyforge.org> An HTML attachment was scrubbed... URL: