From issues at mygrid.org.uk Fri Jul 1 04:14:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 1 Jul 2011 09:14:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-661) New admin feature: merge user accounts Message-ID: <13421585.2502.1309508095487.JavaMail.jira@rosalind.cs.man.ac.uk> 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: Jiten Bhagat Priority: Critical Fix For: 1.0.1 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 Fri Jul 1 04:34:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 1 Jul 2011 09:34:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-662) Allow those responsible for a service to edit it's WSDL location Message-ID: <22914152.2503.1309509295351.JavaMail.jira@rosalind.cs.man.ac.uk> 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: Jiten Bhagat Priority: Blocker Fix For: 1.0.1 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. -- 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 Jul 1 04:44:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 1 Jul 2011 09:44:55 +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: <17624154.2504.1309509895370.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-662?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-662: -------------------------------- Description: 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. was: 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. > 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: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > 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. -- 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 Jul 1 04:48:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 1 Jul 2011 09:48:55 +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: <16013036.2505.1309510135363.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-662?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-662: -------------------------------- Description: 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. Also, from Marco: {quote} Re: keep old ref. This would be very useful when you find a 'depricated' reference used in a workflow or application. That is how I discoverd this problem: Taverna told me the service didn't exist anymore, so I changed the wsdl reference in the workflow. It would be nice if I could find the new reference on biocatalogue through the old reference. {quote} was: 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. > 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: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > 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. > Also, from Marco: > {quote} > Re: keep old ref. This would be very useful when you find a 'depricated' reference used in a workflow or application. That is how I discoverd this problem: Taverna told me the service didn't exist anymore, so I changed the wsdl reference in the workflow. It would be nice if I could find the new reference on biocatalogue through the old reference. > {quote} -- 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 Jul 1 04:50:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 1 Jul 2011 09:50:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-663) Ability to link services by saying that one is the "better" or "newer" version Message-ID: <9875387.2506.1309510255346.JavaMail.jira@rosalind.cs.man.ac.uk> Ability to link services by saying that one is the "better" or "newer" version ------------------------------------------------------------------------------ Key: BIOCAT-663 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-663 Project: BioCatalogue Issue Type: New Feature Components: Misc Codebase Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.1.0 >From Marco: {quote} We also have a new and extended version of this service. This is another type of reference that would be useful for us: refer to a biocatalogue entry that has this better version. We wouldn't want to remove the old entry, because some users might still use it. {quote} -- 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 Jul 1 05:12:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 1 Jul 2011 10:12:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-655) Show curator and admin badges in the UI In-Reply-To: <24162756.2294.1309338475347.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27111994.2507.1309511575397.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-655?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17249#comment-17249 ] Jiten Bhagat commented on BIOCAT-655: ------------------------------------- This needs to be added to the user listings too > Show curator and admin badges in the UI > --------------------------------------- > > Key: BIOCAT-655 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-655 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 1 hour > Remaining Estimate: 0 minutes > > Currently, there is no way of seeing whether a user is an admin or curator in the catalogue. Show badges (similar to how it's done in myExperiment). -- 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 Jul 4 04:02:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 4 Jul 2011 09:02:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-657) Investigate why certain test scripts are failing! In-Reply-To: <30607250.2305.1309341535354.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29434215.2599.1309766575507.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-657?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-657: ----------------------------------- Fix Version/s: Future (was: 1.0.1) > Investigate why certain test scripts are failing! > ------------------------------------------------- > > Key: BIOCAT-657 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-657 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > Fix For: Future > > Attachments: diff.jpg > > > For example: > - http://www.biocatalogue.org/service_tests/4876 > - Many of the INB test scripts > Eric was investigating this but it's not clear what came out of it. So may need to dig up some old emails, etc. -- 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 Jul 4 05:39:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 4 Jul 2011 10:39:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-655) Show curator and admin badges in the UI In-Reply-To: <24162756.2294.1309338475347.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30053354.2600.1309772395476.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-655?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17269#comment-17269 ] Mannie Tagarira commented on BIOCAT-655: ---------------------------------------- Seems to be working @ /users/{id} Role id 1 == Admin Role id 2 == Curator Any other role id == no badge > Show curator and admin badges in the UI > --------------------------------------- > > Key: BIOCAT-655 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-655 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 1 hour > Remaining Estimate: 0 minutes > > Currently, there is no way of seeing whether a user is an admin or curator in the catalogue. Show badges (similar to how it's done in myExperiment). -- 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 Jul 4 05:47:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 4 Jul 2011 10:47:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-659) New curation feature: deactivate users In-Reply-To: <6729550.2318.1309343035349.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <33547294.2601.1309772875388.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-659?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17270#comment-17270 ] Mannie Tagarira commented on BIOCAT-659: ---------------------------------------- Confirmation that deactivated users no longer appear in the listings. Just a thought; consider the possibility of adding functionality to reverse this process. What if a user was incorrectly regarded as spam and therefore deactivated? > New curation feature: deactivate users > -------------------------------------- > > Key: BIOCAT-659 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-659 > Project: BioCatalogue > Issue Type: New Feature > Components: User Management, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 2 hours > Remaining Estimate: 0 minutes > > To get rid of spam users, we need the ability to quickly deactivate users from the web interface -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon Jul 4 05:53:26 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 4 Jul 2011 05:53:26 -0400 (EDT) Subject: [BioCatalogue-developers] [2446] trunk/app/views/users/index.html.erb: users should only be presented with the option to sign in when they are not logged in Message-ID: <20110704095326.C3617185834E@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jul 4 06:22:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Jul 2011 11:22:57 +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: <3657037.2602.1309774977230.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 ] Jiten Bhagat updated BIOCAT-661: -------------------------------- Fix Version/s: 1.0.2 (was: 1.0.1) > 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: Jiten Bhagat > Priority: Critical > Fix For: 1.0.2 > > > 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 noreply at rubyforge.org Mon Jul 4 06:24:23 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 4 Jul 2011 06:24:23 -0400 (EDT) Subject: [BioCatalogue-developers] [2447] trunk/app/controllers/users_controller.rb: users should only be presented with the option to sign up when they are not logged in Message-ID: <20110704102423.BB1C3185836C@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jul 4 06:24:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Jul 2011 11:24:55 +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: <31844618.2603.1309775095354.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-662?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-662: -------------------------------- Fix Version/s: 1.0.2 (was: 1.0.1) > 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: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.2 > > > 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. > Also, from Marco: > {quote} > Re: keep old ref. This would be very useful when you find a 'depricated' reference used in a workflow or application. That is how I discoverd this problem: Taverna told me the service didn't exist anymore, so I changed the wsdl reference in the workflow. It would be nice if I could find the new reference on biocatalogue through the old reference. > {quote} -- 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 Jul 4 06:29:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Jul 2011 11:29:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-664) New admin feature: activate users Message-ID: <12844958.2604.1309775395406.JavaMail.jira@rosalind.cs.man.ac.uk> 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: Jiten Bhagat Fix For: 1.0.2 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 Mon Jul 4 06:31:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Jul 2011 11:31:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-659) New curation feature: deactivate users In-Reply-To: <6729550.2318.1309343035349.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <33062499.2605.1309775515448.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-659?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17271#comment-17271 ] Jiten Bhagat commented on BIOCAT-659: ------------------------------------- > Just a thought; consider the possibility of adding functionality to reverse this process. What if a user was incorrectly regarded as spam and therefore deactivated? Good idea. http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-664 > New curation feature: deactivate users > -------------------------------------- > > Key: BIOCAT-659 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-659 > Project: BioCatalogue > Issue Type: New Feature > Components: User Management, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 2 hours > Remaining Estimate: 0 minutes > > To get rid of spam users, we need the ability to quickly deactivate users from the web interface -- 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 Jul 4 06:31:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Jul 2011 11:31:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-659) New curation feature: deactivate users In-Reply-To: <6729550.2318.1309343035349.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27934379.2606.1309775518177.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-659?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17271#comment-17271 ] Jiten Bhagat edited comment on BIOCAT-659 at 04/07/11 11:30: ------------------------------------------------------------- {quote} Just a thought; consider the possibility of adding functionality to reverse this process. What if a user was incorrectly regarded as spam and therefore deactivated? {quote} Good idea. http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-664 was (Author: jbhagat): > Just a thought; consider the possibility of adding functionality to reverse this process. What if a user was incorrectly regarded as spam and therefore deactivated? Good idea. http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-664 > New curation feature: deactivate users > -------------------------------------- > > Key: BIOCAT-659 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-659 > Project: BioCatalogue > Issue Type: New Feature > Components: User Management, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 2 hours > Remaining Estimate: 0 minutes > > To get rid of spam users, we need the ability to quickly deactivate users from the web interface -- 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 Jul 4 06:33:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Jul 2011 11:33:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-659) New curation feature: deactivate users In-Reply-To: <6729550.2318.1309343035349.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20250936.2607.1309775635397.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-659?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-659. --------------------------------- Resolution: Implemented > New curation feature: deactivate users > -------------------------------------- > > Key: BIOCAT-659 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-659 > Project: BioCatalogue > Issue Type: New Feature > Components: User Management, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 2 hours > Remaining Estimate: 0 minutes > > To get rid of spam users, we need the ability to quickly deactivate users from the web interface -- 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 Jul 4 06:36:56 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 4 Jul 2011 11:36:56 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-653) New curation feature: ability to delete empty service provider in the web UI In-Reply-To: <6424713.2283.1309277875346.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10579801.2608.1309775816286.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-653?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17272#comment-17272 ] Mannie Tagarira commented on BIOCAT-653: ---------------------------------------- Seems to work fine. The "delete" button only shows up when the service provider has no services which is a good thing. > New curation feature: ability to delete empty service provider in the web UI > ---------------------------------------------------------------------------- > > Key: BIOCAT-653 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-653 > Project: BioCatalogue > Issue Type: New Feature > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > Time Spent: 2 hours > Remaining Estimate: 0 minutes > > Need to the ability to delete *empty* service providers (only) in the web interface, only for curators. -- 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 Jul 4 06:39:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Jul 2011 11:39:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-655) Show curator and admin badges in the UI In-Reply-To: <24162756.2294.1309338475347.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1263467.2609.1309775995382.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-655?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-655. --------------------------------- Resolution: Fixed > Show curator and admin badges in the UI > --------------------------------------- > > Key: BIOCAT-655 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-655 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 1 hour > Remaining Estimate: 0 minutes > > Currently, there is no way of seeing whether a user is an admin or curator in the catalogue. Show badges (similar to how it's done in myExperiment). -- 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 Jul 4 06:43:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Jul 2011 11:43:55 +0100 (BST) 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: <16826697.2610.1309776235373.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 ] Jiten Bhagat updated BIOCAT-654: -------------------------------- Description: 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. was:With the new ability to make users curators through the web interface, make Carole a curator too. > 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: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > 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 Mon Jul 4 09:54:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Jul 2011 14:54:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-643) Test out v1.0.1 on the test site In-Reply-To: <863672.1687.1308666415346.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4987182.2611.1309787695509.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-643?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-643 stopped by Jiten Bhagat. > Test out v1.0.1 on the test site > -------------------------------- > > Key: BIOCAT-643 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-643 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > This includes running the monitoring manually to check that everything is running as expected. -- 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 Jul 4 09:54:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Jul 2011 14:54:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-643) Test out v1.0.1 on the test site In-Reply-To: <863672.1687.1308666415346.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24256310.2612.1309787698340.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-643?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-643. --------------------------------- Resolution: Implemented > Test out v1.0.1 on the test site > -------------------------------- > > Key: BIOCAT-643 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-643 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > This includes running the monitoring manually to check that everything is running as expected. -- 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 Jul 4 12:48:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Jul 2011 17:48:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-653) New curation feature: ability to delete empty service provider in the web UI In-Reply-To: <6424713.2283.1309277875346.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27546225.2616.1309798135544.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-653?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-653. --------------------------------- Resolution: Implemented > New curation feature: ability to delete empty service provider in the web UI > ---------------------------------------------------------------------------- > > Key: BIOCAT-653 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-653 > Project: BioCatalogue > Issue Type: New Feature > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > Time Spent: 2 hours > Remaining Estimate: 0 minutes > > Need to the ability to delete *empty* service providers (only) in the web interface, only for curators. -- 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 Jul 4 12:50:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Jul 2011 17:50:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (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: <7883678.2617.1309798255445.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 ] Jiten Bhagat resolved BIOCAT-611. --------------------------------- Resolution: Implemented > 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: 1.0.1 > > 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 Mon Jul 4 12:50:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Jul 2011 17:50:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (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: <12380651.2618.1309798257677.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-611?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17273#comment-17273 ] Jiten Bhagat commented on BIOCAT-611: ------------------------------------- Need to do a final update and clone of the VM and then archive it somewhere. > 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: 1.0.1 > > 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 Mon Jul 4 12:51:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Jul 2011 17:51:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Reopened: (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: <18549893.2619.1309798261781.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 ] Jiten Bhagat reopened BIOCAT-611: --------------------------------- > 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: 1.0.1 > > 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 Tue Jul 5 10:31:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 15:31:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Reopened: (BIOCAT-655) Show curator and admin badges in the UI In-Reply-To: <24162756.2294.1309338475347.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24652510.2676.1309876315518.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-655?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat reopened BIOCAT-655: --------------------------------- Still need to add badges on the user listings! > Show curator and admin badges in the UI > --------------------------------------- > > Key: BIOCAT-655 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-655 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 1 hour > Remaining Estimate: 0 minutes > > Currently, there is no way of seeing whether a user is an admin or curator in the catalogue. Show badges (similar to how it's done in myExperiment). -- 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 Jul 5 10:33:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 15:33:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-655) Show curator and admin badges in the UI In-Reply-To: <24162756.2294.1309338475347.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24860913.2677.1309876435396.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-655?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-655: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.1) > Show curator and admin badges in the UI > --------------------------------------- > > Key: BIOCAT-655 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-655 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.0 > > Time Spent: 1 hour > Remaining Estimate: 0 minutes > > Currently, there is no way of seeing whether a user is an admin or curator in the catalogue. Show badges (similar to how it's done in myExperiment). -- 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 Jul 5 10:33:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 15:33:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-655) Show curator and admin badges in the UI In-Reply-To: <24162756.2294.1309338475347.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4462403.2678.1309876437843.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-655?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-655: -------------------------------- Priority: Trivial (was: Critical) > Show curator and admin badges in the UI > --------------------------------------- > > Key: BIOCAT-655 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-655 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Trivial > Fix For: 1.1.0 > > Time Spent: 1 hour > Remaining Estimate: 0 minutes > > Currently, there is no way of seeing whether a user is an admin or curator in the catalogue. Show badges (similar to how it's done in myExperiment). -- 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 Jul 5 11:15:48 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 5 Jul 2011 11:15:48 -0400 (EDT) Subject: [BioCatalogue-developers] [2448] tags/release-1.0.1/: Tagged v1.0.1 release Message-ID: <20110705151548.C557B1858363@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jul 5 11:32:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:32:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-610) Archived resources appear as having no annotations via the API even when they do have annotations In-Reply-To: <32100862.1325.1307699335367.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <33232089.2681.1309879975446.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-610?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-610: -------------------------------- Fix Version/s: 1.0.1 (was: 1.1.0) > Archived resources appear as having no annotations via the API even when they do have annotations > ------------------------------------------------------------------------------------------------- > > Key: BIOCAT-610 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-610 > Project: BioCatalogue > Issue Type: Bug > Components: REST API > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.0.1 > > > /services/6/annotations > /soap_operations/428/annotations -- 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 Jul 5 11:32:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:32:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-609) The email sent to BioCat admins about service providers with no services and/or hostnames does not always generate valid URLs In-Reply-To: <7440241.1324.1307697295474.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32922047.2682.1309879979105.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-609?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-609: -------------------------------- Fix Version/s: 1.0.1 (was: 1.1.0) > The email sent to BioCat admins about service providers with no services and/or hostnames does not always generate valid URLs > ----------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-609 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-609 > Project: BioCatalogue > Issue Type: Bug > Components: Service Provider Management > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Minor > Fix For: 1.0.1 > > > Generated URL: > http://http//www.biocatalogue.org/service_providers/342 -- 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 Jul 5 11:33:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:33:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-600) Some web services (which are not archived) have incorrect monitoring information In-Reply-To: <2567019.952.1307461195351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18392068.2683.1309879982002.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-600?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-600: -------------------------------- Fix Version/s: 1.0.1 (was: 1.1.0) > Some web services (which are not archived) have incorrect monitoring information > -------------------------------------------------------------------------------- > > Key: BIOCAT-600 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-600 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > > http://www.biocatalogue.org/services/2705#availability-checks > This service has a blue icon and no monitoring information, which is correct. However the "Availablity Check" tab says it has 2 tests available which appears to be incorrect. -- 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 Jul 5 11:33:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:33:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-597) Investigate monitoring for archived services In-Reply-To: <16684682.944.1307435395526.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31257190.2684.1309879984381.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-597?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-597: -------------------------------- Fix Version/s: 1.0.1 (was: 1.1.0) > Investigate monitoring for archived services > -------------------------------------------- > > Key: BIOCAT-597 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-597 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > An archived service has a blue monitoring status icon (highlighting that NO monitoring information is available). Under the monitoring tab, no monitoring tests are shown but the tab itself says X tests exist. > See any of the VBI services: http://www.biocatalogue.org/service_providers/3#services -- 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 Jul 5 11:34:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:34:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-135) Fix WSDL parsing - not picking up all descriptions Message-ID: <4377427.2685.1309880095410.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-135?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-135: -------------------------------- Assignee: Jiten Bhagat (was: Eric Nzuobontane) Fix Version/s: 1.2.0 (was: 1.1.0) > Fix WSDL parsing - not picking up all descriptions > -------------------------------------------------- > > Key: BIOCAT-135 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-135 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > E.g.: http://edoc3.bibliothek.uni-halle.de:8080/axis/vascoda.wsdl has some descriptions about the operation etc BUT the WSDL parsing isn't picking this 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 Tue Jul 5 11:36:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:36:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-253) Monitoring history limit should not be hard coded Message-ID: <17998815.2686.1309880215546.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-253?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-253: -------------------------------- Assignee: Mannie Tagarira (was: Eric Nzuobontane) > Monitoring history limit should not be hard coded > ------------------------------------------------- > > Key: BIOCAT-253 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-253 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Minor > Fix For: 1.1.0 > > > Currently, the limit of 5 entries for monitoring histories is hard coded in the finder methods... need to take this out and define it in one place and then possibly make it configurable. -- 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 Jul 5 11:38:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:38:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-243) Make ALL routes/pages HTTPS (SSL) Message-ID: <856990.2688.1309880335869.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-243: -------------------------------- Summary: Make ALL routes/pages HTTPS (SSL) (was: Make ALL routes/pages HTTPS) > 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: 1.1.0 > > > 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 Tue Jul 5 11:40:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:40:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-649) Investigate whether those responsible for a service can see disabled service tests In-Reply-To: <3163840.2126.1309249555347.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29425965.2690.1309880459056.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-649?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-649: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Investigate whether those responsible for a service can see disabled service tests > ---------------------------------------------------------------------------------- > > Key: BIOCAT-649 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-649 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring, Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.1.0 > > > It is important for those who are responsible for a service to be able to see disabled service tests in the interface AND enable then again. > Check that this is the case. -- 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 Jul 5 11:42:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:42:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-665) Refactor and improve Annotations plugin to support polymorphic values Message-ID: <4683348.2691.1309880575408.JavaMail.jira@rosalind.cs.man.ac.uk> Refactor and improve Annotations plugin to support polymorphic values --------------------------------------------------------------------- Key: BIOCAT-665 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-665 Project: BioCatalogue Issue Type: Improvement Components: Annotations Plugin Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Blocker 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 Tue Jul 5 11:36:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:36:58 +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: <30369334.2687.1309880219277.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-568: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > 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: Blocker > Fix For: 1.1.0 > > > 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 Tue Jul 5 11:44:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:44:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (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: <23764617.2692.1309880695398.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-621?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16871#comment-16871 ] Jiten Bhagat edited comment on BIOCAT-621 at 05/07/11 16:43: ------------------------------------------------------------- Bumping this to v1.1.0 so that a better solution can be put in place for the longer term. was (Author: jbhagat): Bumping this to v1.0.2 so that a better solution can be put in place for the longer term. > 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: 1.1.0 > > > 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 Tue Jul 5 11:46:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:46:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-519) Implement an initial "Examples" tab on the Service profile page In-Reply-To: <23290831.528.1289908589158.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4399340.2693.1309880815418.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-519?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-519: -------------------------------- Priority: Blocker (was: Critical) > Implement an initial "Examples" tab on the Service profile page > --------------------------------------------------------------- > > Key: BIOCAT-519 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-519 > Project: BioCatalogue > Issue Type: New Feature > Components: Service Container, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > Original Estimate: 2 days > Remaining Estimate: 2 days > > An important need has been identified to show users examples of usage for services. > The proposed plan is to implement a new tab "Examples" for the Service profile page which can show the following: > - Links to examples > - Example scripts (both the test scripts and actual examples) > - Example workflows -- 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 Jul 5 11:46:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:46:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-465) Test OAuth on the live site In-Reply-To: <10881481.9000.1284042795322.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19673310.2694.1309880818019.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-465?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-465: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Test OAuth on the live site > --------------------------- > > Key: BIOCAT-465 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-465 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > 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 Tue Jul 5 11:47:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:47:02 +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: <11367165.2695.1309880822209.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 ] Jiten Bhagat updated BIOCAT-499: -------------------------------- Fix Version/s: 1.0.1 (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: 1.0.1 > > > 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 Tue Jul 5 11:40:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:40:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-658) Ability to test out test scripts via the interface to check if they work with the test harness In-Reply-To: <1216271.2306.1309341655352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18049459.2689.1309880455382.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-658?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-658: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) > Ability to test out test scripts via the interface to check if they work with the test harness > ---------------------------------------------------------------------------------------------- > > Key: BIOCAT-658 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-658 > Project: BioCatalogue > Issue Type: New Feature > Components: Service Monitoring > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.2.0 > > > Request from Rob Finn (maintainer of the HMMER Janelia REST service): > {quote} > Is there a way to test if this is going to pass? That would be a useful feature, rather than waiting for the system to automatically run it (however, as a web developer I understand that this many not be straight forward todo). > {quote} > It would be a very useful feature to allow test script submitters to immediately run their scripts and see if they pass/fail in the test harness. This allows for debugging. > This is a tricky thing to get right as it could lead to DOS attacks, etc. So need to approach this with some caution. -- 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 Jul 5 11:48:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:48:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-303) Investigate database timout errors when deleting entries Message-ID: <24784449.2696.1309880935485.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-303?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17289#comment-17289 ] Jiten Bhagat commented on BIOCAT-303: ------------------------------------- This is likely due to memory allocations on the Solr instance > 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: 1.1.0 > > 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 Tue Jul 5 11:50:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:50:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-663) Ability to link services by saying that one is the "better" or "newer" version In-Reply-To: <9875387.2506.1309510255346.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23386033.2697.1309881055377.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-663?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-663: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) > Ability to link services by saying that one is the "better" or "newer" version > ------------------------------------------------------------------------------ > > Key: BIOCAT-663 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-663 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > From Marco: > {quote} > We also have a new and extended version of this service. This is another type of reference that would be useful for us: refer to a biocatalogue entry that has this better version. We wouldn't want to remove the old entry, because some users might still use it. > {quote} -- 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 Jul 5 11:50:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:50:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-638) The monitoring framework should allow for users who wish to supply their own REST endpoints for testing (some of which may contain sensitive information) In-Reply-To: <27341174.1627.1308576295454.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9682243.2698.1309881057686.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-638?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-638: -------------------------------- Priority: Critical (was: Major) > The monitoring framework should allow for users who wish to supply their own REST endpoints for testing (some of which may contain sensitive information) > --------------------------------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-638 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-638 > Project: BioCatalogue > Issue Type: Improvement > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.1.0 > > > Trish Whetzel would like to be able to provide a specific endpoint for testing. This endpoint will contain information which is to be kept private and so the current mechanism for testing REST endpoints (using example_endpoint annotations) is inappropriate. -- 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 Jul 5 11:51:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:51:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-648) Disabled status of service tests not shown in monitoring tab on service profile page In-Reply-To: <31783970.2125.1309249435437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2991781.2699.1309881060105.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-648: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Disabled status of service tests not shown in monitoring tab on service profile page > ------------------------------------------------------------------------------------ > > Key: BIOCAT-648 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring, Web Interface > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > > When viewing the various service tests under the "Monitoring" tab in the service profile page, disabled tests are shown to admins/curators BUT their status (i.e. that it is disabled) is not shown! Only when you click through to the actual service test's page do you see that it is disabled. -- 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 Jul 5 11:52:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:52:55 +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: <1074173.2700.1309881175383.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-634?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-634: -------------------------------- Priority: Critical (was: Major) > 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: Critical > Fix For: 1.1.0 > > > 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 Tue Jul 5 11:54:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:54:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-633) Add "scope" parameter to /tags index so you can get a subset of tags In-Reply-To: <24019167.1523.1308229975349.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18845838.2701.1309881295371.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-633?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-633: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) > Add "scope" parameter to /tags index so you can get a subset of tags > -------------------------------------------------------------------- > > Key: BIOCAT-633 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-633 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > Currently, the /tags index only gives the full list of tags in the catalogue. > Implement a {{scope}} parameter to allow consumers to specify resources that the tags should be limited too. > For example: > {code} > /tags?scope=soap_operations > {code} > This can get tricky, because does the above mean "all tags on SoapOperations only" OR "all tags on SoapOperations and anything below the SoapOperations structure"?? -- 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 Jul 5 11:54:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:54:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-618) Inspect the current state of OAuth and the possibility of using it to provide API keys to agents for use in the test scripts harness In-Reply-To: <18646049.1348.1307707195355.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12271027.2702.1309881297626.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-618?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-618: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) > Inspect the current state of OAuth and the possibility of using it to provide API keys to agents for use in the test scripts harness > ------------------------------------------------------------------------------------------------------------------------------------ > > Key: BIOCAT-618 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-618 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.2.0 > > -- 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 Tue Jul 5 11:56:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:56:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-612) Potentially add the system and API version numbers at the root of ALL API responses (XML and JSON) In-Reply-To: <14740.1329.1307700175359.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7076637.2703.1309881415389.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-612?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-612: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) > Potentially add the system and API version numbers at the root of ALL API responses (XML and JSON) > -------------------------------------------------------------------------------------------------- > > Key: BIOCAT-612 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-612 > Project: BioCatalogue > Issue Type: Improvement > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > -- 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 Tue Jul 5 11:56:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:56:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-608) Improve the way display names for services are set In-Reply-To: <4320008.1302.1307631055357.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14217838.2704.1309881418048.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-608?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-608: -------------------------------- Priority: Blocker (was: Major) > Improve the way display names for services are set > -------------------------------------------------- > > Key: BIOCAT-608 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-608 > Project: BioCatalogue > Issue Type: Improvement > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > > Currently, when a new display name is required for a service, this gets set as a "display_name" *annotation* which takes precedence in the UI and API over the {{name}} field (or whatever else) in the actual model object's table. > This is BAD for things like sorting and also not very efficient at all. > Change this so that {{Service#name}} gets set to the new value instead of using these display_name annotations. -- 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 Jul 5 11:58:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:58:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-604) Improve the stats generation process In-Reply-To: <21474347.1076.1307623855384.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6448316.2705.1309881535372.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-604?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-604: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) Description: The current stats generation for the stats dashboard has become too cumbersome - it often causes the background job to fail or freeze and block up the whole queue. This is probably due to how much it tries to process. This needs to be improved! One possibility is to break up the whole process into a set of sub processes where each maintains it's own stats data. With an overall stats wrapper over all the data. was: The current stats generation for the stats dashboard has become too cumbersome - it often causes the background job to fail or freeze and block up the whole queue. This is probably due to how much it tries to process. This needs to be improved! > Improve the stats generation process > ------------------------------------ > > Key: BIOCAT-604 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-604 > Project: BioCatalogue > Issue Type: Improvement > Components: Stats Dashboard > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > The current stats generation for the stats dashboard has become too cumbersome - it often causes the background job to fail or freeze and block up the whole queue. This is probably due to how much it tries to process. > This needs to be improved! > One possibility is to break up the whole process into a set of sub processes where each maintains it's own stats data. With an overall stats wrapper over all the data. -- 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 Jul 5 11:58:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:58:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-592) Write a test script that performs user access simulation and load testing In-Reply-To: <2616439.780.1305818515353.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21242401.2706.1309881537590.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-592?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-592: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) > Write a test script that performs user access simulation and load testing > ------------------------------------------------------------------------- > > Key: BIOCAT-592 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-592 > Project: BioCatalogue > Issue Type: Task > Components: Performance / Optimisations, Testing > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > We need to be able to test the system under load so as to figure out issues with the set up (eg: with the Solr issues being experienced). > A script that simulates a large load and with a mixture of requests may help with 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 Tue Jul 5 11:58:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 16:58:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-598) Figure out what to do with service providers with no services In-Reply-To: <22732435.949.1307456575352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6847823.2707.1309881539997.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-598?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-598: -------------------------------- Description: As of June 7th 2011, 4 providers exist with no services. IDs: 333, 314, 304, 322 We have the ability to delete empty service providers by curators. Maybe we also need a curation report for this on the curation dashboard? was: As of June 7th 2011, 4 providers exist with no services. IDs: 333, 314, 304, 322 Component/s: Curation Dashboard > Figure out what to do with service providers with no services > ------------------------------------------------------------- > > Key: BIOCAT-598 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-598 > Project: BioCatalogue > Issue Type: Task > Components: Curation Dashboard, Service Provider Management > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > > As of June 7th 2011, 4 providers exist with no services. > IDs: 333, 314, 304, 322 > We have the ability to delete empty service providers by curators. Maybe we also need a curation report for this on the curation dashboard? -- 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 Jul 5 12:00:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:00:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-579) Implement functionality to allow for services to be added to and removed from a user's favourites via the API In-Reply-To: <14465616.66.1298903907810.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26006800.2708.1309881655375.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-579?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-579: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) Priority: Blocker (was: Major) > Implement functionality to allow for services to be added to and removed from a user's favourites via the API > ------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-579 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-579 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > 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 Tue Jul 5 12:00:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:00:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-576) Provide a special API key for agents In-Reply-To: <475530.652.1297958229376.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1511252.2709.1309881657972.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-576?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-576: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) Affects Version/s: (was: 1.0.0) > Provide a special API key for agents > ------------------------------------ > > Key: BIOCAT-576 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-576 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > Original Estimate: 4 days > Remaining Estimate: 4 days > > For agents to be able to create content from outside the BioCatalogue, a mechanism is required to authenticate them. This needed in the case of the test harness for example which submits test results via the API. -- 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 Jul 5 12:02:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:02:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-540) Move to using Bundler to handle gem dependencies In-Reply-To: <18008377.73.1290164217231.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31814519.2710.1309881775480.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-540?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-540: -------------------------------- Fix Version/s: Future (was: 1.1.0) > Move to using Bundler to handle gem dependencies > ------------------------------------------------ > > Key: BIOCAT-540 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-540 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase, Server Management > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > Stuart has successfully and easily moved to using Bundler (http://gembundler.com/) for managing gem dependencies in Sysmo-SEEK. > We should look to do the same as it makes managing gem dependencies much easier. Also, Rails 3 uses Bundler by default. > Stuart's email to the e-lab-hackers list: > {quote} > Hi, > Last week I mentioned that in SEEK I switched over to Bundler. The only thing I need to check is that it worked with passenger, and I've now confirmed this works without any problems or additional effort. > To switch to using bundler, I simply followed the instructions at http://gembundler.com/rails23.html . The only extra things I found I needed to do was define some gems that weren't already defined in my environment.rb, and also in a couple of places I seemed to need to add a require 'xxx' . My functional tests picked all of these up. > Overall it took me about 2hrs altogether, and much of this time was spent testing and waiting for gems to download. > The only downside I've found and not yet solved is that it doesn't work very happily with RadRails 2, so I can currently no longer run the application and debug within the IDE. > Switching to Bundler for SEEK is a big advantage, because as other projects are now starting to use SEEK it makes the installation much simpler. It also means that I no longer need to maintain the installation instructions whenever I add or remove gems, or change versions. > Stuart. > {quote} -- 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 Jul 5 12:02:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:02:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-520) Show warning on any test/example scripts or any other code In-Reply-To: <30307420.527.1289908470640.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3302781.2711.1309881778041.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-520?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-520: -------------------------------- Assignee: Jiten Bhagat (was: Mannie Tagarira) > Show warning on any test/example scripts or any other code > ---------------------------------------------------------- > > Key: BIOCAT-520 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-520 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > A warning message is required to make the user aware that any non-verified bits of code could have adverse/destructive effects and that the user should be cautious and/or verify before usage. -- 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 Jul 5 12:03:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:03:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-520) Show warning on any test/example scripts or any other code In-Reply-To: <30307420.527.1289908470640.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28088642.2712.1309881780361.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-520?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-520: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Show warning on any test/example scripts or any other code > ---------------------------------------------------------- > > Key: BIOCAT-520 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-520 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > > A warning message is required to make the user aware that any non-verified bits of code could have adverse/destructive effects and that the user should be cautious and/or verify before usage. -- 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 Jul 5 12:04:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:04:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-489) Update stats to take into account archived items In-Reply-To: <17224897.9910.1285881915438.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8747064.2713.1309881895386.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-489?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-489: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) > Update stats to take into account archived items > ------------------------------------------------ > > Key: BIOCAT-489 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-489 > Project: BioCatalogue > Issue Type: Improvement > Components: Stats Dashboard > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > So the totals should reflect only unarchived things, and maybe a separate archived count can be shown 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 Tue Jul 5 12:06:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:06:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-361) Add a "Users responsible for this service" section on the service's profile page In-Reply-To: <23419427.1675.1274978476997.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10069787.2714.1309882015383.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-361?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-361: -------------------------------- Priority: Blocker (was: Major) > Add a "Users responsible for this service" section on the service's profile page > -------------------------------------------------------------------------------- > > Key: BIOCAT-361 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-361 > Project: BioCatalogue > Issue Type: New Feature > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > Original Estimate: 2 hours > Remaining Estimate: 2 hours > -- 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 Jul 5 12:06:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:06:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-325) Implement filter for "Archived Services" In-Reply-To: <2148229.59.1273658417012.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12469067.2715.1309882017958.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-325?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-325: -------------------------------- Priority: Blocker (was: Major) > Implement filter for "Archived Services" > ---------------------------------------- > > Key: BIOCAT-325 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-325 > Project: BioCatalogue > Issue Type: Sub-task > Components: Search / Filtering / Browsing, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > Original Estimate: 3 hours > Remaining Estimate: 3 hours > -- 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 Jul 5 12:07:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:07:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-326) Implement option in services listing to ignore archived services In-Reply-To: <14174500.60.1273658418251.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21522246.2716.1309882022007.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-326?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-326: -------------------------------- Priority: Blocker (was: Major) > Implement option in services listing to ignore archived services > ---------------------------------------------------------------- > > Key: BIOCAT-326 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-326 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > Original Estimate: 3 hours > Remaining Estimate: 3 hours > > A filter / check box to "Include Archived Services" may work. -- 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 Jul 5 12:07:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:07:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-332) Allow linking to alternative services In-Reply-To: <2571312.89.1273678937001.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18714337.2717.1309882024765.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-332?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-332: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) > Allow linking to alternative services > ------------------------------------- > > Key: BIOCAT-332 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-332 > Project: BioCatalogue > Issue Type: New Feature > Components: Service Container, Web Interface > Reporter: Paul Gordon > Assignee: Mannie Tagarira > Fix For: 1.2.0 > > Original Estimate: 6 hours > Remaining Estimate: 6 hours > > Especially in cases of archived services where it would make sense to point to an alternative that isn't deprecated/archived. > Paul's original email: > --- > Hi Jits, > I like the idea or "archiving", because then you could point people to working equivalents if they exist...if you plan on doing that, it might make sense to also link to the alternatives on those screens. > My $0.02, > Paul > --- -- 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 Jul 5 12:07:07 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:07:07 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-318) Improve styling of "Part of Service..." Message-ID: <24207932.2718.1309882027369.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-318?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-318: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) Fix Version/s: 1.2.0 (was: 1.1.0) > Improve styling of "Part of Service..." > --------------------------------------- > > Key: BIOCAT-318 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-318 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Fix For: 1.2.0 > > Original Estimate: 1 hour > Remaining Estimate: 1 hour > > ... in the SoapOperation and RestMethod listings partials. -- 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 Jul 5 12:11:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:11:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-137) Investigate no values for min_occurs and max_occurs, from WSDL parsing Message-ID: <6822639.2719.1309882315441.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-137?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-137: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) > Investigate no values for min_occurs and max_occurs, from WSDL parsing > ---------------------------------------------------------------------- > > Key: BIOCAT-137 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-137 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > min_occurs and max_occurs for soap_inputs and soap_outputs currently have no values whatsoever, and this needs investigating. > It could be due to WSDL parsing or it could just be that we don't need those fields in the DB (in which case we should remove them) -- 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 Jul 5 12:11:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:11:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-299) Allow updating of the geolocation data for service deployments Message-ID: <27031219.2720.1309882317817.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-299?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-299: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) Affects Version/s: (was: 1.0.0) > Allow updating of the geolocation data for service deployments > -------------------------------------------------------------- > > Key: BIOCAT-299 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-299 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard, Service Container, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.2.0 > > > An existing script (regelocate.rb) can do this on an ad hoc basis, but support for this needs to be available in the main web UI and curation dashboard. -- 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 Jul 5 12:12:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:12:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-416) Dynamically-generated search suggestions drop-down menu is in the wrong place in IE8 In-Reply-To: <3147156.6627.1277388195335.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30701755.2721.1309882320320.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-416?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-416: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) > Dynamically-generated search suggestions drop-down menu is in the wrong place in IE8 > ------------------------------------------------------------------------------------ > > Key: BIOCAT-416 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-416 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.2.0 > > Attachments: screenshot-1.jpg > > > The drop-down menu appears in the wrong place - some 3cm below and 2cm to the right from the edge of the search box. Screenshot attached. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 5 12:12:05 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:12:05 +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: <1370204.2722.1309882325080.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-509?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-509: -------------------------------- Description: 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. was: 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: 1) 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. > 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: 1.1.0 > > > 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 Tue Jul 5 12:13:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:13:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-295) Investigate double render error with "error_to_back_or_home" helper Message-ID: <5095677.2723.1309882435413.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-295?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-295: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Investigate double render error with "error_to_back_or_home" helper > ------------------------------------------------------------------- > > Key: BIOCAT-295 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-295 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Environment: Ruby on Rails > Reporter: Eric Nzuobontane > Assignee: Mannie Tagarira > Priority: Minor > Fix For: 1.1.0 > > > When error_to_back_or_home helper is used in a before_filter with render/redirect, a multiple redirect error is raise. This even when a false is returned as returning false does not halt the filter chain -- 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 Jul 5 12:13:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:13:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-213) All external links should open in a new tab/window Message-ID: <31830815.2724.1309882437733.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-213?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-213: -------------------------------- Fix Version/s: Future (was: 1.1.0) > All external links should open in a new tab/window > -------------------------------------------------- > > Key: BIOCAT-213 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-213 > Project: BioCatalogue > Issue Type: New Feature > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Will be extremely useful if any external link e.g documentation URL could open in a new tab or window. otherwise navigation is sometimes difficult (a lot of click on the 'go back' button on firefox) -- 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 Jul 5 12:18:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:18:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-243) Make ALL routes/pages HTTPS (SSL) Message-ID: <13581677.2725.1309882735401.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-243: -------------------------------- Priority: Blocker (was: Critical) > 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: Blocker > Fix For: 1.1.0 > > > 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 Tue Jul 5 12:18:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:18:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-638) The monitoring framework should allow for users who wish to supply their own REST endpoints for testing (some of which may contain sensitive information) In-Reply-To: <27341174.1627.1308576295454.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16282527.2726.1309882737628.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-638?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-638: -------------------------------- Priority: Blocker (was: Critical) > The monitoring framework should allow for users who wish to supply their own REST endpoints for testing (some of which may contain sensitive information) > --------------------------------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-638 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-638 > Project: BioCatalogue > Issue Type: Improvement > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > Fix For: 1.1.0 > > > Trish Whetzel would like to be able to provide a specific endpoint for testing. This endpoint will contain information which is to be kept private and so the current mechanism for testing REST endpoints (using example_endpoint annotations) is inappropriate. -- 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 Jul 5 12:18:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Jul 2011 17:18:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-450) Update functional tests In-Reply-To: <16071792.7950.1280933655385.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5879482.2727.1309882739876.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-450?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-450: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) > Update functional tests > ----------------------- > > Key: BIOCAT-450 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-450 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.2.0 > > -- 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 Jul 5 12:27:42 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 5 Jul 2011 12:27:42 -0400 (EDT) Subject: [BioCatalogue-developers] [2449] branches/v1.1.0/: Branch for ALL v1.1.0 work Message-ID: <20110705162742.0DAD0185836C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Jul 5 12:32:53 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 5 Jul 2011 12:32:53 -0400 (EDT) Subject: [BioCatalogue-developers] [2450] branches/v1.1.0/script/biocatalogue: Updated some of the reports Message-ID: <20110705163253.859171D780D5@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jul 6 04:54:59 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 6 Jul 2011 09:54:59 +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: <10987997.2735.1309942499878.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-634?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-634: ----------------------------------- Priority: Blocker (was: Critical) > 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: 1.1.0 > > > 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 Jul 6 04:54:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 6 Jul 2011 09:54:55 +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: <27101368.2734.1309942495485.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-641?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-641: ----------------------------------- Summary: Find a better way to differentiate (at a glance) between services or soap operations with the same name (was: Find a better way to differentiate (at a glace) between services or soap operations with the same name) > 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: 1.1.0 > > Attachments: -service_providers-240#services.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 noreply at rubyforge.org Wed Jul 6 05:23:39 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 6 Jul 2011 05:23:39 -0400 (EDT) Subject: [BioCatalogue-developers] [2451] branches/v1.1.0/app/views/test_scripts/_about_testscripts.html.erb: [BIOCAT-650] updated the help text shown about test scripts Message-ID: <20110706092340.952F518583AD@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jul 6 05:26:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 6 Jul 2011 10:26:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (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: <33208149.2742.1309944415401.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-650?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17294#comment-17294 ] Mannie Tagarira commented on BIOCAT-650: ---------------------------------------- Added information about test scripts to the wiki and updated the help text shown about test scripts. Maybe a one liner should be added to the form used to submit test scripts which will remind users to take a look at the instructions. > 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: Blocker > Fix For: 1.1.0 > > > 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 Jul 6 05:26:58 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 6 Jul 2011 10:26:58 +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: <16825396.2743.1309944418073.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-650?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-650: ----------------------------------- Priority: Critical (was: Blocker) > 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: 1.1.0 > > > 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 Jul 6 05:35:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 6 Jul 2011 10:35:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-647) If a service has a query parameter AND a template parameter of the same name, one of them is ignored In-Reply-To: <17763498.1827.1308919675350.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2734648.2744.1309944955376.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-647?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17295#comment-17295 ] Mannie Tagarira commented on BIOCAT-647: ---------------------------------------- Should we really allow users to add query and template parameters with the same name? Having query and template params with the same name may cause some confusion to people actually looking to use the service. Consider the case where a service has 2 "db" parameters which have different semantics; one "db" may be a primary database whereas the second "db" may a secondary/fallback database. Seeing two "db" params may imply that these 2 entities are the same whereas this might not be the case. Would it not be better to encourage users to name the params differently? > If a service has a query parameter AND a template parameter of the same name, one of them is ignored > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-647 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-647 > Project: BioCatalogue > Issue Type: Bug > Components: REST Services Support > Affects Versions: 1.0.1 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > Fix For: 1.1.0 > > > Registering the following endpoint doesn't generate the correct URL template > {code:none} > POST /iphiphpih/{id}?id={value} > {code} > the template becomes "http://example.org/iphiphpih/{id}" > it misses out the "id" query parameter -- 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 Jul 6 05:40:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 6 Jul 2011 10:40:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-647) If a service has a query parameter AND a template parameter of the same name, one of them is ignored In-Reply-To: <17763498.1827.1308919675350.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24631477.2745.1309945255358.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-647?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17296#comment-17296 ] Jiten Bhagat commented on BIOCAT-647: ------------------------------------- I totally agree! > If a service has a query parameter AND a template parameter of the same name, one of them is ignored > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-647 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-647 > Project: BioCatalogue > Issue Type: Bug > Components: REST Services Support > Affects Versions: 1.0.1 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > Fix For: 1.1.0 > > > Registering the following endpoint doesn't generate the correct URL template > {code:none} > POST /iphiphpih/{id}?id={value} > {code} > the template becomes "http://example.org/iphiphpih/{id}" > it misses out the "id" query parameter -- 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 Jul 6 06:52:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 6 Jul 2011 11:52:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-644) Failing to create new REST endpoints In-Reply-To: <5731097.1711.1308825655356.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32165124.2746.1309949575588.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-644?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17297#comment-17297 ] Mannie Tagarira commented on BIOCAT-644: ---------------------------------------- According to http://gis.638310.n2.nabble.com/rails-port-problem-td6296694.html, ERROROAuth::Signature::UnknownSignatureMethod is not the problem. > 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: Blocker > Fix For: 1.1.0 > > > 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 Jul 6 06:52:58 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 6 Jul 2011 11:52:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-644) Failing to create new REST endpoints In-Reply-To: <5731097.1711.1308825655356.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20996421.2747.1309949578804.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-644?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-644 started by Mannie Tagarira. > 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: Blocker > Fix For: 1.1.0 > > > 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 Jul 6 07:04:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 6 Jul 2011 12:04:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-644) Failing to create new REST endpoints In-Reply-To: <5731097.1711.1308825655356.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26329307.2748.1309950295369.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-644?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17298#comment-17298 ] Mannie Tagarira commented on BIOCAT-644: ---------------------------------------- I managed to replicate this issue but only because SOLR was either not running or not running properly (not enough memory, etc). I have added better logging facilities to help track this bug if it occurs again. I have also fixed the bug which was not deleting RestResources when an error occurred. > 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: Blocker > Fix For: 1.1.0 > > > 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 noreply at rubyforge.org Wed Jul 6 08:03:28 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 6 Jul 2011 08:03:28 -0400 (EDT) Subject: [BioCatalogue-developers] [2452] branches/v1.1.0/app/models: [BIOCAT-644] Failing to create new REST endpoints Message-ID: <20110706120328.45E4918583AD@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jul 6 08:07:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 6 Jul 2011 13:07:55 +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: <5459767.2749.1309954075605.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-644?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-644: ----------------------------------- Priority: Major (was: Blocker) > 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 > Fix For: 1.1.0 > > > 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 Jul 6 08:25:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 6 Jul 2011 13:25:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-647) If a service has a query parameter AND a template parameter of the same name, one of them is ignored In-Reply-To: <17763498.1827.1308919675350.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6240795.2750.1309955155425.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-647?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-647: ----------------------------------- Priority: Major (was: Blocker) > If a service has a query parameter AND a template parameter of the same name, one of them is ignored > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-647 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-647 > Project: BioCatalogue > Issue Type: Bug > Components: REST Services Support > Affects Versions: 1.0.1 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > > Registering the following endpoint doesn't generate the correct URL template > {code:none} > POST /iphiphpih/{id}?id={value} > {code} > the template becomes "http://example.org/iphiphpih/{id}" > it misses out the "id" query parameter -- 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 Jul 6 08:47:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 6 Jul 2011 13:47:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-649) Investigate whether those responsible for a service can see disabled service tests In-Reply-To: <3163840.2126.1309249555347.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13467614.2751.1309956475414.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-649?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-649. ------------------------------------ Resolution: Fixed This is indeed the case. > Investigate whether those responsible for a service can see disabled service tests > ---------------------------------------------------------------------------------- > > Key: BIOCAT-649 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-649 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring, Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.1.0 > > > It is important for those who are responsible for a service to be able to see disabled service tests in the interface AND enable then again. > Check that this is the case. -- 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 Jul 6 10:22:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 6 Jul 2011 15:22:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-243) Make ALL routes/pages HTTPS (SSL) Message-ID: <4201695.2752.1309962175447.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-243 started by Mannie Tagarira. > 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: Blocker > Fix For: 1.1.0 > > > 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 Thu Jul 7 04:14:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 7 Jul 2011 09:14:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-243) Make ALL routes/pages HTTPS (SSL) Message-ID: <3501063.2755.1310026495526.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-243 stopped by Mannie Tagarira. > 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: Blocker > Fix For: 1.1.0 > > > 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 noreply at rubyforge.org Thu Jul 7 05:37:50 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 7 Jul 2011 05:37:50 -0400 (EDT) Subject: [BioCatalogue-developers] [2453] branches/scape/: New branch for SCAPE instance Message-ID: <20110707093751.6CCC01858346@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Jul 7 05:40:29 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 7 Jul 2011 05:40:29 -0400 (EDT) Subject: [BioCatalogue-developers] [2454] branches/v1.1.0: [BIOCAT-253] Message-ID: <20110707094029.4916519783C0@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Jul 7 06:03:03 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 7 Jul 2011 06:03:03 -0400 (EDT) Subject: [BioCatalogue-developers] [2455] branches/v1.1.0: reverting to revision 2453 Message-ID: <20110707100303.9AF9219783C0@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Jul 7 06:10:18 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 7 Jul 2011 06:10:18 -0400 (EDT) Subject: [BioCatalogue-developers] [2456] branches/v1.1.0/.pydevproject: deleted .pydevproject Message-ID: <20110707101018.7AAE41858346@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Jul 7 06:43:50 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 7 Jul 2011 06:43:50 -0400 (EDT) Subject: [BioCatalogue-developers] [2457] branches/v1.1.0: [BIOCAT-253] Message-ID: <20110707104350.3FF3C19783C0@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jul 7 06:45:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 7 Jul 2011 11:45:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-253) Monitoring history limit should not be hard coded Message-ID: <12813971.2761.1310035555400.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-253?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17302#comment-17302 ] Mannie Tagarira commented on BIOCAT-253: ---------------------------------------- fixed in revision 2457 > Monitoring history limit should not be hard coded > ------------------------------------------------- > > Key: BIOCAT-253 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-253 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Minor > Fix For: 1.1.0 > > > Currently, the limit of 5 entries for monitoring histories is hard coded in the finder methods... need to take this out and define it in one place and then possibly make it configurable. -- 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 Jul 7 06:45:58 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 7 Jul 2011 11:45:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-253) Monitoring history limit should not be hard coded Message-ID: <31511421.2762.1310035558060.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-253?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-253. ------------------------------------ Resolution: Fixed > Monitoring history limit should not be hard coded > ------------------------------------------------- > > Key: BIOCAT-253 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-253 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Minor > Fix For: 1.1.0 > > > Currently, the limit of 5 entries for monitoring histories is hard coded in the finder methods... need to take this out and define it in one place and then possibly make it configurable. -- 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 Jul 7 07:01:56 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:01:56 +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: <32291250.2763.1310036516127.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-607?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-607: -------------------------------- Fix Version/s: 1.1.0 (was: 1.2.0) Priority: Blocker (was: Major) > 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 Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > > Currently, values in annotations are just a string. This needs to be stripped out into first class objects such as: > - AnnotationValueTag > - AnnotationValueText > - AnnotationValueRef > 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 Thu Jul 7 07:03:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:03:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-665) Refactor and improve Annotations plugin to support polymorphic values In-Reply-To: <4683348.2691.1309880575408.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25247178.2764.1310036635374.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-665?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-665. --------------------------------- Resolution: Duplicate > Refactor and improve Annotations plugin to support polymorphic values > --------------------------------------------------------------------- > > Key: BIOCAT-665 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-665 > Project: BioCatalogue > Issue Type: Improvement > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > 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 Thu Jul 7 07:03:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:03:57 +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: <19570617.2765.1310036637599.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-601?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-601: -------------------------------- Fix Version/s: 1.1.0 (was: 1.2.0) Affects Version/s: (was: 1.0.0) > 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: 1.1.0 > > -- 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 Thu Jul 7 07:04:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:04:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-267) In Annotations plugin - check the setting of "source" when creating annotations Message-ID: <5101092.2766.1310036640140.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-267?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-267: -------------------------------- Fix Version/s: 1.1.0 (was: Future) Priority: Critical (was: Major) > 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: 1.1.0 > > > 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 Thu Jul 7 07:11:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:11:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-666) May need to delete the db index on the 'value' column in the annotations table Message-ID: <161349.2767.1310037115390.JavaMail.jira@rosalind.cs.man.ac.uk> May need to delete the db index on the 'value' column in the annotations table ------------------------------------------------------------------------------ Key: BIOCAT-666 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-666 Project: BioCatalogue Issue Type: Sub-task Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical 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 noreply at rubyforge.org Thu Jul 7 07:12:34 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 7 Jul 2011 07:12:34 -0400 (EDT) Subject: [BioCatalogue-developers] [2458] branches/v1.1.0: simplified the config options for MONITORING_HISTORY_LIMIT and SHOW_MONITORING_GRAPH Message-ID: <20110707111234.AA4F31858300@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jul 7 07:30:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:30:55 +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: <18857569.2769.1310038255352.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-607?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-607: -------------------------------- Description: 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. was: Currently, values in annotations are just a string. This needs to be stripped out into first class objects such as: - AnnotationValueTag - AnnotationValueText - AnnotationValueRef 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. > 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 Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > > 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 Thu Jul 7 07:40:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:40:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-666) May need to delete the db index on the 'value' column in the annotations table In-Reply-To: <161349.2767.1310037115390.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5340888.2770.1310038855571.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-666?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-666: -------------------------------- Component/s: Annotations (in App) > May need to delete the db index on the 'value' column in the annotations table > ------------------------------------------------------------------------------ > > Key: BIOCAT-666 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-666 > Project: BioCatalogue > Issue Type: Sub-task > Components: Annotations (in App) > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > 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 Thu Jul 7 07:40:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 7 Jul 2011 12:40:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-644) Failing to create new REST endpoints In-Reply-To: <5731097.1711.1308825655356.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17131048.2771.1310038857981.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-644?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-644 stopped by Mannie Tagarira. > 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 > Fix For: 1.1.0 > > > 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 Thu Jul 7 07:41:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:41:00 +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: <14604372.2772.1310038860997.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-607?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-607: -------------------------------- Component/s: Annotations (in App) > 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: 1.1.0 > > > 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 Thu Jul 7 07:41:03 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:41:03 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-666) May need to manually delete the db index on the 'value' column in the annotations table In-Reply-To: <161349.2767.1310037115390.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7393516.2773.1310038863293.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-666?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-666: -------------------------------- Summary: May need to manually delete the db index on the 'value' column in the annotations table (was: May need to delete the db index on the 'value' column in the annotations table) Description: Would need to add this to the new migration > May need to manually delete the db index on the 'value' column in the annotations table > --------------------------------------------------------------------------------------- > > Key: BIOCAT-666 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-666 > Project: BioCatalogue > Issue Type: Sub-task > Components: Annotations (in App) > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.0 > > > Would need to add this to the new migration -- 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 Jul 7 07:42:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 7 Jul 2011 12:42:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-647) If a service has a query parameter AND a template parameter of the same name, one of them is ignored In-Reply-To: <17763498.1827.1308919675350.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13710450.2774.1310038975370.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-647?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-647. ------------------------------------ Resolution: Won't Fix > If a service has a query parameter AND a template parameter of the same name, one of them is ignored > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-647 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-647 > Project: BioCatalogue > Issue Type: Bug > Components: REST Services Support > Affects Versions: 1.0.1 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > > Registering the following endpoint doesn't generate the correct URL template > {code:none} > POST /iphiphpih/{id}?id={value} > {code} > the template becomes "http://example.org/iphiphpih/{id}" > it misses out the "id" query parameter -- 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 Jul 7 07:42:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:42:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-666) May need to manually delete the db index on the 'value' column in the annotations table In-Reply-To: <161349.2767.1310037115390.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25348879.2775.1310038977757.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-666?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-666: -------------------------------- Description: May need to add this to the new migration script (was: Would need to add this to the new migration) > May need to manually delete the db index on the 'value' column in the annotations table > --------------------------------------------------------------------------------------- > > Key: BIOCAT-666 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-666 > Project: BioCatalogue > Issue Type: Sub-task > Components: Annotations (in App) > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.0 > > > May need to add this to the new migration script -- 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 Jul 7 07:42:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:42:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-667) Implement migration to move all annotation values into appropriate models Message-ID: <5396534.2776.1310038979944.JavaMail.jira@rosalind.cs.man.ac.uk> Implement migration to move all annotation values into appropriate models ------------------------------------------------------------------------- Key: BIOCAT-667 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-667 Project: BioCatalogue Issue Type: Sub-task Components: Annotations (in App) Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Blocker Fix For: 1.1.0 Add this to the v3 migration script from the annotations plugin -- 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 Jul 7 07:44:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:44:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-668) Update annotations plugin to support polymorphic values Message-ID: <31613240.2777.1310039095351.JavaMail.jira@rosalind.cs.man.ac.uk> Update annotations plugin to support polymorphic values ------------------------------------------------------- Key: BIOCAT-668 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-668 Project: BioCatalogue Issue Type: Sub-task Components: Annotations Plugin Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Blocker 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 Thu Jul 7 07:46:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:46:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-669) Test new migration script Message-ID: <30217599.2778.1310039215357.JavaMail.jira@rosalind.cs.man.ac.uk> Test new migration script ------------------------- Key: BIOCAT-669 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-669 Project: BioCatalogue Issue Type: Sub-task Components: Annotations (in App) Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical Fix For: 1.1.0 Can test this out on a small dataset with all kinds of annotations in it, then test it on the latest db snapshot -- 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 Jul 7 07:46:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:46:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-667) Implement migration script to move all annotation values into appropriate models In-Reply-To: <5396534.2776.1310038979944.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <850784.2779.1310039219526.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-667?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-667: -------------------------------- Summary: Implement migration script to move all annotation values into appropriate models (was: Implement migration to move all annotation values into appropriate models) > Implement migration script to move all annotation values into appropriate models > -------------------------------------------------------------------------------- > > Key: BIOCAT-667 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-667 > Project: BioCatalogue > Issue Type: Sub-task > Components: Annotations (in App) > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > > Add this to the v3 migration script from the annotations plugin -- 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 Jul 7 07:47:01 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 7 Jul 2011 12:47:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-398) Update /soap_operations/{id}/annotations.json endpoint to show the inputs and the outputs for the SOAP operation In-Reply-To: <4137965.6232.1276690395403.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3610538.2780.1310039221930.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-398?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-398. ------------------------------------ Resolution: No longer relevant This seems to have already been implemented. > Update /soap_operations/{id}/annotations.json endpoint to show the inputs and the outputs for the SOAP operation > ---------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-398 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-398 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API, SOAP Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > > GET /soap_operations/{id}/annotations.json?also=inputs,outputs > and > GET /soap_operations/{id}/annotations.xml?also=inputs,outputs > should return (roughly) the same content in different formats. > The JSON alternative currently behaves as thought no query parameters were provided, i.e. behaves just like > GET /soap_operations/{id}/annotations.json > would behave... -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 7 07:49:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:49:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-670) Write a one off verification test script to test the annotations migration Message-ID: <10011429.2781.1310039395361.JavaMail.jira@rosalind.cs.man.ac.uk> Write a one off verification test script to test the annotations migration -------------------------------------------------------------------------- Key: BIOCAT-670 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-670 Project: BioCatalogue Issue Type: Sub-task Components: Annotations (in App) Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.1.0 After migrating the current set of annotations to the new mechanism for supporting polymorphic annotation values, it is important to verify the data integrity of this! So write a verification test script that can be used to compare before and after state and check total data integrity and consistency! -- 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 Jul 7 07:49:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 7 Jul 2011 12:49:57 +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: <7564779.2782.1310039397675.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-644?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-644: ----------------------------------- Priority: Minor (was: Major) > 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: 1.1.0 > > > 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 Thu Jul 7 07:53:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:53:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-671) Benchmark/profile before/after the changes made to make the annotations support polymorphic values Message-ID: <4494613.2783.1310039635377.JavaMail.jira@rosalind.cs.man.ac.uk> Benchmark/profile before/after the changes made to make the annotations support polymorphic values -------------------------------------------------------------------------------------------------- Key: BIOCAT-671 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-671 Project: BioCatalogue Issue Type: Sub-task Components: Annotations (in App) Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical Fix For: 1.1.0 As part of this, do some benchmarking/profiling of the current state of annotations (eg: tags retrieval, filters, etc) to compare before/after. -- 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 Jul 7 07:53:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:53:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-668) Update annotations plugin to support polymorphic values In-Reply-To: <31613240.2777.1310039095351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21158167.2784.1310039637551.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-668?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-668 started by Jiten Bhagat. > Update annotations plugin to support polymorphic values > ------------------------------------------------------- > > Key: BIOCAT-668 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-668 > Project: BioCatalogue > Issue Type: Sub-task > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > 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 Thu Jul 7 07:55:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 12:55:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-668) Update annotations plugin to support polymorphic values In-Reply-To: <31613240.2777.1310039095351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19328607.2787.1310039759887.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-668?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-668: -------------------------------- Description: The plugin itself should: - Have default support for Text values. - Provide a new migration script that can be extended. > Update annotations plugin to support polymorphic values > ------------------------------------------------------- > > Key: BIOCAT-668 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-668 > Project: BioCatalogue > Issue Type: Sub-task > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > > The plugin itself should: > - Have default support for Text values. > - Provide a new migration script that can be extended. -- 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 Jul 7 09:05:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 14:05:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-672) Need to take into account the annotation versions Message-ID: <23658552.2791.1310043955350.JavaMail.jira@rosalind.cs.man.ac.uk> Need to take into account the annotation versions ------------------------------------------------- Key: BIOCAT-672 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-672 Project: BioCatalogue Issue Type: Sub-task Components: Annotations Plugin Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Blocker Fix For: 1.1.0 Annotations are versioned in a separate table (annotation_versions). This take into account changes to the old text 'value' column. Now that values are moved out and made to be polymorphic, the migration of the annotations needs to migrate all the existing versions. But to where? Maybe have the TextField model be versioned too, separately. So any changes to it's content/value column results in a new version of itself BUT not a new version of the 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 Thu Jul 7 09:07:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 14:07:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-672) Need to take into account the annotation versions In-Reply-To: <23658552.2791.1310043955350.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8024692.2792.1310044075377.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-672?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-672: -------------------------------- Description: Annotations are versioned in a separate table (annotation_versions). This take into account changes to the old text 'value' column. Now that values are moved out and made to be polymorphic, the migration of the annotations needs to migrate all the existing versions. But to where? Maybe have the TextField model be versioned too, separately. So any changes to it's content/value column results in a new version of itself BUT not a new version of the annotation. The migration of the old annotations needs to take this into consideration. It needs to emulate the state that this new way of versioning would have created. was: Annotations are versioned in a separate table (annotation_versions). This take into account changes to the old text 'value' column. Now that values are moved out and made to be polymorphic, the migration of the annotations needs to migrate all the existing versions. But to where? Maybe have the TextField model be versioned too, separately. So any changes to it's content/value column results in a new version of itself BUT not a new version of the annotation. > Need to take into account the annotation versions > ------------------------------------------------- > > Key: BIOCAT-672 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-672 > Project: BioCatalogue > Issue Type: Sub-task > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > > Annotations are versioned in a separate table (annotation_versions). This take into account changes to the old text 'value' column. > Now that values are moved out and made to be polymorphic, the migration of the annotations needs to migrate all the existing versions. But to where? > Maybe have the TextField model be versioned too, separately. So any changes to it's content/value column results in a new version of itself BUT not a new version of the annotation. > The migration of the old annotations needs to take this into consideration. It needs to emulate the state that this new way of versioning would have created. -- 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 Jul 7 09:27:56 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 7 Jul 2011 09:27:56 -0400 (EDT) Subject: [BioCatalogue-developers] [2459] branches/v1.1.0: [BIOCAT-648] added styles to make the disabled service tests more obvious to curators and admins Message-ID: <20110707132756.7204519783C0@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jul 7 09:30:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 7 Jul 2011 14:30:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-648) Disabled status of service tests not shown in monitoring tab on service profile page In-Reply-To: <31783970.2125.1309249435437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22755740.2796.1310045455375.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-648: ----------------------------------- Attachment: updated tabs.jpg > Disabled status of service tests not shown in monitoring tab on service profile page > ------------------------------------------------------------------------------------ > > Key: BIOCAT-648 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring, Web Interface > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > Attachments: updated tabs.jpg > > > When viewing the various service tests under the "Monitoring" tab in the service profile page, disabled tests are shown to admins/curators BUT their status (i.e. that it is disabled) is not shown! Only when you click through to the actual service test's page do you see that it is disabled. -- 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 Jul 7 09:32:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 7 Jul 2011 14:32:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-648) Disabled status of service tests not shown in monitoring tab on service profile page In-Reply-To: <31783970.2125.1309249435437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16554879.2797.1310045575391.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-648: ----------------------------------- Attachment: updated listings.jpg > Disabled status of service tests not shown in monitoring tab on service profile page > ------------------------------------------------------------------------------------ > > Key: BIOCAT-648 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring, Web Interface > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > Attachments: updated listings.jpg, updated tabs.jpg > > > When viewing the various service tests under the "Monitoring" tab in the service profile page, disabled tests are shown to admins/curators BUT their status (i.e. that it is disabled) is not shown! Only when you click through to the actual service test's page do you see that it is disabled. -- 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 Jul 7 09:32:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 7 Jul 2011 14:32:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-648) Disabled status of service tests not shown in monitoring tab on service profile page In-Reply-To: <31783970.2125.1309249435437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5786437.2798.1310045577315.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17304#comment-17304 ] Mannie Tagarira commented on BIOCAT-648: ---------------------------------------- In the listings, the disabled test is highlighted by red outline. In the "quick links" section and the tabs, the names of disabled tests are grayed out. > Disabled status of service tests not shown in monitoring tab on service profile page > ------------------------------------------------------------------------------------ > > Key: BIOCAT-648 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring, Web Interface > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > Attachments: updated listings.jpg, updated tabs.jpg > > > When viewing the various service tests under the "Monitoring" tab in the service profile page, disabled tests are shown to admins/curators BUT their status (i.e. that it is disabled) is not shown! Only when you click through to the actual service test's page do you see that it is disabled. -- 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 Jul 7 09:42:54 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 7 Jul 2011 09:42:54 -0400 (EDT) Subject: [BioCatalogue-developers] [2460] branches/scape: Adding the skinning for SCAPE after branching off from the main BioCatalogue codebase Message-ID: <20110707134254.BC0F519783C0@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jul 7 09:53:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 14:53:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-648) Disabled status of service tests not shown in monitoring tab on service profile page In-Reply-To: <31783970.2125.1309249435437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15775019.2799.1310046835369.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17305#comment-17305 ] Jiten Bhagat commented on BIOCAT-648: ------------------------------------- I don't like the red outline. It doesn't match with any UI pattern on the rest of the site. Instead, why not collapse and grey out the box just like with the services listings? > Disabled status of service tests not shown in monitoring tab on service profile page > ------------------------------------------------------------------------------------ > > Key: BIOCAT-648 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring, Web Interface > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > Attachments: updated listings.jpg, updated tabs.jpg > > > When viewing the various service tests under the "Monitoring" tab in the service profile page, disabled tests are shown to admins/curators BUT their status (i.e. that it is disabled) is not shown! Only when you click through to the actual service test's page do you see that it is disabled. -- 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 Jul 7 09:53:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 14:53:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-648) Disabled status of service tests not shown in monitoring tab on service profile page In-Reply-To: <31783970.2125.1309249435437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14524089.2800.1310046838238.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17306#comment-17306 ] Jiten Bhagat commented on BIOCAT-648: ------------------------------------- Alternatively, break it out into two sections: active tests and disabled tests (like we have for unarchived and archived soap operations). > Disabled status of service tests not shown in monitoring tab on service profile page > ------------------------------------------------------------------------------------ > > Key: BIOCAT-648 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring, Web Interface > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > Attachments: updated listings.jpg, updated tabs.jpg > > > When viewing the various service tests under the "Monitoring" tab in the service profile page, disabled tests are shown to admins/curators BUT their status (i.e. that it is disabled) is not shown! Only when you click through to the actual service test's page do you see that it is disabled. -- 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 Jul 7 10:34:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 7 Jul 2011 15:34:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-648) Disabled status of service tests not shown in monitoring tab on service profile page In-Reply-To: <31783970.2125.1309249435437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14744827.2802.1310049295386.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-648: ----------------------------------- Attachment: updated listings v2.jpg > Disabled status of service tests not shown in monitoring tab on service profile page > ------------------------------------------------------------------------------------ > > Key: BIOCAT-648 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring, Web Interface > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > Attachments: updated listings v2.jpg, updated listings.jpg, updated tabs.jpg > > > When viewing the various service tests under the "Monitoring" tab in the service profile page, disabled tests are shown to admins/curators BUT their status (i.e. that it is disabled) is not shown! Only when you click through to the actual service test's page do you see that it is disabled. -- 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 Jul 7 10:34:58 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 7 Jul 2011 15:34:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-648) Disabled status of service tests not shown in monitoring tab on service profile page In-Reply-To: <31783970.2125.1309249435437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3704010.2803.1310049298168.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-648. ------------------------------------ Resolution: Fixed > Disabled status of service tests not shown in monitoring tab on service profile page > ------------------------------------------------------------------------------------ > > Key: BIOCAT-648 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring, Web Interface > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > Attachments: updated listings v2.jpg, updated listings.jpg, updated tabs.jpg > > > When viewing the various service tests under the "Monitoring" tab in the service profile page, disabled tests are shown to admins/curators BUT their status (i.e. that it is disabled) is not shown! Only when you click through to the actual service test's page do you see that it is disabled. -- 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 Jul 7 10:37:15 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 7 Jul 2011 10:37:15 -0400 (EDT) Subject: [BioCatalogue-developers] [2461] branches/v1.1.0: updated styles for service test listings to be consistent with the rest of the catalogue . Message-ID: <20110707143715.D3B871D780D5@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jul 7 12:05:56 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Jul 2011 17:05:56 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-648) Disabled status of service tests not shown in monitoring tab on service profile page In-Reply-To: <31783970.2125.1309249435437.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4894139.2807.1310054756840.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17309#comment-17309 ] Jiten Bhagat commented on BIOCAT-648: ------------------------------------- Perfect! And it reuses the same CSS class, so any changes in the future will consistently affect the site. > Disabled status of service tests not shown in monitoring tab on service profile page > ------------------------------------------------------------------------------------ > > Key: BIOCAT-648 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-648 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring, Web Interface > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > Attachments: updated listings v2.jpg, updated listings.jpg, updated tabs.jpg > > > When viewing the various service tests under the "Monitoring" tab in the service profile page, disabled tests are shown to admins/curators BUT their status (i.e. that it is disabled) is not shown! Only when you click through to the actual service test's page do you see that it is disabled. -- 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 Jul 8 06:42:05 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 8 Jul 2011 06:42:05 -0400 (EDT) Subject: [BioCatalogue-developers] [2462] trunk/config/initializers/biocat_main.rb: Minor change to the way annotation attribute identifiers are generated. Message-ID: <20110708104205.42CAD18583A3@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jul 11 06:04:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 11 Jul 2011 11:04:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-673) Go through all SOAP services and figure our which are RPC encoded/literal vs Document encoded/literal Message-ID: <1392262.2851.1310378695376.JavaMail.jira@rosalind.cs.man.ac.uk> Go through all SOAP services and figure our which are RPC encoded/literal vs Document encoded/literal ----------------------------------------------------------------------------------------------------- Key: BIOCAT-673 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-673 Project: BioCatalogue Issue Type: Task Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: Future >From Carole: {quote} I should have asked for this statistic RPC/encoded RPC/literal Document/encoded Document/literal how many of each kind do we have in our SOAP services? {quote} Since we don't capture the RPC/Doc status of WSDLs we need to run through all the relevant cached WSDLs and work this out manually. -- 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 Jul 12 09:32:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 12 Jul 2011 14:32:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-674) Possibly open up the Annotations bulk_create endpoint for all users Message-ID: <26739837.3024.1310477575433.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.1.0 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 noreply at rubyforge.org Tue Jul 12 10:33:54 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 12 Jul 2011 10:33:54 -0400 (EDT) Subject: [BioCatalogue-developers] [2463] branches/v1.1.0: [BIOCAT-638] Message-ID: <20110712143354.37DA91858367@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jul 12 10:35:56 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 12 Jul 2011 15:35:56 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-638) The monitoring framework should allow for users who wish to supply their own REST endpoints for testing (some of which may contain sensitive information) In-Reply-To: <27341174.1627.1308576295454.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26618275.3027.1310481356005.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-638?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-638: ----------------------------------- Priority: Major (was: Blocker) Implemented functionaliy to allow users to add ONE custom endpoint for monitoring. The actual endpoint will be kept out of view from the public. Users can update the endpoint being monitoring (at the expense of monitoring history for that endpoint). The service test can also be enabled and disabled like the others. Please confirm. > The monitoring framework should allow for users who wish to supply their own REST endpoints for testing (some of which may contain sensitive information) > --------------------------------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-638 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-638 > Project: BioCatalogue > Issue Type: Improvement > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > > Trish Whetzel would like to be able to provide a specific endpoint for testing. This endpoint will contain information which is to be kept private and so the current mechanism for testing REST endpoints (using example_endpoint annotations) is inappropriate. -- 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 Jul 12 10:37:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 12 Jul 2011 15:37:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-638) The monitoring framework should allow for users who wish to supply their own REST endpoints for testing (some of which may contain sensitive information) In-Reply-To: <27341174.1627.1308576295454.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27264127.3028.1310481475393.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-638?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-638: ----------------------------------- Attachment: public view.jpg > The monitoring framework should allow for users who wish to supply their own REST endpoints for testing (some of which may contain sensitive information) > --------------------------------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-638 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-638 > Project: BioCatalogue > Issue Type: Improvement > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > Attachments: public view.jpg > > > Trish Whetzel would like to be able to provide a specific endpoint for testing. This endpoint will contain information which is to be kept private and so the current mechanism for testing REST endpoints (using example_endpoint annotations) is inappropriate. -- 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 Jul 12 10:53:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 12 Jul 2011 15:53:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-668) Update annotations plugin to support polymorphic values In-Reply-To: <31613240.2777.1310039095351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28448969.3039.1310482435619.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-668?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel\#worklog-{worklog.getId()} ] Jiten Bhagat logged work on BIOCAT-668: --------------------------------------- Author: Jiten Bhagat Created on: 2011-07-12 15:52 Start Date: 2011-07-08 10:00 Worklog Time Spent: 3 days Issue Time Tracking ------------------- Remaining Estimate: 0 minutes Time Spent: 3 days Worklog Id: (was: 10514) > Update annotations plugin to support polymorphic values > ------------------------------------------------------- > > Key: BIOCAT-668 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-668 > Project: BioCatalogue > Issue Type: Sub-task > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > Time Spent: 3 days > Remaining Estimate: 0 minutes > > The plugin itself should: > - Have default support for Text values. > - Provide a new migration script that can be extended. -- 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 Jul 12 11:18:32 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 12 Jul 2011 11:18:32 -0400 (EDT) Subject: [BioCatalogue-developers] [2464] branches/v1.1.0/app: [BIOCAT-638] Message-ID: <20110712151832.58BD11858367@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jul 12 11:20:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 12 Jul 2011 16:20:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-638) The monitoring framework should allow for users who wish to supply their own REST endpoints for testing (some of which may contain sensitive information) In-Reply-To: <27341174.1627.1308576295454.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17532238.3040.1310484055547.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-638?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17342#comment-17342 ] Mannie Tagarira edited comment on BIOCAT-638 at 12/07/11 16:19: ---------------------------------------------------------------- Implemented functionaliy to allow users to add ONE custom endpoint for monitoring. The actual endpoint will be kept out of view from the public. Users can update the endpoint being monitoring. The service test can also be enabled and disabled like the others. Please confirm. was (Author: mannie): Implemented functionaliy to allow users to add ONE custom endpoint for monitoring. The actual endpoint will be kept out of view from the public. Users can update the endpoint being monitoring (at the expense of monitoring history for that endpoint). The service test can also be enabled and disabled like the others. Please confirm. > The monitoring framework should allow for users who wish to supply their own REST endpoints for testing (some of which may contain sensitive information) > --------------------------------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-638 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-638 > Project: BioCatalogue > Issue Type: Improvement > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > Attachments: public view.jpg > > > Trish Whetzel would like to be able to provide a specific endpoint for testing. This endpoint will contain information which is to be kept private and so the current mechanism for testing REST endpoints (using example_endpoint annotations) is inappropriate. -- 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 Jul 14 06:30:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 11:30:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-652) INB services have test scripts that were never passing (!) In-Reply-To: <3954854.2281.1309277635375.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4923109.3054.1310639455508.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-652?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-652: ----------------------------------- Attachment: INBtemplateTester.pl tmp.log All the INB test scripts are essentially templated. The following lines are the only lines that are variable: lines 16-18 my($TESTkey)='...'; my($TESTauthURI)='...'; my($TESTserviceName)='...'; Refer to the attached perl script. Having run a small subset of the INB service tests and found the same results across all test scripts, I have concluded that the all the INB test scripts fail as a result of parsing error (refer to the attached log). The test scripts consistently exit with a status code of 1 (via line 45 of the script). > INB services have test scripts that were never passing (!) > ---------------------------------------------------------- > > Key: BIOCAT-652 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-652 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Blocker > Fix For: 1.1.0 > > Attachments: INBtemplateTester.pl, tmp.log > > > For example: http://www.biocatalogue.org/service_tests/2688 > This needs some serious investigation - digging into emails, logs, etc to figure out why this has happened and left this way. > In the meantime, need to disable all these service tests. -- 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 Jul 14 06:31:00 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 11:31:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-652) INB services have test scripts that were never passing (!) In-Reply-To: <3954854.2281.1309277635375.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27149977.3055.1310639460820.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-652?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17352#comment-17352 ] Mannie Tagarira edited comment on BIOCAT-652 at 14/07/11 11:30: ---------------------------------------------------------------- All the INB test scripts are essentially templated. The following lines are the only lines that are variable: lines 16-18 {code:none} my($TESTkey)='...'; my($TESTauthURI)='...'; my($TESTserviceName)='...'; {code} Refer to the attached perl script. Having run a small subset of the INB service tests and found the same results across all test scripts, I have concluded that the all the INB test scripts fail as a result of parsing error (refer to the attached log). The test scripts consistently exit with a status code of 1 (via line 45 of the script). was (Author: mannie): All the INB test scripts are essentially templated. The following lines are the only lines that are variable: lines 16-18 {code:perl} my($TESTkey)='...'; my($TESTauthURI)='...'; my($TESTserviceName)='...'; {code} Refer to the attached perl script. Having run a small subset of the INB service tests and found the same results across all test scripts, I have concluded that the all the INB test scripts fail as a result of parsing error (refer to the attached log). The test scripts consistently exit with a status code of 1 (via line 45 of the script). > INB services have test scripts that were never passing (!) > ---------------------------------------------------------- > > Key: BIOCAT-652 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-652 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Blocker > Fix For: 1.1.0 > > Attachments: INBtemplateTester.pl, tmp.log > > > For example: http://www.biocatalogue.org/service_tests/2688 > This needs some serious investigation - digging into emails, logs, etc to figure out why this has happened and left this way. > In the meantime, need to disable all these service tests. -- 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 Jul 14 06:31:03 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 11:31:03 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-652) INB services have test scripts that were never passing (!) In-Reply-To: <3954854.2281.1309277635375.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31907201.3056.1310639463560.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-652?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17352#comment-17352 ] Mannie Tagarira edited comment on BIOCAT-652 at 14/07/11 11:30: ---------------------------------------------------------------- All the INB test scripts are essentially templated. The following lines are the only lines that are variable: lines 16-18 {code:perl} my($TESTkey)='...'; my($TESTauthURI)='...'; my($TESTserviceName)='...'; {code} Refer to the attached perl script. Having run a small subset of the INB service tests and found the same results across all test scripts, I have concluded that the all the INB test scripts fail as a result of parsing error (refer to the attached log). The test scripts consistently exit with a status code of 1 (via line 45 of the script). was (Author: mannie): All the INB test scripts are essentially templated. The following lines are the only lines that are variable: lines 16-18 my($TESTkey)='...'; my($TESTauthURI)='...'; my($TESTserviceName)='...'; Refer to the attached perl script. Having run a small subset of the INB service tests and found the same results across all test scripts, I have concluded that the all the INB test scripts fail as a result of parsing error (refer to the attached log). The test scripts consistently exit with a status code of 1 (via line 45 of the script). > INB services have test scripts that were never passing (!) > ---------------------------------------------------------- > > Key: BIOCAT-652 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-652 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Blocker > Fix For: 1.1.0 > > Attachments: INBtemplateTester.pl, tmp.log > > > For example: http://www.biocatalogue.org/service_tests/2688 > This needs some serious investigation - digging into emails, logs, etc to figure out why this has happened and left this way. > In the meantime, need to disable all these service tests. -- 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 Jul 14 06:42:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 11:42:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (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: <10639202.3057.1310640175408.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-617?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17353#comment-17353 ] Mannie Tagarira commented on BIOCAT-617: ---------------------------------------- 3 hours spent. > 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: 1.1.0 > > > 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 Thu Jul 14 06:44:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 11:44:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (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: <31313719.3058.1310640295363.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-617?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17353#comment-17353 ] Mannie Tagarira edited comment on BIOCAT-617 at 14/07/11 11:43: ---------------------------------------------------------------- approximately 3 hours spent on this task. was (Author: mannie): 3 hours spent. > 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: 1.1.0 > > > 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 Thu Jul 14 06:44:59 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 11:44:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-652) INB services have test scripts that were never passing (!) In-Reply-To: <3954854.2281.1309277635375.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20754736.3059.1310640299587.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-652?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17355#comment-17355 ] Mannie Tagarira commented on BIOCAT-652: ---------------------------------------- approximately 2 hours spent on this task. > INB services have test scripts that were never passing (!) > ---------------------------------------------------------- > > Key: BIOCAT-652 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-652 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Blocker > Fix For: 1.1.0 > > Attachments: INBtemplateTester.pl, tmp.log > > > For example: http://www.biocatalogue.org/service_tests/2688 > This needs some serious investigation - digging into emails, logs, etc to figure out why this has happened and left this way. > In the meantime, need to disable all these service tests. -- 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 Jul 14 06:45:01 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 11:45:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-657) Investigate why certain test scripts are failing! In-Reply-To: <30607250.2305.1309341535354.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16547901.3060.1310640301944.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17354#comment-17354 ] Mannie Tagarira edited comment on BIOCAT-657 at 14/07/11 11:44: ---------------------------------------------------------------- approximately 2 days spent on this task. was (Author: mannie): approximately 2 hours spent on this task. > Investigate why certain test scripts are failing! > ------------------------------------------------- > > Key: BIOCAT-657 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-657 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > Fix For: Future > > Attachments: diff.jpg > > > For example: > - http://www.biocatalogue.org/service_tests/4876 > - Many of the INB test scripts > Eric was investigating this but it's not clear what came out of it. So may need to dig up some old emails, etc. -- 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 Jul 14 06:45:06 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 11:45:06 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-657) Investigate why certain test scripts are failing! In-Reply-To: <30607250.2305.1309341535354.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25880027.3061.1310640306058.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17354#comment-17354 ] Mannie Tagarira commented on BIOCAT-657: ---------------------------------------- approximately 2 hours spent on this task. > Investigate why certain test scripts are failing! > ------------------------------------------------- > > Key: BIOCAT-657 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-657 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > Fix For: Future > > Attachments: diff.jpg > > > For example: > - http://www.biocatalogue.org/service_tests/4876 > - Many of the INB test scripts > Eric was investigating this but it's not clear what came out of it. So may need to dig up some old emails, etc. -- 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 Jul 14 06:59:27 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 14 Jul 2011 06:59:27 -0400 (EDT) Subject: [BioCatalogue-developers] [2465] branches/v1.1.0/vendor/embrace_scripts: Changed a call to a missing variable in the script listing writer; this was causing the script to throw and exception when " python script_listing_writer.py" was run from cmd line. Message-ID: <20110714105927.99DF61858367@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jul 14 08:18:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 13:18:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (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: <31013302.3086.1310645935408.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-617?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel\#worklog-{worklog.getId()} ] Mannie Tagarira logged work on BIOCAT-617: ------------------------------------------ Author: Mannie Tagarira Created on: 2011-07-14 13:18 Start Date: 2011-06-20 13:17 Worklog Time Spent: 3 hours Issue Time Tracking ------------------- Remaining Estimate: 0 minutes Time Spent: 3 hours Worklog Id: (was: 10515) > 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: 1.1.0 > > 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 Thu Jul 14 08:18:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 13:18:57 +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: <15087925.3087.1310645937750.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-617?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-617: ----------------------------------- Comment: was deleted (was: approximately 3 hours spent on this task.) > 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: 1.1.0 > > 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 Thu Jul 14 08:20:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 13:20:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-652) INB services have test scripts that were never passing (!) In-Reply-To: <3954854.2281.1309277635375.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11988780.3088.1310646055363.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-652?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel\#worklog-{worklog.getId()} ] Mannie Tagarira logged work on BIOCAT-652: ------------------------------------------ Author: Mannie Tagarira Created on: 2011-07-14 13:19 Start Date: 2011-07-14 21:40 Worklog Time Spent: 3 hours Issue Time Tracking ------------------- Remaining Estimate: 0 minutes Time Spent: 3 hours Worklog Id: (was: 10516) > INB services have test scripts that were never passing (!) > ---------------------------------------------------------- > > Key: BIOCAT-652 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-652 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Blocker > Fix For: 1.1.0 > > Attachments: INBtemplateTester.pl, tmp.log > > Time Spent: 3 hours > Remaining Estimate: 0 minutes > > For example: http://www.biocatalogue.org/service_tests/2688 > This needs some serious investigation - digging into emails, logs, etc to figure out why this has happened and left this way. > In the meantime, need to disable all these service tests. -- 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 Jul 14 08:20:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 13:20:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-657) Investigate why certain test scripts are failing! In-Reply-To: <30607250.2305.1309341535354.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22514079.3089.1310646057695.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-657?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel\#worklog-{worklog.getId()} ] Mannie Tagarira logged work on BIOCAT-657: ------------------------------------------ Author: Mannie Tagarira Created on: 2011-07-14 13:20 Start Date: 2011-06-30 13:20 Worklog Time Spent: 2 days Issue Time Tracking ------------------- Remaining Estimate: 0 minutes Time Spent: 2 days Worklog Id: (was: 10517) > Investigate why certain test scripts are failing! > ------------------------------------------------- > > Key: BIOCAT-657 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-657 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > Fix For: Future > > Attachments: diff.jpg > > Time Spent: 2 days > Remaining Estimate: 0 minutes > > For example: > - http://www.biocatalogue.org/service_tests/4876 > - Many of the INB test scripts > Eric was investigating this but it's not clear what came out of it. So may need to dig up some old emails, etc. -- 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 Jul 14 08:21:00 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 13:21:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-657) Investigate why certain test scripts are failing! In-Reply-To: <30607250.2305.1309341535354.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20336838.3090.1310646060119.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-657?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-657: ----------------------------------- Comment: was deleted (was: approximately 2 days spent on this task.) > Investigate why certain test scripts are failing! > ------------------------------------------------- > > Key: BIOCAT-657 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-657 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > Fix For: Future > > Attachments: diff.jpg > > > For example: > - http://www.biocatalogue.org/service_tests/4876 > - Many of the INB test scripts > Eric was investigating this but it's not clear what came out of it. So may need to dig up some old emails, etc. -- 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 Jul 14 08:21:02 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 13:21:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-652) INB services have test scripts that were never passing (!) In-Reply-To: <3954854.2281.1309277635375.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20688232.3091.1310646062712.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-652?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-652: ----------------------------------- Comment: was deleted (was: approximately 2 hours spent on this task.) > INB services have test scripts that were never passing (!) > ---------------------------------------------------------- > > Key: BIOCAT-652 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-652 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Blocker > Fix For: 1.1.0 > > Attachments: INBtemplateTester.pl, tmp.log > > Time Spent: 3 hours > Remaining Estimate: 0 minutes > > For example: http://www.biocatalogue.org/service_tests/2688 > This needs some serious investigation - digging into emails, logs, etc to figure out why this has happened and left this way. > In the meantime, need to disable all these service tests. -- 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 Jul 14 09:56:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 14:56:55 +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: <32389946.3093.1310651815373.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-641?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-641: ----------------------------------- Attachment: fix for simple listings.jpg This has been fixed for simple service listings but still needs to be attended to in grid view. > 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: 1.1.0 > > Attachments: -service_providers-240#services.jpg, fix for simple listings.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 Thu Jul 14 09:58:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 14:58:55 +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: <19329286.3094.1310651935359.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-641?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-641: ----------------------------------- Attachment: grid view.jpg > 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: 1.1.0 > > 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 Thu Jul 14 09:58:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 14 Jul 2011 14:58:57 +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: <951832.3095.1310651937665.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-641?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-641: ----------------------------------- Attachment: soap operations.jpg > 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: 1.1.0 > > 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 noreply at rubyforge.org Thu Jul 14 10:11:15 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 14 Jul 2011 10:11:15 -0400 (EDT) Subject: [BioCatalogue-developers] [2466] branches/v1.1.0/app/views/services/listing/_simple.html.erb: [ BIOCAT-641] Added the WSDL location or base URL of the service in simple view Message-ID: <20110714141115.7DA8B1858367@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jul 18 03:56:01 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 18 Jul 2011 03:56:01 -0400 (EDT) Subject: [BioCatalogue-developers] [2467] branches/v1.1.0: [BIOCAT-598] Added a curation report in the dashboard allowing curators and admins to see a list of service providers without any services Message-ID: <20110718075601.A5F95167835D@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jul 18 03:57:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 18 Jul 2011 08:57:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-598) Figure out what to do with service providers with no services In-Reply-To: <22732435.949.1307456575352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7219667.3125.1310975875550.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-598?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-598. ------------------------------------ Resolution: Fixed A curation report has been created. > Figure out what to do with service providers with no services > ------------------------------------------------------------- > > Key: BIOCAT-598 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-598 > Project: BioCatalogue > Issue Type: Task > Components: Curation Dashboard, Service Provider Management > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > > As of June 7th 2011, 4 providers exist with no services. > IDs: 333, 314, 304, 322 > We have the ability to delete empty service providers by curators. Maybe we also need a curation report for this on the curation dashboard? -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon Jul 18 04:00:55 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 18 Jul 2011 04:00:55 -0400 (EDT) Subject: [BioCatalogue-developers] [2468] branches/v1.1.0/app/controllers/application_controller.rb: [ BIOCAT-295] Fix for the "error_to_back_or_home" helper which was causing infinite redirects Message-ID: <20110718080055.EDF1A1858376@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jul 18 04:33:09 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 18 Jul 2011 04:33:09 -0400 (EDT) Subject: [BioCatalogue-developers] [2469] branches/v1.1.0/lib/auto_link_override.rb: [BIOCAT-413] The AUTO_LINK_RE override which was put in place to patch up a previous issue was no longer needed . Message-ID: <20110718083309.3DE1E1858376@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jul 18 04:34:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 18 Jul 2011 09:34:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-413) Some urls in annotation fields are not formed properly In-Reply-To: <30372087.6609.1277371035302.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5367106.3126.1310978095399.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-413?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-413. ------------------------------------ Resolution: Fixed Reverted back to the pre "auto_link" patch. The issue we were trying to fix seems to no longer be an issue so we don't need the patch anymore. > Some urls in annotation fields are not formed properly > ------------------------------------------------------ > > Key: BIOCAT-413 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-413 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Sergejs Aleksejevs > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > > For example, "support at genouest.org" does not link to that email address, it links to "genouest.org" ("support@" is shown as is). > Example: > http://www.biocatalogue.org/services/2046 -- 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 Jul 18 04:36:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 18 Jul 2011 09:36:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-295) Investigate double render error with "error_to_back_or_home" helper Message-ID: <15889428.3127.1310978215378.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-295?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-295. ------------------------------------ Resolution: Fixed Fixed in rev. 2468 > Investigate double render error with "error_to_back_or_home" helper > ------------------------------------------------------------------- > > Key: BIOCAT-295 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-295 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Environment: Ruby on Rails > Reporter: Eric Nzuobontane > Assignee: Mannie Tagarira > Priority: Minor > Fix For: 1.1.0 > > > When error_to_back_or_home helper is used in a before_filter with render/redirect, a multiple redirect error is raise. This even when a false is returned as returning false does not halt the filter chain -- 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 Jul 18 04:38:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 18 Jul 2011 09:38:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-638) The monitoring framework should allow for users who wish to supply their own REST endpoints for testing (some of which may contain sensitive information) In-Reply-To: <27341174.1627.1308576295454.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18168058.3128.1310978335394.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-638?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-638. ------------------------------------ Resolution: Fixed > The monitoring framework should allow for users who wish to supply their own REST endpoints for testing (some of which may contain sensitive information) > --------------------------------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-638 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-638 > Project: BioCatalogue > Issue Type: Improvement > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > Attachments: public view.jpg > > > Trish Whetzel would like to be able to provide a specific endpoint for testing. This endpoint will contain information which is to be kept private and so the current mechanism for testing REST endpoints (using example_endpoint annotations) is inappropriate. -- 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 Jul 18 04:40:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 18 Jul 2011 09:40:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-652) INB services have test scripts that were never passing (!) In-Reply-To: <3954854.2281.1309277635375.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31242094.3129.1310978455377.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-652?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-652. ------------------------------------ Resolution: Not A Bug Is there really anything we can do to fix this? If so, mark this task as unresolved. > INB services have test scripts that were never passing (!) > ---------------------------------------------------------- > > Key: BIOCAT-652 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-652 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Blocker > Fix For: 1.1.0 > > Attachments: INBtemplateTester.pl, tmp.log > > Time Spent: 3 hours > Remaining Estimate: 0 minutes > > For example: http://www.biocatalogue.org/service_tests/2688 > This needs some serious investigation - digging into emails, logs, etc to figure out why this has happened and left this way. > In the meantime, need to disable all these service tests. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon Jul 18 08:26:34 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 18 Jul 2011 08:26:34 -0400 (EDT) Subject: [BioCatalogue-developers] [2470] branches/v1.1.0/config/initializers/biocat_main.rb: removed the requirement of "auto_link_override.rb" from the app Message-ID: <20110718122636.58CDA1858361@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jul 18 10:01:20 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 18 Jul 2011 10:01:20 -0400 (EDT) Subject: [BioCatalogue-developers] [2471] branches/v1.1.0: [BIOCAT-579] Message-ID: <20110718140120.6BC921858376@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jul 18 10:01:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 18 Jul 2011 15:01:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-579) Implement functionality to allow for services to be added to and removed from a user's favourites via the API In-Reply-To: <14465616.66.1298903907810.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2952566.3135.1310997715409.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-579?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-579. ------------------------------------ Resolution: Fixed Added 2 new JSON endpoints to allow for the favouriting and unfavouriting of services via the API POST /services/{id}/favourite POST /services/{id}/unfavourite Revision 2471. > Implement functionality to allow for services to be added to and removed from a user's favourites via the API > ------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-579 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-579 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > 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 Tue Jul 19 09:15:56 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 19 Jul 2011 14:15:56 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-465) Test OAuth on the live site In-Reply-To: <10881481.9000.1284042795322.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15652177.3152.1311081356367.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-465?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-465. ------------------------------------ Resolution: Responded > Test OAuth on the live site > --------------------------- > > Key: BIOCAT-465 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-465 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > 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 Tue Jul 19 09:33:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 19 Jul 2011 14:33:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-675) Write documentation on how to use OAuth n third party apps Message-ID: <16265318.3153.1311082435356.JavaMail.jira@rosalind.cs.man.ac.uk> Write documentation on how to use OAuth n third party apps ---------------------------------------------------------- Key: BIOCAT-675 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-675 Project: BioCatalogue Issue Type: Task Components: Documentation, REST API, Wiki Affects Versions: 1.0.0 Reporter: Mannie Tagarira Assignee: Mannie Tagarira Priority: Blocker 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 Tue Jul 19 09:59:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 19 Jul 2011 14:59:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Reopened: (BIOCAT-465) Test OAuth on the live site In-Reply-To: <10881481.9000.1284042795322.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23653378.3154.1311083995379.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-465?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira reopened BIOCAT-465: ------------------------------------ > Test OAuth on the live site > --------------------------- > > Key: BIOCAT-465 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-465 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > 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 noreply at rubyforge.org Tue Jul 19 10:38:51 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 19 Jul 2011 10:38:51 -0400 (EDT) Subject: [BioCatalogue-developers] [2472] branches/v1.1.0/app: Added a fix for a bug in OAuth. Message-ID: <20110719143851.5FA3418581B2@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Fri Jul 22 03:58:56 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 22 Jul 2011 08:58:56 +0100 Subject: [BioCatalogue-developers] [2472] branches/v1.1.0/app: Added a fix for a bug in OAuth. In-Reply-To: <20110719143851.5FA3418581B2@rubyforge.org> References: <20110719143851.5FA3418581B2@rubyforge.org> Message-ID: <4E292DC0.2050401@cs.man.ac.uk> Hi Mannie, I don't understand why the deletion of tokens isn't just something like: class ClientApp... has_many :tokens, :dependent => :destroy ? Jits On 19/07/2011 15:38, noreply at rubyforge.org wrote: > > Revision > 2472 > Author > mannie > Date > 2011-07-19 10:38:51 -0400 (Tue, 19 Jul 2011) > > > Log Message > > Added a fix for a bug in OAuth. whenever an registered application is deleted from the catalogue, the tokens associated with it remain. If an accepted token exists and the application to which it is associated is deleted, the catalogue would throw a 500 error. > > Now, tokens without an associated client application are omitted from the UI (which fixes the error code 500 issue). Also, tokens are now deleted before the client application is. > > > Modified Paths > > * branches/v1.1.0/app/controllers/oauth_clients_controller.rb > <#branchesv110appcontrollersoauth_clients_controllerrb> > * branches/v1.1.0/app/views/oauth_clients/index.html.erb > <#branchesv110appviewsoauth_clientsindexhtmlerb> > > > Diff > > > Modified: > branches/v1.1.0/app/controllers/oauth_clients_controller.rb > (2471 => 2472) > > > --- branches/v1.1.0/app/controllers/oauth_clients_controller.rb 2011-07-18 14:01:19 UTC (rev 2471) > +++ branches/v1.1.0/app/controllers/oauth_clients_controller.rb 2011-07-19 14:38:51 UTC (rev 2472) > @@ -13,11 +13,11 @@ > before_filter :get_client_application, :only => [ :show, :edit, :update, :destroy ] > > before_filter :authorise, :only => [ :show, :edit, :update, :destroy ] > - > + > if ENABLE_SSL&& Rails.env.production? > ssl_required :all > end > - > + > def index > @client_applications = current_user.client_applications > @tokens = current_user.tokens.find :all, :conditions => 'oauth_tokens.invalidated_at is null and oauth_tokens.authorized_at is not null' > @@ -53,8 +53,17 @@ > end > > def destroy > - @client_application.destroy > - flash[:notice] = "Destroyed the client application registration" > + begin > + ClientApplication.transaction do > + @client_application.tokens.each { |t| t.destroy } > + @client_application.destroy > + end > + > + flash[:notice] = "Destroyed the client application registration" > + rescue > + flash[:error] = "Could not delete the application" > + end > + > redirect_to :action => "index" > end > > > > Modified: > branches/v1.1.0/app/views/oauth_clients/index.html.erb (2471 > => 2472) > > > --- branches/v1.1.0/app/views/oauth_clients/index.html.erb 2011-07-18 14:01:19 UTC (rev 2471) > +++ branches/v1.1.0/app/views/oauth_clients/index.html.erb 2011-07-19 14:38:51 UTC (rev 2472) > @@ -24,6 +24,8 @@ >
> > <% @tokens.each do |token|%> > +<% next if token.client_application.nil? %> > + >
> <%= link_to image_tag("delete_faded_darker.png", :mouseover => "delete.png") + content_tag(:span, " Revoke Access"), > { :controller => :oauth, :action => :revoke, :token => token.token }, > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Fri Jul 22 04:08:58 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 22 Jul 2011 09:08:58 +0100 Subject: [BioCatalogue-developers] [2467] branches/v1.1.0: [BIOCAT-598] Added a curation report in the dashboard allowing curators and admins to see a list of service providers without any services In-Reply-To: <20110718075601.A5F95167835D@rubyforge.org> References: <20110718075601.A5F95167835D@rubyforge.org> Message-ID: <4E29301A.1090303@cs.man.ac.uk> This: > + def self.providers_without_services > + providers = [] > + > + ServiceProvider.all.each do |p| > + providers<< p if p.service_deployments.empty? > + end > + > + return providers > + end ... needs optimising as it's a potential perf hog. It will do the following: 1 x query to service_providers to load the WHOLE list of providers, then n x queries to the service_deployments table per provider. The typical N+1 problem. Few things you can do to improve this: 1. Call p.service_deployments.count (SLIGHTLY BETTER, still N+1 queries though). 2. Use ServiceProvider.find(:all, :include => :service_deployments). This tells Rails to eager load the deployments too. (SLIGHTLY BETTER, but essentially loading everything just to check a simple thing). 3. Do a *single* custom query to get back just the list of providers you want. I fixed something like this recently - see ServiceProvider#has_service_submitter? for the kind of query I'm talking about (BEST!) Let me know if you think of a more performant way of doing this! Jits On 18/07/2011 08:56, noreply at rubyforge.org wrote: > > Revision > 2467 > Author > mannie > Date > 2011-07-18 03:56:01 -0400 (Mon, 18 Jul 2011) > > > Log Message > > [BIOCAT-598] Added a curation report in the dashboard allowing curators and admins to see a list of service providers without any services > > > Modified Paths > > * branches/v1.1.0/app/controllers/curation_controller.rb > <#branchesv110appcontrollerscuration_controllerrb> > * branches/v1.1.0/app/views/curation/show.html.erb > <#branchesv110appviewscurationshowhtmlerb> > * branches/v1.1.0/config/routes.rb <#branchesv110configroutesrb> > * branches/v1.1.0/lib/bio_catalogue/curation/reports.rb > <#branchesv110libbio_cataloguecurationreportsrb> > > > Added Paths > > * branches/v1.1.0/app/views/curation/providers_without_services.html.erb > <#branchesv110appviewscurationproviders_without_serviceshtmlerb> > > > Diff > > > Modified: > branches/v1.1.0/app/controllers/curation_controller.rb (2466 > => 2467) > > > --- branches/v1.1.0/app/controllers/curation_controller.rb 2011-07-14 14:11:14 UTC (rev 2466) > +++ branches/v1.1.0/app/controllers/curation_controller.rb 2011-07-18 07:56:01 UTC (rev 2467) > @@ -90,6 +90,13 @@ > end > end > > + def providers_without_services > + @service_providers = BioCatalogue::Curation::Reports.providers_without_services > + > + respond_to do |format| > + format.html # providers_without_services.html.erb > + end > + end > > protected > > > > Added: > branches/v1.1.0/app/views/curation/providers_without_services.html.erb > (0 => 2467) > > > --- branches/v1.1.0/app/views/curation/providers_without_services.html.erb (rev 0) > +++ branches/v1.1.0/app/views/curation/providers_without_services.html.erb 2011-07-18 07:56:01 UTC (rev 2467) > @@ -0,0 +1,30 @@ > +<% > + > +# BioCatalogue: app/views/curation/providers_without_services.html.erb > +# > +# Copyright (c) 2011, University of Manchester, The European Bioinformatics > +# Institute (EMBL-EBI) and the University of Southampton. > +# See license.txt for details > + > +%> > + > +<%= render :partial => 'header', :locals => { :sub => "- Reports - Providers Without Services" } %> > + > +
> + This will identify all service providers without any Services associated with them. > +
> + > +
> +<% if @service_providers.nil? %> > +

Potential system error. Please contact an admin/developer with this message: "@service_providers collection was nil on the providers_without_services curation reports page"

> +<% else %> > + > +

> +<%= pluralize(@service_providers.length, "provider") -%> found > +

> + > +<%= render :partial => "service_providers/listing", :locals => { :items => @service_providers } %> > + > +
> +<% end %> > + > > > Modified: branches/v1.1.0/app/views/curation/show.html.erb > (2466 => 2467) > > > --- branches/v1.1.0/app/views/curation/show.html.erb 2011-07-14 14:11:14 UTC (rev 2466) > +++ branches/v1.1.0/app/views/curation/show.html.erb 2011-07-18 07:56:01 UTC (rev 2467) > @@ -2,45 +2,47 @@ > > # BioCatalogue: app/views/curation/show.html.erb > # > -# Copyright (c) 2010, University of Manchester, The European Bioinformatics > +# Copyright (c) 2010, University of Manchester, The European Bioinformatics > # Institute (EMBL-EBI) and the University of Southampton. > # See license.txt for details > > %> > > -

> - Curation Dashboard > -

> +

Curation Dashboard

> >
>
> -

> - Reports > - <%= info_icon_with_tooltip "Please note that some of these reports can take a while to produce and can cause load on the server. Please try to avoid generating these reports during potentially busy hours." -%> > -

> - > +

Reports > + <%= info_icon_with_tooltip "Please note that some of these reports can take a while to produce and can cause load on the server. Please try to avoid generating these reports during potentially busy hours." -%>

> + >
> - > + > <%= link_to "Potential Duplicate SOAP Operations within a SOAP Service", curation_reports_potential_duplicate_operations_within_service_path, :class => "button_slim" -%> > -

> -<%= link_to "Services Missing Annotations", curation_reports_services_missing_annotations_path, :class => "button_slim" -%> > -

> -<%= link_to "Links Checker Report", '/links_checker_report.html', :popup => true, :class => "button_slim" -%> > -

> -<%= link_to "Service Annotation Levels", curation_annotation_level_path, :popup => true, :class => "button_slim", :title => "Use sparingly! Calculates annotation levels on the fly"-%> > -

> -<%= link_to "All Service Tests", service_tests_url, :popup => true, :class => "button_slim", :title => "All service tests. Both URL checks and test scripts"-%> > +
> +
> + <%= link_to "Service Providers Without Services", curation_reports_providers_without_services_path, :popup => true, :class => "button_slim" -%> > +
> +
> + <%= link_to "Services Missing Annotations", curation_reports_services_missing_annotations_path, :class => "button_slim" -%> > +
> +
> + <%= link_to "Links Checker Report", '/links_checker_report.html', :popup => true, :class => "button_slim" -%> > +
> +
> + <%= link_to "Service Annotation Levels", curation_annotation_level_path, :popup => true, :class => "button_slim", :title => "Use sparingly! Calculates annotation levels on the fly"-%> > +
> +
> + <%= link_to "All Service Tests", service_tests_url, :popup => true, :class => "button_slim", :title => "All service tests. Both URL checks and test scripts"-%> >
> - > + >
>

Tools

> - > + >
> - > + > <%= link_to "Copy Annotations From Item to Item", curation_tools_copy_annotations_path, :class => "button_slim" -%> >
> - > + > >
> > - > > > Modified: branches/v1.1.0/config/routes.rb (2466 => 2467) > > > --- branches/v1.1.0/config/routes.rb 2011-07-14 14:11:14 UTC (rev 2466) > +++ branches/v1.1.0/config/routes.rb 2011-07-18 07:56:01 UTC (rev 2467) > @@ -31,6 +31,11 @@ > :action => 'potential_duplicate_operations_within_service', > :conditions => { :method => :get } > > + map.curation_reports_providers_without_services '/curation/reports/providers_without_services', > + :controller => 'curation', > + :action => 'providers_without_services', > + :conditions => { :method => :get } > + > map.curation_reports_services_missing_annotations '/curation/reports/services_missing_annotations', > :controller => 'curation', > :action => 'services_missing_annotations', > > > Modified: > branches/v1.1.0/lib/bio_catalogue/curation/reports.rb (2466 => > 2467) > > > --- branches/v1.1.0/lib/bio_catalogue/curation/reports.rb 2011-07-14 14:11:14 UTC (rev 2466) > +++ branches/v1.1.0/lib/bio_catalogue/curation/reports.rb 2011-07-18 07:56:01 UTC (rev 2467) > @@ -61,6 +61,16 @@ > return services > end > > + def self.providers_without_services > + providers = [] > + > + ServiceProvider.all.each do |p| > + providers<< p if p.service_deployments.empty? > + end > + > + return providers > + end > + > end > end > end > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jul 25 05:57:21 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 25 Jul 2011 05:57:21 -0400 (EDT) Subject: [BioCatalogue-developers] [2473] branches/v1.1.0/app: Updated the deletion of OAuth tokens associated with a client application to be done the Rails way . Message-ID: <20110725095721.35FED1858361@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jul 25 08:18:03 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 25 Jul 2011 08:18:03 -0400 (EDT) Subject: [BioCatalogue-developers] [2474] branches/v1.1.0/lib/bio_catalogue/curation/reports.rb: Performance enhancement for the curation report showing which service providers have no services . Message-ID: <20110725121804.3BED3185838A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jul 25 08:28:21 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 25 Jul 2011 08:28:21 -0400 (EDT) Subject: [BioCatalogue-developers] [2475] branches/v1.1.0/lib/bio_catalogue/curation/reports.rb: Slight performance enhancement for the curation report showing which service providers have no services . Message-ID: <20110725122821.CA1EC1858367@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jul 26 07:22:50 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 26 Jul 2011 12:22:50 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-676) Update the map_routes method in the Annotations and Favourites plugins to account for :requirements In-Reply-To: <20360330.0.1311679364973.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20068393.1.1311679370115.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-676?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-676: ----------------------------------- Description: Consider: in routes.rb {code:none} Annotations.map_routes(map, {}, {}, :protocol => "") Favourites.map_routes(map, {}, {}, :protocol => "") {code} in plugin routing.rb {code:none} def self.map_routes(map, collection={}, member={}, requirements={}) map.resources :favourites, :collection => { }.merge(collection), :member => { }.merge(member), :requirements => { }.merge(requirements) end {code} Make sure the versions used by the app are updated to take into consideration these changes. was: Consider: in routes.rb {code:ruby} Annotations.map_routes(map, {}, {}, :protocol => "") Favourites.map_routes(map, {}, {}, :protocol => "") {code} in plugin routing.rb {code:ruby} def self.map_routes(map, collection={}, member={}, requirements={}) map.resources :favourites, :collection => { }.merge(collection), :member => { }.merge(member), :requirements => { }.merge(requirements) end {code} Make sure the versions used by the app are updated to take into consideration these changes. > Update the map_routes method in the Annotations and Favourites plugins to account for :requirements > --------------------------------------------------------------------------------------------------- > > Key: BIOCAT-676 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-676 > Project: BioCatalogue > Issue Type: Task > Components: Annotations Plugin > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > > Consider: > in routes.rb > {code:none} > Annotations.map_routes(map, {}, {}, :protocol => "") > Favourites.map_routes(map, {}, {}, :protocol => "") > {code} > in plugin routing.rb > {code:none} > def self.map_routes(map, collection={}, member={}, requirements={}) > map.resources :favourites, > :collection => { }.merge(collection), > :member => { }.merge(member), > :requirements => { }.merge(requirements) > end > {code} > Make sure the versions used by the app are updated to take into consideration these changes. -- 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 Jul 26 07:22:44 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 26 Jul 2011 12:22:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-676) Update the map_routes method in the Annotations and Favourites plugins to account for :requirements Message-ID: <20360330.0.1311679364973.JavaMail.jira@rosalind.cs.man.ac.uk> Update the map_routes method in the Annotations and Favourites plugins to account for :requirements --------------------------------------------------------------------------------------------------- Key: BIOCAT-676 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-676 Project: BioCatalogue Issue Type: Task Components: Annotations Plugin Reporter: Mannie Tagarira Assignee: Jiten Bhagat Priority: Blocker Fix For: 1.1.0 Consider: in routes.rb {code:ruby} Annotations.map_routes(map, {}, {}, :protocol => "") Favourites.map_routes(map, {}, {}, :protocol => "") {code} in plugin routing.rb {code:ruby} def self.map_routes(map, collection={}, member={}, requirements={}) map.resources :favourites, :collection => { }.merge(collection), :member => { }.merge(member), :requirements => { }.merge(requirements) end {code} Make sure the versions used by the app are updated to take into consideration these changes. -- 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 Jul 26 07:24:44 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 26 Jul 2011 12:24:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-676) Update the map_routes method in the Annotations and Favourites plugins to account for :requirements In-Reply-To: <20360330.0.1311679364973.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32500105.2.1311679484733.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-676?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-676: ----------------------------------- Description: Consider: in routes.rb {code:none} Annotations.map_routes(map, {}, {}, :protocol => "https") Favourites.map_routes(map, {}, {}, :protocol => "https") {code} in plugin routing.rb {code:none} def self.map_routes(map, collection={}, member={}, requirements={}) map.resources :favourites, :collection => { }.merge(collection), :member => { }.merge(member), :requirements => { }.merge(requirements) end {code} Make sure the versions used by the app are updated to take into consideration these changes. was: Consider: in routes.rb {code:none} Annotations.map_routes(map, {}, {}, :protocol => "") Favourites.map_routes(map, {}, {}, :protocol => "") {code} in plugin routing.rb {code:none} def self.map_routes(map, collection={}, member={}, requirements={}) map.resources :favourites, :collection => { }.merge(collection), :member => { }.merge(member), :requirements => { }.merge(requirements) end {code} Make sure the versions used by the app are updated to take into consideration these changes. > Update the map_routes method in the Annotations and Favourites plugins to account for :requirements > --------------------------------------------------------------------------------------------------- > > Key: BIOCAT-676 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-676 > Project: BioCatalogue > Issue Type: Task > Components: Annotations Plugin > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > > Consider: > in routes.rb > {code:none} > Annotations.map_routes(map, {}, {}, :protocol => "https") > Favourites.map_routes(map, {}, {}, :protocol => "https") > {code} > in plugin routing.rb > {code:none} > def self.map_routes(map, collection={}, member={}, requirements={}) > map.resources :favourites, > :collection => { }.merge(collection), > :member => { }.merge(member), > :requirements => { }.merge(requirements) > end > {code} > Make sure the versions used by the app are updated to take into consideration these changes. -- 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 Jul 26 11:39:45 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 26 Jul 2011 16:39:45 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-677) Update the DRAMA testing procedure in the wiki to take into account some of the new functionality Message-ID: <1700665.3.1311694785977.JavaMail.jira@rosalind.cs.man.ac.uk> Update the DRAMA testing procedure in the wiki to take into account some of the new functionality -------------------------------------------------------------------------------------------------- Key: BIOCAT-677 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-677 Project: BioCatalogue Issue Type: Task Components: Wiki Reporter: Mannie Tagarira Assignee: Mannie Tagarira Priority: Blocker Fix For: 1.1.0 Update http://www.biocatalogue.org/wiki/doku.php?id=development:system_testing Main things to consider: - REST endpoint (registration and annotation) - REST parameters and representations - Monitoring endpoint -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Wed Jul 27 05:00:48 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 27 Jul 2011 10:00:48 +0100 Subject: [BioCatalogue-developers] Fwd: Re: [Biocatalogue-support] [BioCatalogue] Service 'Mutalyzer' has a test change status from UNCHECKED to WARNING In-Reply-To: <4E2FD26A.1070205@cs.man.ac.uk> References: <4E2FD26A.1070205@cs.man.ac.uk> Message-ID: <4E2FD3C0.8090103@cs.man.ac.uk> Hi Mannie, Since you've spent some (painful) time with the test scripts stuff, would you be able to handle this today please? Thanks! Jits -------- Original Message -------- Subject: Re: [Biocatalogue-support] [BioCatalogue] Service 'Mutalyzer' has a test change status from UNCHECKED to WARNING Date: Wed, 27 Jul 2011 09:55:06 +0100 From: Jiten Bhagat To: p.e.m.taschner at lumc.nl CC: biocatalogue-support at rubyforge.org Dear Peter, Our apologies for this. We'll investigate this today with our EBI colleagues and get back to you. Regards, Jiten On 27/07/2011 08:34, P.E.M.Taschner at lumc.nl wrote: > Dear BioCatalogue Team, > > We have tried several times to find the problem resulting in the test status WARNING for our test script sp.py, but did not succeed. The test script works fine from our end, but it is unclear how the test was performed by your service. It was unclear what should be entered in the field "executable name". We did use sp.py, sp.python, test.py, but that did not affect the test results. We would appreciate it very much if you would be able to help us. > Thanking you very much in anitcipation, > > Best regards, > > Peter Taschner > > Dr. Peter E.M. Taschner > Department of Human Genetics S-4-P > Center for Human and Clinical Genetics > Leiden University Medical Center > P.O. Box 9600 > 2300 RC Leiden > The Netherlands > Tel. +31-71- 526 9424 Fax +31-71-526 8285 > Visiting address: Building 2, Room R04-005, Einthovenweg 20, Leiden > > > -----Original Message----- > From: contact at biocatalogue.org [mailto:contact at biocatalogue.org] > Sent: woensdag 27 juli 2011 1:30 > To: Taschner, P.E.M. (HG) > Subject: [BioCatalogue] Service 'Mutalyzer' has a test change status from UNCHECKED to WARNING > > > > Dear Member, > > A monitoring test status change has occurred! Service 'Mutalyzer' has a test (TestScript, ID: 745) change status from UNCHECKED to WARNING. Last test result message: Something did not go right with this check. Go to Service: http://www.biocatalogue.org/services/2749 > > If you have any questions please reply to this mail. > > Kind regards, > > The BioCatalogue Team > _______________________________________________ > Biocatalogue-support mailing list > Biocatalogue-support at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jul 27 05:28:44 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 27 Jul 2011 10:28:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-678) Create update script on staging VM image Message-ID: <18461761.4.1311758924787.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.1.0 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 Jul 27 06:52:44 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 27 Jul 2011 11:52:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-679) Test SSL on the BioCatalogue sandbox Message-ID: <7008757.20.1311763964719.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.1.0 -- 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 Jul 27 06:54:44 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 27 Jul 2011 11:54:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-668) Update annotations plugin to support polymorphic values In-Reply-To: <31613240.2777.1310039095351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23337614.21.1311764084785.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-668?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-668 stopped by Jiten Bhagat. > Update annotations plugin to support polymorphic values > ------------------------------------------------------- > > Key: BIOCAT-668 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-668 > Project: BioCatalogue > Issue Type: Sub-task > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > Time Spent: 3 days > Remaining Estimate: 0 minutes > > The plugin itself should: > - Have default support for Text values. > - Provide a new migration script that can be extended. -- 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 Jul 27 06:54:47 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 27 Jul 2011 11:54:47 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-668) Update annotations plugin to support polymorphic values In-Reply-To: <31613240.2777.1310039095351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32290420.22.1311764087067.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-668?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-668. --------------------------------- Resolution: Fixed > Update annotations plugin to support polymorphic values > ------------------------------------------------------- > > Key: BIOCAT-668 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-668 > Project: BioCatalogue > Issue Type: Sub-task > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > Time Spent: 3 days > Remaining Estimate: 0 minutes > > The plugin itself should: > - Have default support for Text values. > - Provide a new migration script that can be extended. -- 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 Jul 27 06:54:49 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 27 Jul 2011 11:54:49 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-668) Update annotations plugin to support polymorphic values In-Reply-To: <31613240.2777.1310039095351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15446367.23.1311764089524.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-668?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17390#comment-17390 ] Jiten Bhagat commented on BIOCAT-668: ------------------------------------- Initial work on this has been done. > Update annotations plugin to support polymorphic values > ------------------------------------------------------- > > Key: BIOCAT-668 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-668 > Project: BioCatalogue > Issue Type: Sub-task > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > Time Spent: 3 days > Remaining Estimate: 0 minutes > > The plugin itself should: > - Have default support for Text values. > - Provide a new migration script that can be extended. -- 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 Jul 27 07:39:19 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 27 Jul 2011 07:39:19 -0400 (EDT) Subject: [BioCatalogue-developers] [2476] branches/v1.1.0: [BIOCAT-243] Make ALL routes/pages HTTPS (SSL) Message-ID: <20110727113919.473C63C8043@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Wed Jul 27 07:40:42 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 27 Jul 2011 12:40:42 +0100 Subject: [BioCatalogue-developers] Fwd: Re: [Biocatalogue-support] [BioCatalogue] Service 'Mutalyzer' has a test change status from UNCHECKED to WARNING In-Reply-To: <65DFE3D7-2D46-4A2A-93A0-A3A7D5D1887E@gmail.com> References: <4E2FD26A.1070205@cs.man.ac.uk> <4E2FD3C0.8090103@cs.man.ac.uk> <65DFE3D7-2D46-4A2A-93A0-A3A7D5D1887E@gmail.com> Message-ID: <4E2FF93A.6080404@cs.man.ac.uk> Good findings Mannie. Could you liaise with Peter Taschner to sort this out please? Seems like adding some return statements might be all that is needed. Thanks, Jits On 27/07/2011 11:26, Mannie Tagarira wrote: > Hi Jits, > > I think I figured out what is going on but I can't really say for sure; all I have are hypotheses. > > The first one would be the lack of "return" or "exit" statements in the script. Every bit of information is displayed via print statements. > > Secondly: for whatever reason, my environment is not recognising the "#!/usr/bin/env python" directive (see environment.log) and have had to change it to "#!/usr/bin/python". FYI: Test scripts using both directives do exist in the catalogue and (surprise surprise) they are all failing. I don't believe this is *the* issue though, but let's not rule it out as a possibility. > > Lastly, I would say the issue might just be boiling down to missing or incompatible libraries (see libs.log). > > > > > > Mannie > > > > On 27 Jul 2011, at 10:00, Jiten Bhagat wrote: > >> Hi Mannie, >> >> Since you've spent some (painful) time with the test scripts stuff, would you be able to handle this today please? >> >> Thanks! >> Jits >> >> -------- Original Message -------- >> Subject: Re: [Biocatalogue-support] [BioCatalogue] Service 'Mutalyzer' has a test change status from UNCHECKED to WARNING >> Date: Wed, 27 Jul 2011 09:55:06 +0100 >> From: Jiten Bhagat >> To: p.e.m.taschner at lumc.nl >> CC: biocatalogue-support at rubyforge.org >> >> Dear Peter, >> >> Our apologies for this. We'll investigate this today with our EBI >> colleagues and get back to you. >> >> Regards, >> Jiten >> >> >> On 27/07/2011 08:34, >> P.E.M.Taschner at lumc.nl >> wrote: >>> Dear BioCatalogue Team, >>> >>> We have tried several times to find the problem resulting in the test status WARNING for our test script sp.py, but did not succeed. The test script works fine from our end, but it is unclear how the test was performed by your service. It was unclear what should be entered in the field "executable name". We did use sp.py, sp.python, test.py, but that did not affect the test results. We would appreciate it very much if you would be able to help us. >>> Thanking you very much in anitcipation, >>> >>> Best regards, >>> >>> Peter Taschner >>> >>> Dr. Peter E.M. Taschner >>> Department of Human Genetics S-4-P >>> Center for Human and Clinical Genetics >>> Leiden University Medical Center >>> P.O. Box 9600 >>> 2300 RC Leiden >>> The Netherlands >>> Tel. +31-71- 526 9424 Fax +31-71-526 8285 >>> Visiting address: Building 2, Room R04-005, Einthovenweg 20, Leiden >>> >>> >>> -----Original Message----- >>> From: >> contact at biocatalogue.org [mailto:contact at biocatalogue.org >> ] >>> Sent: woensdag 27 juli 2011 1:30 >>> To: Taschner, P.E.M. (HG) >>> Subject: [BioCatalogue] Service 'Mutalyzer' has a test change status from UNCHECKED to WARNING >>> >>> >>> >>> Dear Member, >>> >>> A monitoring test status change has occurred! Service 'Mutalyzer' has a test (TestScript, ID: 745) change status from UNCHECKED to WARNING. Last test result message: Something did not go right with this check. Go to Service: >> http://www.biocatalogue.org/services/2749 >> >>> If you have any questions please reply to this mail. >>> >>> Kind regards, >>> >>> The BioCatalogue Team >>> _______________________________________________ >>> Biocatalogue-support mailing list >>> >> Biocatalogue-support at rubyforge.org >> >> http://rubyforge.org/mailman/listinfo/biocatalogue-support >> >> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jul 27 07:40:49 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 27 Jul 2011 12:40:49 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-243) Make ALL routes/pages HTTPS (SSL) Message-ID: <26329780.66.1311766849219.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17393#comment-17393 ] Mannie Tagarira commented on BIOCAT-243: ---------------------------------------- This has been done but is unstable at the moment; task BIOCAT-676 is required > 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: Blocker > Fix For: 1.1.0 > > > 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 Jul 27 07:47:44 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 27 Jul 2011 12:47:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-243) Make ALL routes/pages HTTPS (SSL) Message-ID: <23327768.71.1311767264724.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-243: ----------------------------------- Priority: Critical (was: Blocker) > 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: 1.1.0 > > > 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 Jul 27 07:49:44 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 27 Jul 2011 12:49:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-465) Test OAuth on the live site In-Reply-To: <10881481.9000.1284042795322.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17442981.72.1311767384745.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-465?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17394#comment-17394 ] Mannie Tagarira commented on BIOCAT-465: ---------------------------------------- Testing was carried out; a bug was found and a fix was made in branch v1.1.0. > Test OAuth on the live site > --------------------------- > > Key: BIOCAT-465 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-465 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > 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 Jul 27 07:51:44 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 27 Jul 2011 12:51:44 +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: <9882228.73.1311767504767.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-568: ----------------------------------- Priority: Critical (was: Blocker) > 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: 1.1.0 > > > 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 Jul 27 07:51:50 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 27 Jul 2011 12:51:50 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-676) Update the map_routes method in the Annotations and Favourites plugins to account for :requirements In-Reply-To: <20360330.0.1311679364973.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3427810.74.1311767510248.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-676?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17395#comment-17395 ] Mannie Tagarira commented on BIOCAT-676: ---------------------------------------- The Favourites has been updated within the codebase; the Annotations plugin still needs to be updated. > Update the map_routes method in the Annotations and Favourites plugins to account for :requirements > --------------------------------------------------------------------------------------------------- > > Key: BIOCAT-676 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-676 > Project: BioCatalogue > Issue Type: Task > Components: Annotations Plugin > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > > Consider: > in routes.rb > {code:none} > Annotations.map_routes(map, {}, {}, :protocol => "https") > Favourites.map_routes(map, {}, {}, :protocol => "https") > {code} > in plugin routing.rb > {code:none} > def self.map_routes(map, collection={}, member={}, requirements={}) > map.resources :favourites, > :collection => { }.merge(collection), > :member => { }.merge(member), > :requirements => { }.merge(requirements) > end > {code} > Make sure the versions used by the app are updated to take into consideration these changes. -- 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 Jul 27 07:54:35 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 27 Jul 2011 12:54:35 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-675) Write documentation on how to use OAuth in third party apps In-Reply-To: <16265318.3153.1311082435356.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21539085.75.1311767675509.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-675?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-675: ----------------------------------- Summary: Write documentation on how to use OAuth in third party apps (was: Write documentation on how to use OAuth n third party apps) > Write documentation on how to use OAuth in third party apps > ----------------------------------------------------------- > > Key: BIOCAT-675 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-675 > Project: BioCatalogue > Issue Type: Task > Components: Documentation, REST API, Wiki > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > 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 Jul 27 07:57:44 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 27 Jul 2011 12:57:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-680) Contact Trish Whetzel and inform her of the new custom monitoring endpoint feature Message-ID: <6216212.76.1311767864720.JavaMail.jira@rosalind.cs.man.ac.uk> Contact Trish Whetzel and inform her of the new custom monitoring endpoint feature ---------------------------------------------------------------------------------- Key: BIOCAT-680 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-680 Project: BioCatalogue Issue Type: Task Reporter: Mannie Tagarira Assignee: Jiten Bhagat Priority: Blocker -- 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 Jul 27 08:00:44 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 27 Jul 2011 13:00:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-675) Write documentation on how to use OAuth in third party apps In-Reply-To: <16265318.3153.1311082435356.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23448296.77.1311768044748.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-675?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-675. ------------------------------------ Resolution: Fixed http://www.biocatalogue.org/wiki/doku.php?id=public:api#ruby > Write documentation on how to use OAuth in third party apps > ----------------------------------------------------------- > > Key: BIOCAT-675 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-675 > Project: BioCatalogue > Issue Type: Task > Components: Documentation, REST API, Wiki > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > 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 Jul 27 08:02:44 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 27 Jul 2011 13:02:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-465) Test OAuth on the live site In-Reply-To: <10881481.9000.1284042795322.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24318034.78.1311768164759.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-465?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17394#comment-17394 ] Mannie Tagarira edited comment on BIOCAT-465 at 27/07/11 13:00: ---------------------------------------------------------------- Testing was carried out; a bug was found and a fix was made in branch v1.1.0. This needs to be merged into trunk. was (Author: mannie): Testing was carried out; a bug was found and a fix was made in branch v1.1.0. > Test OAuth on the live site > --------------------------- > > Key: BIOCAT-465 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-465 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > 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 Jul 27 08:02:46 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 27 Jul 2011 13:02:46 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-465) Test OAuth on the live site In-Reply-To: <10881481.9000.1284042795322.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30538662.79.1311768166985.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-465?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-465. ------------------------------------ Resolution: Fixed > Test OAuth on the live site > --------------------------- > > Key: BIOCAT-465 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-465 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > 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 Jul 27 08:38:44 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 27 Jul 2011 13:38:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-677) Update the DRAMA testing procedure in the wiki to take into account some of the new functionality In-Reply-To: <1700665.3.1311694785977.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24829310.122.1311770324744.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-677?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-677. ------------------------------------ Resolution: Responded > Update the DRAMA testing procedure in the wiki to take into account some of the new functionality > -------------------------------------------------------------------------------------------------- > > Key: BIOCAT-677 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-677 > Project: BioCatalogue > Issue Type: Task > Components: Wiki > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > Fix For: 1.1.0 > > > Update http://www.biocatalogue.org/wiki/doku.php?id=development:system_testing > Main things to consider: > - REST endpoint (registration and annotation) > - REST parameters and representations > - Monitoring endpoint -- 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 Jul 27 09:41:16 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 27 Jul 2011 09:41:16 -0400 (EDT) Subject: [BioCatalogue-developers] [2477] branches/v1.1.0: [BIOCAT-608] Improved the way display names for services are set. Message-ID: <20110727134117.07D393C8043@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jul 27 10:14:08 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 27 Jul 2011 10:14:08 -0400 (EDT) Subject: [BioCatalogue-developers] [2478] branches/v1.1.0/config/routes.rb: Temp fix just to get things working for now Message-ID: <20110727141408.D25DC185838A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jul 27 10:26:31 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 27 Jul 2011 10:26:31 -0400 (EDT) Subject: [BioCatalogue-developers] [2479] branches/v1.1.0/script/biocatalogue/migrate_display_names_jul11.rb: [BIOCAT-608] Script to migrate the display name annotations Message-ID: <20110727142631.51D9E185838A@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jul 27 10:41:44 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 27 Jul 2011 15:41:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-608) Improve the way display names for services are set In-Reply-To: <4320008.1302.1307631055357.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1502565.131.1311777704845.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-608?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-608. --------------------------------- Resolution: Implemented Done > Improve the way display names for services are set > -------------------------------------------------- > > Key: BIOCAT-608 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-608 > Project: BioCatalogue > Issue Type: Improvement > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > > Currently, when a new display name is required for a service, this gets set as a "display_name" *annotation* which takes precedence in the UI and API over the {{name}} field (or whatever else) in the actual model object's table. > This is BAD for things like sorting and also not very efficient at all. > Change this so that {{Service#name}} gets set to the new value instead of using these display_name annotations. -- 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 Jul 27 10:43:44 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 27 Jul 2011 15:43:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-681) Implement the ability to directly set the display name of a service Message-ID: <19283279.132.1311777824765.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.1.0 Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.2.0 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 Jul 27 10:43:47 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 27 Jul 2011 15:43:47 +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: <11351553.133.1311777827142.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-681?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-681: -------------------------------- Fix Version/s: 1.1.0 (was: 1.2.0) Affects Version/s: 1.0.1 (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: 1.1.0 > > > 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 noreply at rubyforge.org Wed Jul 27 10:46:17 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 27 Jul 2011 10:46:17 -0400 (EDT) Subject: [BioCatalogue-developers] [2480] branches/v1.1.0/app/models/service_provider.rb: Fixed a bug where admins were being emailed about service providers with no services when a new service was registered . Message-ID: <20110727144617.7269E3C8043@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jul 27 10:55:22 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 27 Jul 2011 10:55:22 -0400 (EDT) Subject: [BioCatalogue-developers] [2481] branches/v1.1.0/app: [BIOCAT-551] Added sorting by name for the services index. Message-ID: <20110727145522.0F0373C8043@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jul 27 10:55:34 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 27 Jul 2011 15:55:34 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-551) Add sorting by name for the parent Web services. Currenlty sorting only available by "newest" and "earliest". In-Reply-To: <12751319.530.1291979212833.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27516974.135.1311778534759.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-551?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-551. --------------------------------- Resolution: Implemented > Add sorting by name for the parent Web services. Currenlty sorting only available by "newest" and "earliest". > ------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-551 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-551 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Alex Nenadic > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > Sorting of results needed for Taverna 2.30 release, see http://www.mygrid.org.uk/dev/issues/browse/T2-1556 -- 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 Jul 27 11:02:44 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 27 Jul 2011 16:02:44 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-682) Update Annotations plugin to allow acts_as_annotatable models to specify the "name" field Message-ID: <20532854.137.1311778964723.JavaMail.jira@rosalind.cs.man.ac.uk> Update Annotations plugin to allow acts_as_annotatable models to specify the "name" field ----------------------------------------------------------------------------------------- Key: BIOCAT-682 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-682 Project: BioCatalogue Issue Type: Improvement Components: Annotations Plugin Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical Fix For: 1.1.0 Need to update the {{acts_as_annotatable}} mixin in the Annotations plugin to allow the model to specify what the "name" field is. Like how the {{acts_as_annotation_value mixin works}}. This can then be used in queries, etc. -- 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 Jul 27 11:04:44 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 27 Jul 2011 16:04:44 +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: <13753795.138.1311779084748.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-662?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-662: -------------------------------- Description: 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. was: 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. Also, from Marco: {quote} Re: keep old ref. This would be very useful when you find a 'depricated' reference used in a workflow or application. That is how I discoverd this problem: Taverna told me the service didn't exist anymore, so I changed the wsdl reference in the workflow. It would be nice if I could find the new reference on biocatalogue through the old reference. {quote} > 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: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > > 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. -- 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 Jul 27 11:04:47 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 27 Jul 2011 16:04:47 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-683) Show previous WSDL URLs in the UI Message-ID: <17669339.139.1311779087418.JavaMail.jira@rosalind.cs.man.ac.uk> Show previous WSDL URLs in the UI --------------------------------- Key: BIOCAT-683 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-683 Project: BioCatalogue Issue Type: Sub-task Components: Web Interface Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.1.0 >From Marco: {quote} Re: keep old ref. This would be very useful when you find a 'depricated' reference used in a workflow or application. That is how I discoverd this problem: Taverna told me the service didn't exist anymore, so I changed the wsdl reference in the workflow. It would be nice if I could find the new reference on biocatalogue through the old reference. {quote} We already have the {{wsdl_files}} table that stores this info. So now just need to show the previous WSDL URLs in the UI. -- 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 Jul 27 11:06:44 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 27 Jul 2011 16:06:44 +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: <2190342.140.1311779204729.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-662?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-662: -------------------------------- Description: 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. was: 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. > 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: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > > 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 noreply at rubyforge.org Wed Jul 27 11:17:44 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 27 Jul 2011 11:17:44 -0400 (EDT) Subject: [BioCatalogue-developers] [2482] branches/v1.1.0/app/views/services/_favourited_box.rhtml: Minor textual change Message-ID: <20110727151744.E91661858346@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jul 27 12:16:17 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 27 Jul 2011 12:16:17 -0400 (EDT) Subject: [BioCatalogue-developers] [2483] branches/v1.1.0/app: [BIOCAT-361] Initial implementation of a " Users responsible for this service" section on the service's profile page Message-ID: <20110727161617.87AE818583A3@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jul 27 12:24:42 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 27 Jul 2011 12:24:42 -0400 (EDT) Subject: [BioCatalogue-developers] [2484] branches/v1.1.0: Minor bugfixes Message-ID: <20110727162442.4954D18583A3@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jul 27 12:25:43 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 27 Jul 2011 17:25:43 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-361) Add a "Users responsible for this service" section on the service's profile page In-Reply-To: <23419427.1675.1274978476997.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7735742.0.1311783944006.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-361?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17400#comment-17400 ] Jiten Bhagat commented on BIOCAT-361: ------------------------------------- Initial work done. Needs further testing. > Add a "Users responsible for this service" section on the service's profile page > -------------------------------------------------------------------------------- > > Key: BIOCAT-361 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-361 > Project: BioCatalogue > Issue Type: New Feature > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > Original Estimate: 2 hours > Remaining Estimate: 2 hours > -- 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 Jul 28 06:15:43 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 28 Jul 2011 11:15:43 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-676) Update the map_routes method in the Annotations and Favourites plugins to account for :requirements In-Reply-To: <20360330.0.1311679364973.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5208625.1.1311848143546.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-676?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17401#comment-17401 ] Jiten Bhagat commented on BIOCAT-676: ------------------------------------- Annotations plugin has been updated (v0.2.1) to support this. > Update the map_routes method in the Annotations and Favourites plugins to account for :requirements > --------------------------------------------------------------------------------------------------- > > Key: BIOCAT-676 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-676 > Project: BioCatalogue > Issue Type: Task > Components: Annotations Plugin > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.1.0 > > > Consider: > in routes.rb > {code:none} > Annotations.map_routes(map, {}, {}, :protocol => "https") > Favourites.map_routes(map, {}, {}, :protocol => "https") > {code} > in plugin routing.rb > {code:none} > def self.map_routes(map, collection={}, member={}, requirements={}) > map.resources :favourites, > :collection => { }.merge(collection), > :member => { }.merge(member), > :requirements => { }.merge(requirements) > end > {code} > Make sure the versions used by the app are updated to take into consideration these changes. -- 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 Jul 28 06:20:43 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 28 Jul 2011 11:20:43 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-682) Update Annotations plugin to force acts_as_annotatable models to specify the "name" field In-Reply-To: <20532854.137.1311778964723.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23803668.2.1311848443508.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-682?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-682: -------------------------------- Summary: Update Annotations plugin to force acts_as_annotatable models to specify the "name" field (was: Update Annotations plugin to allow acts_as_annotatable models to specify the "name" field) Description: Need to update the {{acts_as_annotatable}} mixin in the Annotations plugin to force the model to specify what the "name" field is. Like how the {{acts_as_annotation_value mixin works}}. This can then be used in queries, etc. was: Need to update the {{acts_as_annotatable}} mixin in the Annotations plugin to allow the model to specify what the "name" field is. Like how the {{acts_as_annotation_value mixin works}}. This can then be used in queries, etc. > Update Annotations plugin to force acts_as_annotatable models to specify the "name" field > ----------------------------------------------------------------------------------------- > > Key: BIOCAT-682 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-682 > Project: BioCatalogue > Issue Type: Improvement > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.0 > > > Need to update the {{acts_as_annotatable}} mixin in the Annotations plugin to force the model to specify what the "name" field is. Like how the {{acts_as_annotation_value mixin works}}. > This can then be used in queries, etc. -- 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 Jul 28 06:36:43 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 28 Jul 2011 11:36:43 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-682) Update Annotations plugin to force acts_as_annotatable models to specify the "name" field In-Reply-To: <20532854.137.1311778964723.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6275129.3.1311849403415.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-682?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17402#comment-17402 ] Jiten Bhagat commented on BIOCAT-682: ------------------------------------- Plugin has been updated. Now need to incorporate these changes into the BioCat main codebase. > Update Annotations plugin to force acts_as_annotatable models to specify the "name" field > ----------------------------------------------------------------------------------------- > > Key: BIOCAT-682 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-682 > Project: BioCatalogue > Issue Type: Improvement > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.0 > > > Need to update the {{acts_as_annotatable}} mixin in the Annotations plugin to force the model to specify what the "name" field is. Like how the {{acts_as_annotation_value mixin works}}. > This can then be used in queries, etc. -- 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 Jul 28 06:38:43 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 28 Jul 2011 11:38:43 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-682) Update Annotations plugin to force acts_as_annotatable models to specify the "name" field In-Reply-To: <20532854.137.1311778964723.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32962700.4.1311849523446.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-682?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17402#comment-17402 ] Jiten Bhagat edited comment on BIOCAT-682 at 28/07/11 11:36: ------------------------------------------------------------- Plugin has been updated (v0.3.0) to support this. Now need to incorporate these changes into the BioCat main codebase. was (Author: jbhagat): Plugin has been updated. Now need to incorporate these changes into the BioCat main codebase. > Update Annotations plugin to force acts_as_annotatable models to specify the "name" field > ----------------------------------------------------------------------------------------- > > Key: BIOCAT-682 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-682 > Project: BioCatalogue > Issue Type: Improvement > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.0 > > > Need to update the {{acts_as_annotatable}} mixin in the Annotations plugin to force the model to specify what the "name" field is. Like how the {{acts_as_annotation_value mixin works}}. > This can then be used in queries, etc. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira